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<h3 style="margin-top: 20px; margin-bottom: 10px;">
Étienne Mollier pushed to branch master at <a href="https://salsa.debian.org/med-team/tnseq-transit">Debian Med / tnseq-transit</a>
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Commits:
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<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/aef1ec004789ae886472c48f72908f244c588648">aef1ec00</a></strong>
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<span> by Étienne Mollier </span> <i> at 2023-08-13T10:59:12+02:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>routine-update: New upstream version
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<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/b687e54ccd8832e49b59f62b5dbe4769c0e97f4b">b687e54c</a></strong>
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<span> by Étienne Mollier </span> <i> at 2023-08-13T10:59:17+02:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 3.3.0</pre>
</li>
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<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/27b776985ea7166dcaa3917b2afa3a0dc1453b93">27b77698</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-08-13T11:02:29+02:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update upstream source from tag 'upstream/3.3.0'
Update to upstream version '3.3.0'
with Debian dir ae07aa8646af34dce9f398de795ab14703709dd3</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/db8135af86daee217f3167f7a473cd0460c8a90c">db8135af</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-08-13T11:02:29+02:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>routine-update: Standards-Version: 4.6.2
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/tnseq-transit/-/commit/898cc600b276228ce95ff463aa822e85dffdcaa1">898cc600</a></strong>
<div>
<span> by Étienne Mollier </span> <i> at 2023-08-13T11:08:43+02:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>routine-update: Ready to upload to unstable
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
23 changed files:
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.gitignore
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CHANGELOG.md
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debian/changelog
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debian/control
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
Changes:
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<li id="a5cc2925ca8258af241be7e5b0381edf30266302">
<a href="https://salsa.debian.org/med-team/tnseq-transit/-/compare/e7fcdb595572f7ea598ca27f80632375a9e0790d...898cc600b276228ce95ff463aa822e85dffdcaa1#a5cc2925ca8258af241be7e5b0381edf30266302"><strong style="font-weight: bold;">.gitignore</strong></a>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="plaintext"># # Mac</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="plaintext"># </span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4" class="line" lang="plaintext">**/*.do_not_sync</span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/compare/e7fcdb595572f7ea598ca27f80632375a9e0790d...898cc600b276228ce95ff463aa822e85dffdcaa1#ab09011fa121d0a2bb9fa4ca76094f2482b902b7"><strong style="font-weight: bold;">CHANGELOG.md</strong></a>
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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -2,6 +2,23 @@</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2" class="line" lang="markdown">All notable changes to this project will be documented in this file.</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5" class="line" lang="markdown"></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Version 3.3.0 2023-08-03</span></span>
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7
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Transit:</span></span>
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8
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC8" class="line" lang="markdown"></span>
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9
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC9" class="line" lang="markdown">Major changes:</span>
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<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10" class="line" lang="markdown"><span class="p"> -</span> added CRISPRi-DR method for identifying chemical-genetic interactions (CGI) in CRISPRi libraries</span>
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11
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12
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13
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC13" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Version 3.2.8 2023-07-22</span></span>
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14
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC14" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### TPP:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
16
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC16" class="line" lang="markdown">Small bug fixes:</span>
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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
17
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC17" class="line" lang="markdown"><span class="p"> -</span> fixed uncompression of gzipped fastq files</span>
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<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
18
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC18" class="line" lang="markdown"><span class="p"> -</span> fixed error condition caused by recent versions of wxPython that require 'proportion' arg in sizers in TPP GUI to be int (not float)</span>
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<td class="new_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
19
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC19" class="line" lang="markdown"><span class="p"> -</span> added link in documentation to make users aware of Transit2</span>
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20
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC20" class="line" lang="markdown"></span>
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21
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC21" class="line" lang="markdown"></span>
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5
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<td class="new_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
22
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC22" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Version 3.2.7 2022-09-22</span></span>
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6
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<td class="new_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
23
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC23" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### TRANSIT:</span></span>
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24
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC24" class="line" lang="markdown"></span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/compare/e7fcdb595572f7ea598ca27f80632375a9e0790d...898cc600b276228ce95ff463aa822e85dffdcaa1#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong style="font-weight: bold;">debian/changelog</strong></a>
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1
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1" class="line" lang="plaintext">tnseq-transit (3.3.0-1) unstable; urgency=medium</span>
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2
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
4
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4" class="line" lang="plaintext"> * Standards-Version: 4.6.2 (routine-update)</span>
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5
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6" class="line" lang="plaintext"> -- Étienne Mollier <emollier@debian.org> Sun, 13 Aug 2023 11:03:02 +0200</span>
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7
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7" class="line" lang="plaintext"></span>
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1
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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
8
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC8" class="line" lang="plaintext">tnseq-transit (3.2.7-1) unstable; urgency=medium</span>
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2
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC9" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10" class="line" lang="plaintext"> [ Nilesh Patra ]</span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/compare/e7fcdb595572f7ea598ca27f80632375a9e0790d...898cc600b276228ce95ff463aa822e85dffdcaa1#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong style="font-weight: bold;">debian/control</strong></a>
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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -16,7 +16,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC16" class="line" lang="plaintext"> python3-statsmodels,</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC17" class="line" lang="plaintext"> python3-pubsub,</span>
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18
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<td class="new_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC18" class="line" lang="plaintext"> bwa</span>
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<td class="old_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
19
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<td class="new_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC19" class="line" lang="plaintext">Standards-Version: 4.6.<span class="idiff left right deletion" style="background-color: #fac5cd;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
19
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC19" class="line" lang="plaintext">Standards-Version: 4.6.<span class="idiff left right addition" style="background-color: #c7f0d2;">2</span></span>
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<td class="new_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC20" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/tnseq-transit</span>
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<td class="old_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="new_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC21" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/tnseq-transit.git</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC22" class="line" lang="plaintext">Homepage: http://saclab.tamu.edu/essentiality/transit/</span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/compare/e7fcdb595572f7ea598ca27f80632375a9e0790d...898cc600b276228ce95ff463aa822e85dffdcaa1#8ecf421955e8c32c6b36c85f5252965c7e6c9f07"><strong style="font-weight: bold;">src/pytpp/tpp_gui.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="110" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="110" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -110,7 +110,7 @@ if hasWx:</td>
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<td class="old_line diff-line-num" data-linenumber="110" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
110
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<td class="new_line diff-line-num" data-linenumber="110" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
110
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">label_replicon_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">StaticText</span><span class="p">(</span><span class="n" style="color: #333;">panel</span><span class="p">,</span> <span class="n" style="color: #333;">label</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'ID names for each replicon: </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">(if genome has multiple contigs)'</span><span class="p">,</span><span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="mi" style="color: #099;">340</span><span class="p">,</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">))</span></span>
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<td class="old_line diff-line-num" data-linenumber="111" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
111
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<td class="new_line diff-line-num" data-linenumber="111" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
111
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">sizer_replicon_ids</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">Add</span><span class="p">(</span><span class="n" style="color: #333;">label_replicon_ids</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">ALIGN_CENTER_VERTICAL</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="112" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
112
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<td class="new_line diff-line-num" data-linenumber="112" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
112
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC112" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">replicon_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">TextCtrl</span><span class="p">(</span><span class="n" style="color: #333;">panel</span><span class="p">,</span><span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">replicon_ids</span><span class="p">,</span><span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="mi" style="color: #099;">400</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="113" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
113
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<td class="new_line diff-line-num old" data-linenumber="113" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">sizer_replicon_ids</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">Add</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">replicon_ids</span><span class="p">,</span> <span class="n" style="color: #333;">proportion</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1<span class="idiff left right deletion" style="background-color: #fac5cd;">.0</span></span><span class="p">,</span> <span class="n" style="color: #333;">flag</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="o" style="font-weight: 600;">|</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">ALL</span><span class="p">,</span> <span class="n" style="color: #333;">border</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">5</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="114" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="113" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
113
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">sizer_replicon_ids</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">Add</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">replicon_ids</span><span class="p">,</span> <span class="n" style="color: #333;">proportion</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">flag</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="o" style="font-weight: 600;">|</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">ALL</span><span class="p">,</span> <span class="n" style="color: #333;">border</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">5</span><span class="p">)</span></span>
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114
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114
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">sizer_replicon_ids</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">Add</span><span class="p">(</span><span class="nc" style="color: #458; font-weight: 600;">TPPIcon</span><span class="p">(</span><span class="n" style="color: #333;">panel</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">ID_ANY</span><span class="p">,</span> <span class="n" style="color: #333;">bmp</span><span class="p">,</span> <span class="s" style="color: #d14;">"Specify names of each contig within the reference genome separated by commas (if using wig_gb_to_csv.py you must use the contig names in the Genbank file). Only required if there are multiple contigs; can leave blank if there is just one sequence.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Enter 'auto' for autogenerated ids."</span><span class="p">),</span> <span class="n" style="color: #333;">flag</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">CENTER</span><span class="p">,</span> <span class="n" style="color: #333;">border</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="115" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
115
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<td class="new_line diff-line-num" data-linenumber="115" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
115
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">sizer_replicon_ids</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">Add</span><span class="p">((</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">),</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">)</span> </span>
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<td class="old_line diff-line-num" data-linenumber="116" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
116
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<td class="new_line diff-line-num" data-linenumber="116" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
116
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;">sizer</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">Add</span><span class="p">(</span><span class="n" style="color: #333;">sizer_replicon_ids</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="142" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="142" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -142,7 +142,7 @@ if hasWx:</td>
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<td class="old_line diff-line-num" data-linenumber="142" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
142
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<td class="new_line diff-line-num" data-linenumber="142" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
142
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">label5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">StaticText</span><span class="p">(</span><span class="n" style="color: #333;">panel</span><span class="p">,</span> <span class="n" style="color: #333;">label</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Prefix to use for output filenames (REQUIRED):'</span><span class="p">,</span><span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="mi" style="color: #099;">340</span><span class="p">,</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">))</span></span>
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<td class="old_line diff-line-num" data-linenumber="143" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
143
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<td class="new_line diff-line-num" data-linenumber="143" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
143
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">sizer5</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">Add</span><span class="p">(</span><span class="n" style="color: #333;">label5</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">ALIGN_CENTER_VERTICAL</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
144
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<td class="new_line diff-line-num" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
144
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">TextCtrl</span><span class="p">(</span><span class="n" style="color: #333;">panel</span><span class="p">,</span><span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">base</span><span class="p">,</span><span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="mi" style="color: #099;">400</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="145" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
145
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<td class="new_line diff-line-num old" data-linenumber="145" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC145" class="line" lang="python"> <span class="n" style="color: #333;">sizer5</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">Add</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">base</span><span class="p">,</span> <span class="n" style="color: #333;">proportion</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1<span class="idiff left right deletion" style="background-color: #fac5cd;">.0</span></span><span class="p">,</span> <span class="n" style="color: #333;">flag</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="o" style="font-weight: 600;">|</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">ALL</span><span class="p">,</span> <span class="n" style="color: #333;">border</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">5</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="146" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
145
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC145" class="line" lang="python"> <span class="n" style="color: #333;">sizer5</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">Add</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">base</span><span class="p">,</span> <span class="n" style="color: #333;">proportion</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">flag</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="o" style="font-weight: 600;">|</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">ALL</span><span class="p">,</span> <span class="n" style="color: #333;">border</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">5</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="146" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
146
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<td class="new_line diff-line-num" data-linenumber="146" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
146
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">sizer5</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">Add</span><span class="p">(</span><span class="nc" style="color: #458; font-weight: 600;">TPPIcon</span><span class="p">(</span><span class="n" style="color: #333;">panel</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">ID_ANY</span><span class="p">,</span> <span class="n" style="color: #333;">bmp</span><span class="p">,</span> <span class="s" style="color: #d14;">"Select a prefix that will be used when writing output files"</span><span class="p">),</span> <span class="n" style="color: #333;">flag</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">CENTER</span><span class="p">,</span> <span class="n" style="color: #333;">border</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="147" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
147
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<td class="new_line diff-line-num" data-linenumber="147" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
147
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">sizer5</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">Add</span><span class="p">((</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">),</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">)</span> </span>
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<td class="old_line diff-line-num" data-linenumber="148" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
148
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<td class="new_line diff-line-num" data-linenumber="148" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
148
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">sizer</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">Add</span><span class="p">(</span><span class="n" style="color: #333;">sizer5</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="247" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="247" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -247,7 +247,7 @@ The Mme1 protocol generally assumes reads do NOT include the primer prefix, and</td>
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247
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<td class="new_line diff-line-num" data-linenumber="247" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
247
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC247" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">bwa_alg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">ComboBox</span><span class="p">(</span><span class="n" style="color: #333;">panel</span><span class="p">,</span><span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"use algorithm 'aln'"</span><span class="p">,</span> <span class="s" style="color: #d14;">"use algorithm 'mem'"</span><span class="p">],</span><span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="mi" style="color: #099;">200</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="p">))</span></span>
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<td class="old_line diff-line-num" data-linenumber="248" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
248
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<td class="new_line diff-line-num" data-linenumber="248" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
248
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC248" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">bwa_alg</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">'aln'</span><span class="p">:</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">bwa_alg</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">SetSelection</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="249" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
249
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<td class="new_line diff-line-num" data-linenumber="249" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
249
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC249" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">bwa_alg</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">SetSelection</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># default</span></span>
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<td class="old_line diff-line-num old" data-linenumber="250" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
250
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<td class="new_line diff-line-num old" data-linenumber="250" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC250" class="line" lang="python"> <span class="n" style="color: #333;">sizer0</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">Add</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">bwa_alg</span><span class="p">,</span> <span class="n" style="color: #333;">proportion</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;"><span class="idiff left right deletion" style="background-color: #fac5cd;">0.5</span></span><span class="p">,</span> <span class="n" style="color: #333;">flag</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="o" style="font-weight: 600;">|</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">ALL</span><span class="p">,</span> <span class="n" style="color: #333;">border</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">## </span></span>
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<td class="old_line diff-line-num new" data-linenumber="251" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="250" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
250
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC250" class="line" lang="python"> <span class="n" style="color: #333;">sizer0</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">Add</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">bwa_alg</span><span class="p">,</span> <span class="n" style="color: #333;">proportion</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;"><span class="idiff left right addition" style="background-color: #c7f0d2;">2</span></span><span class="p">,</span> <span class="n" style="color: #333;">flag</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="o" style="font-weight: 600;">|</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">ALL</span><span class="p">,</span> <span class="n" style="color: #333;">border</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">## </span></span>
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<td class="old_line diff-line-num" data-linenumber="251" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
251
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<td class="new_line diff-line-num" data-linenumber="251" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
251
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC251" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">bwa_alg</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">Bind</span><span class="p">(</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EVT_COMBOBOX</span><span class="p">,</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">OnBwaAlgSelection</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">bwa_alg</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">GetId</span><span class="p">())</span></span>
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<td class="old_line diff-line-num" data-linenumber="252" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
252
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<td class="new_line diff-line-num" data-linenumber="252" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
252
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC252" class="line" lang="python"> <span class="n" style="color: #333;">sizer0</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">Add</span><span class="p">(</span><span class="nc" style="color: #458; font-weight: 600;">TPPIcon</span><span class="p">(</span><span class="n" style="color: #333;">panel</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">ID_ANY</span><span class="p">,</span> <span class="n" style="color: #333;">bmp</span><span class="p">,</span> <span class="s" style="color: #d14;">"'mem' is considered to do a better job at mapping reads, but 'aln' is available as an alternative."</span><span class="p">),</span> <span class="n" style="color: #333;">flag</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">CENTER</span><span class="p">,</span> <span class="n" style="color: #333;">border</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="253" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
253
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<td class="new_line diff-line-num" data-linenumber="253" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
253
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC253" class="line" lang="python"> <span class="n" style="color: #333;">sizer0</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">Add</span><span class="p">((</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">),</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="271" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="271" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -271,7 +271,7 @@ The Mme1 protocol generally assumes reads do NOT include the primer prefix, and</td>
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<td class="old_line diff-line-num" data-linenumber="271" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
271
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<td class="new_line diff-line-num" data-linenumber="271" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
271
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC271" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="272" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
272
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<td class="new_line diff-line-num" data-linenumber="272" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
272
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC272" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">barseq_select</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">ComboBox</span><span class="p">(</span><span class="n" style="color: #333;">panel</span><span class="p">,</span><span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'this is not a Barseq dataset'</span><span class="p">,</span><span class="s" style="color: #d14;">'read catalog file'</span><span class="p">,</span><span class="s" style="color: #d14;">'write catalog file'</span><span class="p">],</span><span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="mi" style="color: #099;">200</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;">## # does a BoxSizer use wx.HORIZONTAL, not wx.EXPAND?</span></span>
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<td class="old_line diff-line-num" data-linenumber="273" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
273
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<td class="new_line diff-line-num" data-linenumber="273" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
273
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC273" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">barseq_select</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">SetSelection</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="274" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
274
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<td class="new_line diff-line-num old" data-linenumber="274" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC274" class="line" lang="python"> <span class="n" style="color: #333;">sizer9</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">Add</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">barseq_select</span><span class="p">,</span> <span class="n" style="color: #333;">proportion</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;"><span class="idiff left right deletion" style="background-color: #fac5cd;">0.5</span></span><span class="p">,</span> <span class="n" style="color: #333;">flag</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="o" style="font-weight: 600;">|</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">ALL</span><span class="p">,</span> <span class="n" style="color: #333;">border</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">## </span></span>
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<td class="new_line diff-line-num new" data-linenumber="274" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
274
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC274" class="line" lang="python"> <span class="n" style="color: #333;">sizer9</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">Add</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">barseq_select</span><span class="p">,</span> <span class="n" style="color: #333;">proportion</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;"><span class="idiff left right addition" style="background-color: #c7f0d2;">2</span></span><span class="p">,</span> <span class="n" style="color: #333;">flag</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="o" style="font-weight: 600;">|</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">ALL</span><span class="p">,</span> <span class="n" style="color: #333;">border</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">## </span></span>
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275
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<td class="new_line diff-line-num" data-linenumber="275" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
275
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC275" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="276" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
276
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<td class="new_line diff-line-num" data-linenumber="276" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
276
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC276" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">picker9</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">lib</span><span class="p">.</span><span class="n" style="color: #333;">filebrowsebutton</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">FileBrowseButton</span><span class="p">(</span><span class="n" style="color: #333;">panel</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">ID_ANY</span><span class="p">,</span> <span class="n" style="color: #333;">dialogTitle</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Please select the Barseq catalog filename'</span><span class="p">,</span> <span class="n" style="color: #333;">fileMode</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">FD_OPEN</span><span class="p">,</span> <span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="mi" style="color: #099;">400</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="p">),</span> <span class="n" style="color: #333;">startDirectory</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">dirname</span><span class="p">(</span><span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">fq2</span><span class="p">),</span> <span class="n" style="color: #333;">initialValue</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">labelText</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span> <span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># no need for this: changeCallback=self.OnChanged9 ; initialValue set below ; no file mask</span></span>
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277
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<td class="new_line diff-line-num" data-linenumber="277" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
277
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC277" class="line" lang="python"> <span class="n" style="color: #333;">sizer9</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">Add</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">picker9</span><span class="p">,</span> <span class="n" style="color: #333;">proportion</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">flag</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">EXPAND</span><span class="o" style="font-weight: 600;">|</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="n" style="color: #333;">ALL</span><span class="p">,</span> <span class="n" style="color: #333;">border</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">5</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/compare/e7fcdb595572f7ea598ca27f80632375a9e0790d...898cc600b276228ce95ff463aa822e85dffdcaa1#88e0c8b85bd56c1ffb341f3c428ad72e4c8fc7c7"><strong style="font-weight: bold;">src/pytpp/tpp_tools.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="686" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -686,7 +686,7 @@ def driver(vars):</td>
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686
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686
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC686" class="line" lang="python"></span>
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687
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687
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC687" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">err</span><span class="p">:</span></span>
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688
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688
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC688" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">message</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="689" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
689
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<td class="new_line diff-line-num old" data-linenumber="689" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC689" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">message</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left deletion" style="background-color: #fac5cd;">"%s"</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">%</span></span><span class="idiff deletion" style="background-color: #fac5cd;"> </span><span class="s" style="color: #d14;"><span class="idiff deletion" style="background-color: #fac5cd;">" "</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">.</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">join</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">(</span></span><span class="n" style="color: #333;">err</span><span class="p">.</span><span class="n" style="color: #333;">args</span><span class="p">)<span class="idiff right deletion" style="background-color: #fac5cd;">)</span></span></span>
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<td class="new_line diff-line-num new" data-linenumber="689" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
689
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC689" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">message</span><span class="p">(</span><span class="n" style="color: #333;">err</span><span class="p">.</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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690
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC690" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">message</span><span class="p">(</span><span class="s" style="color: #d14;">"Exiting."</span><span class="p">)</span></span>
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691
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691
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC691" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">exit</span><span class="p">()</span></span>
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692
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692
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC692" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="700" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="700" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -700,11 +700,15 @@ def driver(vars):</td>
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700
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700
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC700" class="line" lang="python"></span>
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701
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701
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC701" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">message</span><span class="p">(</span><span class="s" style="color: #d14;">"Done."</span><span class="p">)</span></span>
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702
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702
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC702" class="line" lang="python"></span>
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<td class="old_line diff-line-num new" data-linenumber="703" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="703" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
703
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC703" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># gunzip <fastq>.gz file, written to <fastq></span></span>
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<td class="new_line diff-line-num new" data-linenumber="704" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
704
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC704" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="703" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
703
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<td class="new_line diff-line-num" data-linenumber="705" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
705
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC705" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">uncompress</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="704" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
704
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<td class="new_line diff-line-num old" data-linenumber="706" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC704" class="line" lang="python"> <span class="n" style="color: #333;">outfil</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="s" style="color: #d14;">"w+"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="706" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
706
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC706" class="line" lang="python"> <span class="n" style="color: #333;">newfname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filename</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3</span><span class="p">]</span></span>
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<td class="old_line diff-line-num new" data-linenumber="705" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="707" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
707
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC707" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"uncompressing %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">filename</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="705" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="708" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
708
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC708" class="line" lang="python"> <span class="n" style="color: #333;">outfil</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333;">newfname</span><span class="p">,</span> <span class="s" style="color: #d14;">"wb+"</span><span class="p">)</span></span>
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705
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<td class="new_line diff-line-num" data-linenumber="709" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
709
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC709" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">gzip</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">):</span></span>
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706
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<td class="new_line diff-line-num" data-linenumber="710" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
710
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC710" class="line" lang="python"> <span class="n" style="color: #333;">outfil</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="707" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
707
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<td class="new_line diff-line-num old" data-linenumber="711" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC707" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left deletion" style="background-color: #fac5cd;">filename</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">[</span></span><span class="mi" style="color: #099;"><span class="idiff deletion" style="background-color: #fac5cd;">0</span></span><span class="p"><span class="idiff deletion" style="background-color: #fac5cd;">:</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion" style="background-color: #fac5cd;">-</span></span><span class="mi" style="color: #099;"><span class="idiff deletion" style="background-color: #fac5cd;">3</span></span><span class="p"><span class="idiff right deletion" style="background-color: #fac5cd;">]</span></span></span>
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<td class="new_line diff-line-num new" data-linenumber="711" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
711
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC711" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left right addition" style="background-color: #c7f0d2;">newfname</span></span></span>
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708
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712
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC712" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="709" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
709
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<td class="new_line diff-line-num" data-linenumber="713" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
713
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC713" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">copy_fasta</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">,</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span><span class="n" style="color: #333;">maxreads</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">1</span><span class="p">):</span></span>
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710
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<td class="new_line diff-line-num" data-linenumber="714" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
714
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC714" class="line" lang="python"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="724" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="728" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -724,8 +728,15 @@ def copy_fasta(infile,outfile,maxreads=-1):</td>
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724
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<td class="new_line diff-line-num" data-linenumber="728" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
728
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC728" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">extract_reads</span><span class="p">(</span><span class="nb" style="color: #0086b3;">vars</span><span class="p">):</span></span>
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<td class="old_line diff-line-num" data-linenumber="725" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
725
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<td class="new_line diff-line-num" data-linenumber="729" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
729
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC729" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">message</span><span class="p">(</span><span class="s" style="color: #d14;">"extracting reads..."</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="726" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
726
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<td class="new_line diff-line-num" data-linenumber="730" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
730
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC730" class="line" lang="python"></span>
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<td class="old_line diff-line-num new" data-linenumber="727" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="731" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
731
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC731" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">fq1</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">'.gz'</span><span class="p">):</span></span>
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<td class="old_line diff-line-num new" data-linenumber="727" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="732" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
732
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC732" class="line" lang="python"> <span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">fq1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">uncompress</span><span class="p">(</span><span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">fq1</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="727" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="733" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
733
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC733" class="line" lang="python"></span>
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<td class="old_line diff-line-num new" data-linenumber="727" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="734" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
734
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC734" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">fq2</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">'.gz'</span><span class="p">):</span></span>
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<td class="old_line diff-line-num new" data-linenumber="727" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="735" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
735
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC735" class="line" lang="python"> <span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">fq2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">uncompress</span><span class="p">(</span><span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">fq2</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="736" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
736
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC736" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="727" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
727
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<td class="new_line diff-line-num" data-linenumber="737" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
737
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC737" class="line" lang="python"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">''</span><span class="p">,</span><span class="s" style="color: #d14;">''</span><span class="p">]</span></span>
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<td class="old_line diff-line-num" data-linenumber="728" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
728
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<td class="new_line diff-line-num" data-linenumber="738" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
738
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC738" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nf" style="color: #900; font-weight: 600;">enumerate</span><span class="p">([</span><span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">fq1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">fq2</span><span class="p">]):</span></span>
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<td class="old_line diff-line-num new" data-linenumber="729" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="739" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
739
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC739" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="729" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
729
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<td class="new_line diff-line-num" data-linenumber="740" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
740
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC740" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">single_end</span><span class="o" style="font-weight: 600;">==</span><span class="bp" style="color: #999;">True</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="old_line diff-line-num" data-linenumber="730" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
730
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<td class="new_line diff-line-num" data-linenumber="741" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
741
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC741" class="line" lang="python"> <span class="n" style="color: #333;">fil</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="731" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
731
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<td class="new_line diff-line-num" data-linenumber="742" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
742
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC742" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fil</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="736" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="747" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -736,12 +747,6 @@ def extract_reads(vars):</td>
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<td class="old_line diff-line-num" data-linenumber="736" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
736
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<td class="new_line diff-line-num" data-linenumber="747" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
747
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC747" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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737
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<td class="new_line diff-line-num" data-linenumber="748" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
748
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC748" class="line" lang="python"> <span class="n" style="color: #333;">fil</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">close</span><span class="p">()</span></span>
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738
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<td class="new_line diff-line-num" data-linenumber="749" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
749
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC749" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="739" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
739
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<td class="new_line diff-line-num old" data-linenumber="750" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC739" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">fq1</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">'.gz'</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="740" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
740
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<td class="new_line diff-line-num old" data-linenumber="750" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC740" class="line" lang="python"> <span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">fq1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">uncompress</span><span class="p">(</span><span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">fq1</span><span class="p">)</span></span>
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741
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<td class="new_line diff-line-num old" data-linenumber="750" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC741" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="742" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
742
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<td class="new_line diff-line-num old" data-linenumber="750" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC742" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">fq2</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">'.gz'</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="743" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
743
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<td class="new_line diff-line-num old" data-linenumber="750" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC743" class="line" lang="python"> <span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">fq2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">uncompress</span><span class="p">(</span><span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">fq2</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="744" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
744
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<td class="new_line diff-line-num old" data-linenumber="750" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC744" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="745" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
745
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<td class="new_line diff-line-num" data-linenumber="750" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
750
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC750" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">flag</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'FASTQ'</span><span class="p">):</span></span>
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<td class="old_line diff-line-num" data-linenumber="746" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
746
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<td class="new_line diff-line-num" data-linenumber="751" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
751
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC751" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">message</span><span class="p">(</span><span class="s" style="color: #d14;">"fastq2reads: %s -> %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">fq1</span><span class="p">,</span><span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">reads1</span><span class="p">))</span></span>
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<td class="old_line diff-line-num" data-linenumber="747" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
747
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<td class="new_line diff-line-num" data-linenumber="752" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
752
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC752" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">fastq2reads</span><span class="p">(</span><span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">fq1</span><span class="p">,</span><span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">reads1</span><span class="p">,</span><span class="nb" style="color: #0086b3;">vars</span><span class="p">.</span><span class="n" style="color: #333;">maxreads</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/compare/e7fcdb595572f7ea598ca27f80632375a9e0790d...898cc600b276228ce95ff463aa822e85dffdcaa1#176b28a2342a4b0b837f1b361ba78e8f0ea87ce4"><strong style="font-weight: bold;">src/pytransit/__init__.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -2,6 +2,6 @@</td>
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<td class="old_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2
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<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2" class="line" lang="python"><span class="n" style="color: #333;">__all__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"transit_tools"</span><span class="p">,</span> <span class="s" style="color: #d14;">"tnseq_tools"</span><span class="p">,</span> <span class="s" style="color: #d14;">"norm_tools"</span><span class="p">,</span> <span class="s" style="color: #d14;">"stat_tools"</span><span class="p">]</span></span>
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3
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<td class="new_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3" class="line" lang="python"></span>
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4
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
5
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<td class="new_line diff-line-num old" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"v3.<span class="idiff left right deletion" style="background-color: #fac5cd;">2.7</span>"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
5
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"v3.<span class="idiff left right addition" style="background-color: #c7f0d2;">3.0</span>"</span></span>
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6
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6
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"[TRANSIT]"</span></span>
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7
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7
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7" class="line" lang="python"></span></pre></td>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/compare/e7fcdb595572f7ea598ca27f80632375a9e0790d...898cc600b276228ce95ff463aa822e85dffdcaa1#091b664e15a91b5c74f6dbfd56cb3757d2c34f5d"><strong style="font-weight: bold;">src/pytransit/analysis/CGI.py</strong></a>
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1
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">sys</span></span>
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2
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
4
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">wx</span></span>
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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
5
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5" class="line" lang="python"> <span class="n" style="color: #333;">WX_VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">wx</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">version</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6" class="line" lang="python"> <span class="n" style="color: #333;">hasWx</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
7
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
8
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC8" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
9
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC9" class="line" lang="python"> <span class="n" style="color: #333;">hasWx</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10" class="line" lang="python"> <span class="n" style="color: #333;">WX_VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
11
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC11" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
12
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC12" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">hasWx</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
13
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC13" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">wx.xrc</span></span>
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<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
14
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC14" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">wx.lib.buttons</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">GenBitmapTextButton</span></span>
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<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
15
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC15" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">pubsub</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">pub</span></span>
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<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
16
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC16" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">wx.adv</span></span>
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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
17
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC17" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
18
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">os</span></span>
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<td class="new_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
19
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">time</span></span>
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<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
20
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC20" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">math</span></span>
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<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
21
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">random</span></span>
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<td class="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
22
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">numpy</span></span>
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<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
23
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">scipy.stats</span></span>
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<td class="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
24
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC24" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">datetime</span></span>
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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
25
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">pandas</span></span>
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<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
26
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC26" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
27
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC27" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">pytransit.analysis</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">base</span></span>
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<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
28
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC28" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">pytransit.transit_tools</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">transit_tools</span></span>
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<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
29
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC29" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">pytransit.tnseq_tools</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tnseq_tools</span></span>
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<td class="new_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
30
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC30" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">pytransit.norm_tools</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">norm_tools</span></span>
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<td class="new_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
31
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC31" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">pytransit.stat_tools</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">stat_tools</span></span>
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<td class="new_line diff-line-num new" data-linenumber="32" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
32
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC32" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
33
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC33" class="line" lang="python"><span class="n" style="color: #333;">hasR</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<td class="new_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
34
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC34" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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35
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC35" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">rpy2.robjects</span></span>
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<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
36
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">hasR</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<td class="new_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
37
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC37" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
38
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">hasR</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<td class="new_line diff-line-num new" data-linenumber="39" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
39
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC39" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
40
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC40" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">hasR</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
41
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC41" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">rpy2.robjects</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">DataFrame</span><span class="p">,</span> <span class="n" style="color: #333;">globalenv</span><span class="p">,</span> <span class="n" style="color: #333;">IntVector</span><span class="p">,</span> <span class="n" style="color: #333;">FloatVector</span><span class="p">,</span> <span class="n" style="color: #333;">StrVector</span><span class="p">,</span> <span class="n" style="color: #333;">packages</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">rpackages</span></span>
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<td class="new_line diff-line-num new" data-linenumber="42" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
42
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC42" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
43
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC43" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">############# Description ##################</span></span>
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<td class="new_line diff-line-num new" data-linenumber="44" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
44
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC44" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="45" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
45
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC45" class="line" lang="python"><span class="n" style="color: #333;">short_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"CGI"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
46
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC46" class="line" lang="python"><span class="n" style="color: #333;">long_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Chemical Genetic Analysis"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
47
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC47" class="line" lang="python"><span class="n" style="color: #333;">short_desc</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"CGI Analysis of CRISPRi libraries"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
48
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC48" class="line" lang="python"><span class="n" style="color: #333;">long_desc</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"CGI Analysis of CRISPRi libraries"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
49
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC49" class="line" lang="python"><span class="n" style="color: #333;">transposons</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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50
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC50" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="51" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
51
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC51" class="line" lang="python"><span class="n" style="color: #333;">columns</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"Position"</span><span class="p">,</span><span class="s" style="color: #d14;">"Reads"</span><span class="p">,</span><span class="s" style="color: #d14;">"Genes"</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;"># ???</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC52" class="line" lang="python"></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC53" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">############# Analysis Method ##############</span></span>
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54
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC54" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
55
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC55" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">CGI</span><span class="p">(</span><span class="n" style="color: #333;">base</span><span class="p">.</span><span class="n" style="color: #333;">TransitAnalysis</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="56" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
56
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="57" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
57
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">base</span><span class="p">.</span><span class="n" style="color: #333;">TransitAnalysis</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">short_name</span><span class="p">,</span> <span class="n" style="color: #333;">long_name</span><span class="p">,</span> <span class="n" style="color: #333;">short_desc</span><span class="p">,</span> <span class="n" style="color: #333;">long_desc</span><span class="p">,</span> <span class="n" style="color: #333;">transposons</span><span class="p">,</span> <span class="n" style="color: #333;">CGI_Method</span><span class="p">,</span> <span class="n" style="color: #333;">CGI_GUI</span><span class="p">,</span> <span class="p">[])</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
58
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC58" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="59" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
59
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC59" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">################## FILE ###################</span></span>
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<td class="new_line diff-line-num new" data-linenumber="60" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
60
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC60" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
61
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC61" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># there is no output file that could be loaded into the GUI</span></span>
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<td class="new_line diff-line-num new" data-linenumber="62" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
62
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC62" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
63
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC63" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#class HeatmapFile(base.TransitFile):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="64" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
64
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC64" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="65" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
65
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC65" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># def __init__(self):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="66" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
66
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC66" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># base.TransitFile.__init__(self, "#CombinedWig", columns) </span></span>
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<td class="new_line diff-line-num new" data-linenumber="67" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
67
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC67" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
68
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC68" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># def getHeader(self, path):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
69
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC69" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># text = """This is file contains mean counts for each gene. Nzmean is mean accross non-zero sites."""</span></span>
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<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
70
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC70" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># return text</span></span>
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71
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC71" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC72" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">################# GUI ##################</span></span>
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73
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC73" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="74" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
74
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC74" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># right now, CGI is just intended for the command-line; TRI</span></span>
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75
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC75" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
76
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC76" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">CGI_GUI</span><span class="p">(</span><span class="n" style="color: #333;">base</span><span class="p">.</span><span class="n" style="color: #333;">AnalysisGUI</span><span class="p">):</span></span>
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77
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC77" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="78" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
78
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC78" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
79
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">base</span><span class="p">.</span><span class="n" style="color: #333;">AnalysisGUI</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">)</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC80" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="81" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
81
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC81" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">########## METHOD #######################</span></span>
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82
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC82" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="83" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
83
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC83" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">CGI_Method</span><span class="p">(</span><span class="n" style="color: #333;">base</span><span class="p">.</span><span class="n" style="color: #333;">SingleConditionMethod</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
84
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC84" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="85" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
85
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">ctrldata</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span> <span class="c1" style="color: #998; font-style: italic;"># initializers for superclass</span></span>
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<td class="new_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
86
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">annotation_path</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span></span>
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<td class="new_line diff-line-num new" data-linenumber="87" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
87
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">output_file</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span></span>
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<td class="new_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
88
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">replicates</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Sum"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="89" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
89
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">normalization</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"nonorm"</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="90" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
90
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">LOESS</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span></span>
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<td class="new_line diff-line-num new" data-linenumber="91" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
91
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">ignoreCodon</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span></span>
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<td class="new_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
92
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">NTerminus</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
93
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">CTerminus</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="94" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
94
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">wxobj</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span></span>
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<td class="new_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
95
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC95" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># this initialization seems pointless for CGI, but must do this for base class...</span></span>
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<td class="new_line diff-line-num new" data-linenumber="96" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
96
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">base</span><span class="p">.</span><span class="n" style="color: #333;">SingleConditionMethod</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">short_name</span><span class="p">,</span> <span class="n" style="color: #333;">long_name</span><span class="p">,</span> <span class="n" style="color: #333;">short_desc</span><span class="p">,</span> <span class="n" style="color: #333;">long_desc</span><span class="p">,</span> <span class="n" style="color: #333;">ctrldata</span><span class="p">,</span> <span class="n" style="color: #333;">annotation_path</span><span class="p">,</span> <span class="n" style="color: #333;">output_file</span><span class="p">,</span> <span class="n" style="color: #333;">replicates</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">replicates</span><span class="p">,</span> <span class="n" style="color: #333;">normalization</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">normalization</span><span class="p">,</span> <span class="n" style="color: #333;">LOESS</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">LOESS</span><span class="p">,</span> <span class="n" style="color: #333;">NTerminus</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">NTerminus</span><span class="p">,</span> <span class="n" style="color: #333;">CTerminus</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">CTerminus</span><span class="p">,</span> <span class="n" style="color: #333;">wxobj</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">wxobj</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="97" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
97
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC97" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
98
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC98" class="line" lang="python"> <span class="nd">@classmethod</span></span>
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<td class="new_line diff-line-num new" data-linenumber="99" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
99
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC99" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">usage_string</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
100
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC100" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"""usage (6 sub-commands):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="101" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
101
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC101" class="line" lang="python"><span class="s" style="color: #d14;"> python3 ../src/transit.py CGI extract_counts <fastq file> <ids file> > <counts file></span></span>
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<td class="new_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
102
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC102" class="line" lang="python"><span class="s" style="color: #d14;"> python3 ../src/transit.py CGI create_combined_counts <comma seperated headers> <counts file 1> <counts file 2> ... <counts file n> > <combined counts file></span></span>
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<td class="new_line diff-line-num new" data-linenumber="103" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
103
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC103" class="line" lang="python"><span class="s" style="color: #d14;"> python3 ../src/transit.py CGI extract_abund <combined counts file> <metadata file> <control condition> <sgRNA strength file> <uninduced ATC file> <drug> <days> > <fractional abundundance file></span></span>
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<td class="new_line diff-line-num new" data-linenumber="104" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
104
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC104" class="line" lang="python"><span class="s" style="color: #d14;"> python3 ../src/transit.py CGI run_model <fractional abundundance file> > <CRISPRi DR results file></span></span>
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<td class="new_line diff-line-num new" data-linenumber="105" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
105
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC105" class="line" lang="python"><span class="s" style="color: #d14;"> python3 ../src/transit.py CGI visualize <fractional abundance> <gene> <output figure location></span></span>
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<td class="new_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
106
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC106" class="line" lang="python"><span class="s" style="color: #d14;"> note: redirect output from stdout to output files as shown above"""</span></span>
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107
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC107" class="line" lang="python"></span>
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108
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC108" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="109" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
109
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC109" class="line" lang="python"> <span class="nd">@classmethod</span></span>
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<td class="new_line diff-line-num new" data-linenumber="110" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
110
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fromargs</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">rawargs</span><span class="p">):</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
111
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">hasR</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="112" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
112
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC112" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: R and rpy2 (~= 3.0) required to run heatmap."</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="113" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
113
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC113" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"After installing R, you can install rpy2 using the command </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">pip install 'rpy2~=3.0'</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="114" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
114
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="115" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
115
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC115" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="116" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
116
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC116" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">kwargs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transit_tools</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">cleanargs</span><span class="p">(</span><span class="n" style="color: #333;">rawargs</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="117" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
117
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">1</span><span class="p">:</span> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">usage_string</span><span class="p">())</span></span>
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<td class="new_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
118
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
119
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="120" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
120
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">kwargs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span></span>
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<td class="new_line diff-line-num new" data-linenumber="121" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
121
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC121" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
122
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nf" style="color: #900; font-weight: 600;">self</span><span class="p">()</span></span>
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123
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC123" class="line" lang="python"></span>
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124
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC124" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">Run</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
125
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC125" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">,</span><span class="n" style="color: #333;">kwargs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">cmd</span><span class="p">,</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">args</span><span class="p">,</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">kwargs</span></span>
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<td class="new_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
126
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC126" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
127
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC127" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"extract_counts"</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="128" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
128
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC128" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">2</span><span class="p">:</span> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">usage_string</span><span class="p">())</span></span>
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<td class="new_line diff-line-num new" data-linenumber="129" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
129
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">fastq_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="130" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
130
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">ids_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="131" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
131
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">extract_counts</span><span class="p">(</span><span class="n" style="color: #333;">fastq_file</span><span class="p">,</span> <span class="n" style="color: #333;">ids_file</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
132
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC132" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="133" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
133
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC133" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"create_combined_counts"</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="134" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
134
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">2</span><span class="p">:</span> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">usage_string</span><span class="p">())</span></span>
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<td class="new_line diff-line-num new" data-linenumber="135" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
135
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">headers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="136" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
136
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">counts_file_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="137" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
137
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">create_combined_counts</span><span class="p">(</span><span class="n" style="color: #333;">headers</span><span class="p">,</span><span class="n" style="color: #333;">counts_file_list</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="138" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
138
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC138" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
139
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC139" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">cmd</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"extract_abund"</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="140" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
140
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC140" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">7</span><span class="p">:</span> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">usage_string</span><span class="p">())</span></span>
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<td class="new_line diff-line-num new" data-linenumber="141" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
141
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">combined_counts_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="142" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
142
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">metadata_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="143" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
143
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">control_condition</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
144
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">sgRNA_strength_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
145
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC145" class="line" lang="python"> <span class="n" style="color: #333;">no_dep_abund</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="146" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
146
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">drug</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
147
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">days</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="148" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
148
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">extract_abund</span><span class="p">(</span><span class="n" style="color: #333;">combined_counts_file</span><span class="p">,</span><span class="n" style="color: #333;">metadata_file</span><span class="p">,</span><span class="n" style="color: #333;">control_condition</span><span class="p">,</span><span class="n" style="color: #333;">sgRNA_strength_file</span><span class="p">,</span><span class="n" style="color: #333;">no_dep_abund</span><span class="p">,</span><span class="n" style="color: #333;">drug</span><span class="p">,</span><span class="n" style="color: #333;">days</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="149" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
149
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC149" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"run_model"</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
150
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC150" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">1</span><span class="p">:</span> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">usage_string</span><span class="p">())</span></span>
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<td class="new_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
151
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">ifile_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;">#example frac_abund_RIF_D5.txt</span></span>
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<td class="new_line diff-line-num new" data-linenumber="152" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
152
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">run_model</span><span class="p">(</span><span class="n" style="color: #333;">ifile_path</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="153" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
153
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC153" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"visualize"</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="154" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
154
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC154" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">3</span><span class="p">:</span> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">usage_string</span><span class="p">())</span></span>
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<td class="new_line diff-line-num new" data-linenumber="155" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
155
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">frac_abund_file</span><span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="156" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
156
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">gene</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="157" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
157
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">fig_location</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="158" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
158
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">visualize</span><span class="p">(</span><span class="n" style="color: #333;">frac_abund_file</span><span class="p">,</span> <span class="n" style="color: #333;">gene</span><span class="p">,</span> <span class="n" style="color: #333;">fig_location</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="159" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
159
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC159" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="160" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
160
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC160" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">usage_string</span><span class="p">())</span></span>
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<td class="new_line diff-line-num new" data-linenumber="161" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
161
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC161" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
162
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC162" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">reverse_complement</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="163" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
163
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC163" class="line" lang="python"> <span class="n" style="color: #333;">complement</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'A'</span><span class="p">:</span><span class="s" style="color: #d14;">'T'</span><span class="p">,</span><span class="s" style="color: #d14;">'T'</span><span class="p">:</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span><span class="s" style="color: #d14;">'C'</span><span class="p">:</span><span class="s" style="color: #d14;">'G'</span><span class="p">,</span><span class="s" style="color: #d14;">'G'</span><span class="p">:</span><span class="s" style="color: #d14;">'C'</span><span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="164" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
164
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">list</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="165" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
165
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">reverse</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="166" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
166
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC166" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nf" style="color: #900; font-weight: 600;">range</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="167" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
167
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC167" class="line" lang="python"> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">complement</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">get</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span><span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span> <span class="c1" style="color: #998; font-style: italic;"># if unknown, leave as it, e.g > or !</span></span>
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<td class="new_line diff-line-num new" data-linenumber="168" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
168
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC168" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="169" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
169
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC169" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">s</span></span>
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<td class="new_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
170
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC170" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="171" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
171
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC171" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">extract_counts</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">fastq_file</span><span class="p">,</span> <span class="n" style="color: #333;">ids_file</span><span class="p">):</span></span>
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172
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC172" class="line" lang="python"> <span class="n" style="color: #333;">IDs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="173" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
173
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC173" class="line" lang="python"> <span class="n" style="color: #333;">barcodemap</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span> <span class="c1" style="color: #998; font-style: italic;"># hash from barcode to full ids</span></span>
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<td class="new_line diff-line-num new" data-linenumber="174" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
174
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC174" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333;">ids_file</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="175" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
175
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC175" class="line" lang="python"> <span class="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">rstrip</span><span class="p">().</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="176" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
176
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC176" class="line" lang="python"> <span class="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="177" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
177
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">id</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'_'</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="178" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
178
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC178" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">)</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">3</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="new_line diff-line-num new" data-linenumber="179" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
179
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC179" class="line" lang="python"> <span class="n" style="color: #333;">barcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">v</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="180" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
180
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC180" class="line" lang="python"> <span class="n" style="color: #333;">IDs</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="nb" style="color: #0086b3;">id</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
181
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC181" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># reverse-complement of barcodes appears in reads, so hash them that way</span></span>
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<td class="new_line diff-line-num new" data-linenumber="182" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
182
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">barcodemap</span><span class="p">[</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">reverse_complement</span><span class="p">(</span><span class="n" style="color: #333;">barcode</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">id</span></span>
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<td class="new_line diff-line-num new" data-linenumber="183" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
183
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC183" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="184" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
184
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC184" class="line" lang="python"> <span class="n" style="color: #333;">counts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="185" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
185
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC185" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="186" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
186
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC186" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#A,B = "AGCTTCTTTCGAGTACAAAAAC","TCCCAGATTATATCTATCACTGA"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="187" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
187
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC187" class="line" lang="python"> <span class="n" style="color: #333;">A</span><span class="p">,</span><span class="n" style="color: #333;">B</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"GTACAAAAAC"</span><span class="p">,</span><span class="s" style="color: #d14;">"TCCCAGATTA"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="188" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
188
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">lenA</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">A</span><span class="p">)</span></span>
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189
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC189" class="line" lang="python"> <span class="n" style="color: #333;">cnt</span><span class="p">,</span><span class="n" style="color: #333;">nreads</span><span class="p">,</span><span class="n" style="color: #333;">recognized</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="190" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
190
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC190" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333;">fastq_file</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="191" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
191
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">cnt</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="192" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
192
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC192" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cnt</span><span class="o" style="font-weight: 600;">%</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">2</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
193
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">nreads</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="194" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
194
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC194" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">if </span><span class="p">(</span><span class="n" style="color: #333;">nreads</span><span class="o" style="font-weight: 600;">%</span><span class="mi" style="color: #099;">1000000</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">):</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"reads=%s, recognized barcodes=%s (%0.1f%%)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">nreads</span><span class="p">,</span><span class="n" style="color: #333;">recognized</span><span class="p">,</span><span class="mf" style="color: #099;">100.</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">recognized</span><span class="o" style="font-weight: 600;">/</span><span class="nf" style="color: #900; font-weight: 600;">float</span><span class="p">(</span><span class="n" style="color: #333;">nreads</span><span class="p">)))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="195" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
195
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">rstrip</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="196" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
196
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">find</span><span class="p">(</span><span class="n" style="color: #333;">A</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="197" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
197
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC197" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">==-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="new_line diff-line-num new" data-linenumber="198" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
198
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">find</span><span class="p">(</span><span class="n" style="color: #333;">B</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="199" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
199
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC199" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">==-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="200" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
200
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">sz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">lenA</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="201" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
201
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC201" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sz</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">10</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">sz</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">30</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="new_line diff-line-num new" data-linenumber="202" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
202
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">barcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">lenA</span><span class="p">:</span><span class="n" style="color: #333;">b</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;"># these are reverse-complements, but rc(barcodes) stored in hash too</span></span>
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<td class="new_line diff-line-num new" data-linenumber="203" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
203
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC203" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">barcode</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">barcodemap</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="new_line diff-line-num new" data-linenumber="204" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
204
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC204" class="line" lang="python"> <span class="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">barcodemap</span><span class="p">[</span><span class="n" style="color: #333;">barcode</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="205" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
205
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">id</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">counts</span><span class="p">:</span> <span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="nb" style="color: #0086b3;">id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="206" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
206
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="nb" style="color: #0086b3;">id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="207" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
207
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">recognized</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="208" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
208
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC208" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="209" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
209
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC209" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="nb" style="color: #0086b3;">id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">IDs</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
210
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">vals</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">id</span><span class="p">,</span><span class="n" style="color: #333;">counts</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">get</span><span class="p">(</span><span class="nb" style="color: #0086b3;">id</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">)]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="211" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
211
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC211" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">([</span><span class="nf" style="color: #900; font-weight: 600;">str</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">vals</span><span class="p">]))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="212" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
212
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC212" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="213" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
213
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC213" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="214" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
214
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC214" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">create_combined_counts</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span><span class="n" style="color: #333;">headers</span><span class="p">,</span> <span class="n" style="color: #333;">counts_list</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="215" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
215
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC215" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">pandas</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pd</span></span>
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<td class="new_line diff-line-num new" data-linenumber="216" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
216
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">df_list</span> <span class="o" style="font-weight: 600;">=</span><span class="p">[]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="217" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
217
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC217" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">counts_list</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="218" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
218
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC218" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Adding in file # %s </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="219" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
219
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC219" class="line" lang="python"> <span class="n" style="color: #333;">counts_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">read_csv</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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220
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC220" class="line" lang="python"> <span class="n" style="color: #333;">counts_df</span><span class="p">[</span><span class="s" style="color: #d14;">"sgRNA"</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">counts_df</span><span class="p">[</span><span class="n" style="color: #333;">counts_df</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]].</span><span class="nb" style="color: #0086b3;">str</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_v"</span><span class="p">,</span> <span class="n" style="color: #333;">expand</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="221" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
221
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC221" class="line" lang="python"> <span class="n" style="color: #333;">counts_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">counts_df</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">drop</span><span class="p">(</span><span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">counts_df</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="222" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
222
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">counts_df</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">set_index</span><span class="p">(</span><span class="s" style="color: #d14;">"sgRNA"</span><span class="p">,</span><span class="n" style="color: #333;">inplace</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="223" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
223
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">df_list</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">counts_df</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="224" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
224
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC224" class="line" lang="python"> <span class="n" style="color: #333;">combined_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">concat</span><span class="p">(</span><span class="n" style="color: #333;">df_list</span><span class="p">,</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="225" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
225
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC225" class="line" lang="python"> <span class="n" style="color: #333;">combined_df</span><span class="p">.</span><span class="n" style="color: #333;">columns</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">headers</span></span>
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<td class="new_line diff-line-num new" data-linenumber="226" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
226
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC226" class="line" lang="python"> <span class="n" style="color: #333;">combined_df_text</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">combined_df</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_csv</span><span class="p">(</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="227" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
227
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC227" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Number of sgRNAs in combined counts file (present in all counts files): %d </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">%</span><span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">combined_df</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="228" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
228
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC228" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">combined_df_text</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="229" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
229
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC229" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="230" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
230
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC230" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="231" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
231
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC231" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">extract_abund</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span><span class="n" style="color: #333;">combined_counts_file</span><span class="p">,</span><span class="n" style="color: #333;">metadata_file</span><span class="p">,</span><span class="n" style="color: #333;">control_condition</span><span class="p">,</span><span class="n" style="color: #333;">sgRNA_strength_file</span><span class="p">,</span><span class="n" style="color: #333;">no_dep_abund</span><span class="p">,</span><span class="n" style="color: #333;">drug</span><span class="p">,</span><span class="n" style="color: #333;">days</span><span class="p">,</span><span class="n" style="color: #333;">PC</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1e-8</span><span class="p">):</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="232" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
232
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC232" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">pandas</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pd</span></span>
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<td class="new_line diff-line-num new" data-linenumber="233" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
233
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC233" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="234" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
234
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC234" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">read_csv</span><span class="p">(</span><span class="n" style="color: #333;">metadata_file</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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235
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC235" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">[((</span><span class="n" style="color: #333;">metadata</span><span class="p">[</span><span class="s" style="color: #d14;">"drug"</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">drug</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="n" style="color: #333;">metadata</span><span class="p">[</span><span class="s" style="color: #d14;">"drug"</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">control_condition</span><span class="p">))</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">metadata</span><span class="p">[</span><span class="s" style="color: #d14;">"days_predepletion"</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">days</span><span class="p">))]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="236" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
236
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC236" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">if</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">metadata</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="237" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
237
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC237" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"This combination of conditions does not exist in your metadata file. Please select one that does"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="238" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
238
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC238" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="239" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
239
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC239" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">elif </span><span class="p">(</span><span class="n" style="color: #333;">drug</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">metadata</span><span class="p">[</span><span class="s" style="color: #d14;">"drug"</span><span class="p">].</span><span class="n" style="color: #333;">values</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">tolist</span><span class="p">()):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
240
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC240" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"%s is not found in your metadata. Add the drug's information in the metadata file or select a different drug"</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">drug</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="241" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
241
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC241" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="242" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
242
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC242" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">elif </span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">days</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">metadata</span><span class="p">[</span><span class="s" style="color: #d14;">"days_predepletion"</span><span class="p">].</span><span class="n" style="color: #333;">values</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">tolist</span><span class="p">()):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="243" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
243
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC243" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"%d is not found in your metadata days of predepletion column. Add the day's information in the metadata file or select a different day"</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">days</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="244" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
244
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC244" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="245" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
245
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC245" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">elif </span><span class="p">(</span><span class="n" style="color: #333;">control_condition</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">metadata</span><span class="p">[</span><span class="s" style="color: #d14;">"drug"</span><span class="p">].</span><span class="n" style="color: #333;">values</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">tolist</span><span class="p">()):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="246" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
246
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC246" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"%s is not found in your metadata. Add the corresponding information in the metadata file or select a different control"</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">control_condition</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="247" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
247
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC247" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="248" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
248
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC248" class="line" lang="python"> <span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">sort_values</span><span class="p">(</span><span class="n" style="color: #333;">by</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"conc_xMIC"</span><span class="p">])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="249" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
249
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC249" class="line" lang="python"> <span class="n" style="color: #333;">column_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">[</span><span class="s" style="color: #d14;">"column_name"</span><span class="p">].</span><span class="n" style="color: #333;">values</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">tolist</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="250" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
250
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC250" class="line" lang="python"> <span class="n" style="color: #333;">concs_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metadata</span><span class="p">[</span><span class="s" style="color: #d14;">"conc_xMIC"</span><span class="p">].</span><span class="n" style="color: #333;">values</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">tolist</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="251" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
251
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC251" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="252" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
252
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC252" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# Condition Tested : "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">drug</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" D"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">days</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="253" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
253
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC253" class="line" lang="python"> <span class="n" style="color: #333;">headers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="254" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
254
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC254" class="line" lang="python"> <span class="n" style="color: #333;">combined_counts_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">read_csv</span><span class="p">(</span><span class="n" style="color: #333;">combined_counts_file</span><span class="p">,</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">index_col</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="255" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
255
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC255" class="line" lang="python"> <span class="n" style="color: #333;">combined_counts_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">combined_counts_df</span><span class="p">[</span><span class="n" style="color: #333;">column_names</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
256
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC256" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="257" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
257
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC257" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">if</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">combined_counts_df</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="258" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
258
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC258" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"The samples assocaited with the selected drugs do not exist in your combined counts file. Please select one that does and check your metadata file has corresponding column names"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="259" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
259
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC259" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="260" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
260
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC260" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">elif</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">combined_counts_df</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">)</span><span class="o" style="font-weight: 600;"><</span><span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">metadata</span><span class="p">)):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="261" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
261
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC261" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"WARNING: Not all of the samples from the metadata based on this criteron have a column in the combined counts file"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
262
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC262" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="263" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
263
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC263" class="line" lang="python"> <span class="n" style="color: #333;">sgRNA_strength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">read_csv</span><span class="p">(</span><span class="n" style="color: #333;">sgRNA_strength_file</span><span class="p">,</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">index_col</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="264" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
264
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC264" class="line" lang="python"> <span class="n" style="color: #333;">sgRNA_strength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sgRNA_strength</span><span class="p">.</span><span class="n" style="color: #333;">iloc</span><span class="p">[:,</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:]</span></span>
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265
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC265" class="line" lang="python"> <span class="n" style="color: #333;">sgRNA_strength</span><span class="p">.</span><span class="n" style="color: #333;">columns</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"sgRNA strength"</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="266" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
266
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC266" class="line" lang="python"> <span class="n" style="color: #333;">sgRNA_strength</span><span class="p">[</span><span class="s" style="color: #d14;">"sgRNA"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sgRNA_strength</span><span class="p">.</span><span class="n" style="color: #333;">index</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="267" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
267
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC267" class="line" lang="python"> <span class="n" style="color: #333;">sgRNA_strength</span><span class="p">[</span><span class="s" style="color: #d14;">"sgRNA"</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sgRNA_strength</span><span class="p">[</span><span class="s" style="color: #d14;">"sgRNA"</span><span class="p">].</span><span class="nb" style="color: #0086b3;">str</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_v"</span><span class="p">,</span> <span class="n" style="color: #333;">expand</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="268" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
268
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC268" class="line" lang="python"> <span class="n" style="color: #333;">sgRNA_strength</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">set_index</span><span class="p">(</span><span class="s" style="color: #d14;">"sgRNA"</span><span class="p">,</span><span class="n" style="color: #333;">inplace</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="269" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
269
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC269" class="line" lang="python"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="270" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
270
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC270" class="line" lang="python"> <span class="n" style="color: #333;">no_dep_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">read_csv</span><span class="p">(</span><span class="n" style="color: #333;">no_dep_abund</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">index_col</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="271" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
271
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC271" class="line" lang="python"> <span class="n" style="color: #333;">no_dep_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">no_dep_df</span><span class="p">.</span><span class="n" style="color: #333;">iloc</span><span class="p">[:,</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="272" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
272
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC272" class="line" lang="python"> <span class="n" style="color: #333;">no_dep_df</span><span class="p">.</span><span class="n" style="color: #333;">columns</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"uninduced ATC values"</span><span class="p">]</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="273" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
273
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC273" class="line" lang="python"> <span class="n" style="color: #333;">no_dep_df</span><span class="p">[</span><span class="s" style="color: #d14;">"uninduced ATC values"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">no_dep_df</span><span class="p">[</span><span class="s" style="color: #d14;">"uninduced ATC values"</span><span class="p">]</span><span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">no_dep_df</span><span class="p">[</span><span class="s" style="color: #d14;">"uninduced ATC values"</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">sum</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="274" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
274
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC274" class="line" lang="python"> <span class="n" style="color: #333;">no_dep_df</span><span class="p">[</span><span class="s" style="color: #d14;">"sgRNA"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">no_dep_df</span><span class="p">.</span><span class="n" style="color: #333;">index</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="275" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
275
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC275" class="line" lang="python"> <span class="n" style="color: #333;">no_dep_df</span><span class="p">[</span><span class="s" style="color: #d14;">"sgRNA"</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">no_dep_df</span><span class="p">[</span><span class="s" style="color: #d14;">"sgRNA"</span><span class="p">].</span><span class="nb" style="color: #0086b3;">str</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_v"</span><span class="p">,</span> <span class="n" style="color: #333;">expand</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="276" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
276
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC276" class="line" lang="python"> <span class="n" style="color: #333;">no_dep_df</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">set_index</span><span class="p">(</span><span class="s" style="color: #d14;">"sgRNA"</span><span class="p">,</span><span class="n" style="color: #333;">inplace</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="277" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
277
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC277" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="278" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
278
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC278" class="line" lang="python"> <span class="n" style="color: #333;">abund_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">concat</span><span class="p">([</span><span class="n" style="color: #333;">sgRNA_strength</span><span class="p">,</span> <span class="n" style="color: #333;">no_dep_df</span><span class="p">,</span><span class="n" style="color: #333;">combined_counts_df</span><span class="p">],</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="279" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
279
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC279" class="line" lang="python"> <span class="n" style="color: #333;">abund_df</span><span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">abund_df</span><span class="p">[</span><span class="o" style="font-weight: 600;">~</span><span class="p">(</span><span class="n" style="color: #333;">abund_df</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">.</span><span class="nb" style="color: #0086b3;">str</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">contains</span><span class="p">(</span><span class="s" style="color: #d14;">"Negative"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">abund_df</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">.</span><span class="nb" style="color: #0086b3;">str</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">contains</span><span class="p">(</span><span class="s" style="color: #d14;">"Empty"</span><span class="p">))]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="280" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
280
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC280" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Disregarding Empty or Negative sgRNAs</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="281" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
281
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC281" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"%d sgRNAs are all of the following files : sgRNA strength metadata, uninduced ATC counts file, combined counts file</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">%</span><span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">abund_df</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="282" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
282
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC282" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="283" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
283
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC283" class="line" lang="python"> <span class="n" style="color: #333;">headers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"sgRNA strength"</span><span class="p">,</span><span class="s" style="color: #d14;">"uninduced ATC values"</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="284" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
284
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC284" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">col</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nf" style="color: #900; font-weight: 600;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">column_names</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="285" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
285
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC285" class="line" lang="python"> <span class="n" style="color: #333;">abund_df</span><span class="p">[</span><span class="n" style="color: #333;">col</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">abund_df</span><span class="p">[</span><span class="n" style="color: #333;">col</span><span class="p">]</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">abund_df</span><span class="p">[</span><span class="n" style="color: #333;">col</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">sum</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="286" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
286
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC286" class="line" lang="python"> <span class="n" style="color: #333;">abund_df</span><span class="p">[</span><span class="n" style="color: #333;">col</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">abund_df</span><span class="p">[</span><span class="n" style="color: #333;">col</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">PC</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="n" style="color: #333;">abund_df</span><span class="p">[</span><span class="s" style="color: #d14;">"uninduced ATC values"</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">PC</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="287" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
287
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC287" class="line" lang="python"> <span class="n" style="color: #333;">headers</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">str</span><span class="p">(</span><span class="n" style="color: #333;">concs_list</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"_"</span><span class="o" style="font-weight: 600;">+</span><span class="nf" style="color: #900; font-weight: 600;">str</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="288" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
288
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC288" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# "</span><span class="o" style="font-weight: 600;">+</span><span class="nf" style="color: #900; font-weight: 600;">str</span><span class="p">(</span><span class="n" style="color: #333;">concs_list</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" conc_xMIC"</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" - "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">col</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="289" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
289
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC289" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="290" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
290
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC290" class="line" lang="python"> <span class="n" style="color: #333;">abund_df</span><span class="p">.</span><span class="n" style="color: #333;">columns</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">headers</span></span>
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<td class="new_line diff-line-num new" data-linenumber="291" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
291
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC291" class="line" lang="python"> <span class="n" style="color: #333;">abund_df</span><span class="p">[</span><span class="s" style="color: #d14;">"sgRNA"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">abund_df</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">tolist</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="292" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
292
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC292" class="line" lang="python"> <span class="n" style="color: #333;">abund_df</span><span class="p">[[</span><span class="s" style="color: #d14;">"orf-gene"</span><span class="p">,</span><span class="s" style="color: #d14;">"remaining"</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">abund_df</span><span class="p">[</span><span class="s" style="color: #d14;">"sgRNA"</span><span class="p">].</span><span class="nb" style="color: #0086b3;">str</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'_'</span><span class="p">,</span><span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">expand</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="293" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
293
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC293" class="line" lang="python"> <span class="n" style="color: #333;">abund_df</span><span class="p">[[</span><span class="s" style="color: #d14;">"orf"</span><span class="p">,</span><span class="s" style="color: #d14;">"gene"</span><span class="p">]]</span><span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">abund_df</span><span class="p">[</span><span class="s" style="color: #d14;">"orf-gene"</span><span class="p">].</span><span class="nb" style="color: #0086b3;">str</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">':'</span><span class="p">,</span><span class="n" style="color: #333;">expand</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="294" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
294
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC294" class="line" lang="python"> <span class="n" style="color: #333;">abund_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">abund_df</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">drop</span><span class="p">(</span><span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"orf-gene"</span><span class="p">,</span><span class="s" style="color: #d14;">"remaining"</span><span class="p">,</span><span class="s" style="color: #d14;">"sgRNA"</span><span class="p">])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="295" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
295
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC295" class="line" lang="python"> <span class="n" style="color: #333;">abund_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">abund_df</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">dropna</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="296" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
296
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC296" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="297" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
297
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC297" class="line" lang="python"> <span class="n" style="color: #333;">abund_df</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">insert</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">"sgRNA strength"</span><span class="p">,</span> <span class="n" style="color: #333;">abund_df</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">"sgRNA strength"</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="298" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
298
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC298" class="line" lang="python"> <span class="n" style="color: #333;">abund_df</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">insert</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">"uninduced ATC values"</span><span class="p">,</span> <span class="n" style="color: #333;">abund_df</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">"uninduced ATC values"</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="299" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
299
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC299" class="line" lang="python"> <span class="n" style="color: #333;">abund_df</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">insert</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">'gene'</span><span class="p">,</span> <span class="n" style="color: #333;">abund_df</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'gene'</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="300" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
300
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC300" class="line" lang="python"> <span class="n" style="color: #333;">abund_df</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">insert</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">'orf'</span><span class="p">,</span> <span class="n" style="color: #333;">abund_df</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'orf'</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="301" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
301
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC301" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="302" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
302
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC302" class="line" lang="python"> <span class="n" style="color: #333;">abund_df_text</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">abund_df</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_csv</span><span class="p">(</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="303" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
303
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC303" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">abund_df_text</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="304" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
304
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC304" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="305" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
305
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC305" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="306" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
306
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC306" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#####################################################</span></span>
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<td class="new_line diff-line-num new" data-linenumber="307" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
307
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC307" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="308" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
308
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC308" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># derived from logsigmoidfit.R</span></span>
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<td class="new_line diff-line-num new" data-linenumber="309" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
309
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC309" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># see heatmap.py for example of how to put data in a pandas.DataFrame and call an R function like make_heatmapFunc()</span></span>
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310
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC310" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="311" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
311
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC311" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_model</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">frac_abund_file</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="312" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
312
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC312" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">pandas</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pd</span></span>
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<td class="new_line diff-line-num new" data-linenumber="313" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
313
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC313" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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<td class="new_line diff-line-num new" data-linenumber="314" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
314
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC314" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">mne.stats</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">fdr_correction</span></span>
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<td class="new_line diff-line-num new" data-linenumber="315" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
315
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC315" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">statsmodels.api</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">sm</span></span>
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<td class="new_line diff-line-num new" data-linenumber="316" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
316
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC316" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="317" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
317
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC317" class="line" lang="python"> <span class="n" style="color: #333;">frac_abund_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">read_csv</span><span class="p">(</span><span class="n" style="color: #333;">frac_abund_file</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">comment</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'#'</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="318" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
318
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC318" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="319" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
319
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC319" class="line" lang="python"> <span class="n" style="color: #333;">drug_output</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="320" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
320
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC320" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">gene</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nf" style="color: #900; font-weight: 600;">enumerate</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">set</span><span class="p">(</span><span class="n" style="color: #333;">frac_abund_df</span><span class="p">[</span><span class="s" style="color: #d14;">"gene"</span><span class="p">])):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="321" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
321
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC321" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print(i,gene)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="322" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
322
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC322" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Analyzing Gene # %d </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="323" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
323
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC323" class="line" lang="python"> <span class="n" style="color: #333;">gene_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">frac_abund_df</span><span class="p">[</span><span class="n" style="color: #333;">frac_abund_df</span><span class="p">[</span><span class="s" style="color: #d14;">"gene"</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">gene</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="324" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
324
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC324" class="line" lang="python"> <span class="n" style="color: #333;">orf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_df</span><span class="p">[</span><span class="s" style="color: #d14;">"orf"</span><span class="p">].</span><span class="n" style="color: #333;">iloc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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325
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC325" class="line" lang="python"> <span class="n" style="color: #333;">gene_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_df</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">drop</span><span class="p">(</span><span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"orf"</span><span class="p">,</span><span class="s" style="color: #d14;">"gene"</span><span class="p">,</span><span class="s" style="color: #d14;">"uninduced ATC values"</span><span class="p">])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="326" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
326
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC326" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="327" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
327
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC327" class="line" lang="python"> <span class="n" style="color: #333;">melted_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_df</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">melt</span><span class="p">(</span><span class="n" style="color: #333;">id_vars</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"sgRNA"</span><span class="p">,</span><span class="s" style="color: #d14;">"sgRNA strength"</span><span class="p">],</span><span class="n" style="color: #333;">var_name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"conc"</span><span class="p">,</span><span class="n" style="color: #333;">value_name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"abund"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="328" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
328
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC328" class="line" lang="python"> <span class="n" style="color: #333;">melted_df</span><span class="p">[</span><span class="s" style="color: #d14;">"conc"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">melted_df</span><span class="p">[</span><span class="s" style="color: #d14;">"conc"</span><span class="p">].</span><span class="nb" style="color: #0086b3;">str</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_"</span><span class="p">,</span> <span class="n" style="color: #333;">expand</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">astype</span><span class="p">(</span><span class="nb" style="color: #0086b3;">float</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="329" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
329
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC329" class="line" lang="python"> <span class="n" style="color: #333;">min_conc</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">min</span><span class="p">(</span><span class="n" style="color: #333;">melted_df</span><span class="p">[</span><span class="n" style="color: #333;">melted_df</span><span class="p">[</span><span class="s" style="color: #d14;">"conc"</span><span class="p">]</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="s" style="color: #d14;">"conc"</span><span class="p">])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="330" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
330
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC330" class="line" lang="python"> <span class="n" style="color: #333;">melted_df</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">melted_df</span><span class="p">[</span><span class="s" style="color: #d14;">"conc"</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="s" style="color: #d14;">"conc"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">min_conc</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">2</span></span>
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<td class="new_line diff-line-num new" data-linenumber="331" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
331
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC331" class="line" lang="python"> <span class="n" style="color: #333;">melted_df</span><span class="p">[</span><span class="s" style="color: #d14;">"abund"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mf" style="color: #099;">0.01</span><span class="o" style="font-weight: 600;">+</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">0.01</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">exp</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">float</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)))</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">exp</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">float</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">melted_df</span><span class="p">[</span><span class="s" style="color: #d14;">"abund"</span><span class="p">]]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="332" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
332
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC332" class="line" lang="python"> <span class="n" style="color: #333;">melted_df</span><span class="p">[</span><span class="s" style="color: #d14;">"logsig abund"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">nan</span> <span class="nf" style="color: #900; font-weight: 600;">if </span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">x</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">log10</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">float</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="nf" style="color: #900; font-weight: 600;">float</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">melted_df</span><span class="p">[</span><span class="s" style="color: #d14;">"abund"</span><span class="p">]]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="333" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
333
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC333" class="line" lang="python"> <span class="n" style="color: #333;">melted_df</span><span class="p">[</span><span class="s" style="color: #d14;">"log conc"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">log2</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">float</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">melted_df</span><span class="p">[</span><span class="s" style="color: #d14;">"conc"</span><span class="p">]]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="334" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
334
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC334" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="335" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
335
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC335" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="336" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
336
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC336" class="line" lang="python"> <span class="n" style="color: #333;">melted_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">melted_df</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">dropna</span><span class="p">()</span></span>
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337
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC337" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">melted_df</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">)</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">2</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="338" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
338
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC338" class="line" lang="python"> <span class="n" style="color: #333;">drug_output</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">([</span><span class="n" style="color: #333;">orf</span><span class="p">,</span><span class="n" style="color: #333;">gene</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">gene_df</span><span class="p">)]</span><span class="o" style="font-weight: 600;">+</span><span class="p">[</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">nan</span><span class="p">]</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">6</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
339
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC339" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="new_line diff-line-num new" data-linenumber="340" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
340
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC340" class="line" lang="python"> </span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="341" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
341
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC341" class="line" lang="python"> <span class="n" style="color: #333;">Y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">melted_df</span><span class="p">[</span><span class="s" style="color: #d14;">"logsig abund"</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="342" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
342
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC342" class="line" lang="python"> <span class="n" style="color: #333;">X</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">melted_df</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">drop</span><span class="p">(</span><span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"abund"</span><span class="p">,</span> <span class="s" style="color: #d14;">"logsig abund"</span><span class="p">,</span> <span class="s" style="color: #d14;">"sgRNA"</span><span class="p">,</span> <span class="s" style="color: #d14;">"conc"</span><span class="p">])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="343" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
343
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC343" class="line" lang="python"> <span class="n" style="color: #333;">X</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sm</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">add_constant</span><span class="p">(</span><span class="n" style="color: #333;">X</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="344" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
344
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC344" class="line" lang="python"> <span class="n" style="color: #333;">model</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sm</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">OLS</span><span class="p">(</span><span class="n" style="color: #333;">Y</span><span class="p">,</span><span class="n" style="color: #333;">X</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="345" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
345
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC345" class="line" lang="python"> <span class="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">fit</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="346" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
346
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC346" class="line" lang="python"> <span class="n" style="color: #333;">coeffs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</span><span class="p">.</span><span class="n" style="color: #333;">params</span></span>
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<td class="new_line diff-line-num new" data-linenumber="347" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
347
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC347" class="line" lang="python"> <span class="n" style="color: #333;">pvals</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</span><span class="p">.</span><span class="n" style="color: #333;">pvalues</span></span>
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<td class="new_line diff-line-num new" data-linenumber="348" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
348
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC348" class="line" lang="python"> <span class="n" style="color: #333;">drug_output</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">([</span><span class="n" style="color: #333;">orf</span><span class="p">,</span><span class="n" style="color: #333;">gene</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">gene_df</span><span class="p">)]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">coeffs</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">tolist</span><span class="p">()</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">pvals</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">tolist</span><span class="p">())</span></span>
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<td class="new_line diff-line-num new" data-linenumber="349" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
349
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC349" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">flush</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="350" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
350
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC350" class="line" lang="python"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="351" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
351
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC351" class="line" lang="python"> <span class="n" style="color: #333;">drug_out_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">DataFrame</span><span class="p">(</span><span class="n" style="color: #333;">drug_output</span><span class="p">,</span> <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"Orf"</span><span class="p">,</span><span class="s" style="color: #d14;">"Gene"</span><span class="p">,</span><span class="s" style="color: #d14;">"Nobs"</span><span class="p">,</span> <span class="s" style="color: #d14;">"intercept"</span><span class="p">,</span><span class="s" style="color: #d14;">"ceofficient sgRNA_strength"</span><span class="p">,</span><span class="s" style="color: #d14;">"ceofficient concentration dependence"</span><span class="p">,</span><span class="s" style="color: #d14;">"pval intercept"</span><span class="p">,</span><span class="s" style="color: #d14;">"pval pred_logFC"</span><span class="p">,</span><span class="s" style="color: #d14;">"pval concentration dependence"</span><span class="p">])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="352" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
352
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC352" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="353" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
353
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC353" class="line" lang="python"> <span class="n" style="color: #333;">mask</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">isfinite</span><span class="p">(</span><span class="n" style="color: #333;">drug_out_df</span><span class="p">[</span><span class="s" style="color: #d14;">"pval concentration dependence"</span><span class="p">])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="354" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
354
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC354" class="line" lang="python"> <span class="n" style="color: #333;">pval_corrected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">full</span><span class="p">(</span><span class="n" style="color: #333;">drug_out_df</span><span class="p">[</span><span class="s" style="color: #d14;">"pval concentration dependence"</span><span class="p">].</span><span class="n" style="color: #333;">shape</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">nan</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="355" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
355
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC355" class="line" lang="python"> <span class="n" style="color: #333;">pval_corrected</span><span class="p">[</span><span class="n" style="color: #333;">mask</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">fdr_correction</span><span class="p">(</span><span class="n" style="color: #333;">drug_out_df</span><span class="p">[</span><span class="s" style="color: #d14;">"pval concentration dependence"</span><span class="p">][</span><span class="n" style="color: #333;">mask</span><span class="p">])[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
356
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC356" class="line" lang="python"> <span class="n" style="color: #333;">drug_out_df</span><span class="p">[</span><span class="s" style="color: #d14;">"qval concentration dependence"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pval_corrected</span></span>
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<td class="new_line diff-line-num new" data-linenumber="357" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
357
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC357" class="line" lang="python"> <span class="n" style="color: #333;">drug_out_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">drug_out_df</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">replace</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">nan</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="358" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
358
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC358" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="359" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
359
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC359" class="line" lang="python"> <span class="n" style="color: #333;">drug_out_df</span><span class="p">[</span><span class="s" style="color: #d14;">"Z"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">drug_out_df</span><span class="p">[</span><span class="s" style="color: #d14;">"ceofficient concentration dependence"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">drug_out_df</span><span class="p">[</span><span class="s" style="color: #d14;">"ceofficient concentration dependence"</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">mean</span><span class="p">())</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">drug_out_df</span><span class="p">[</span><span class="s" style="color: #d14;">"ceofficient concentration dependence"</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">std</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="360" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
360
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC360" class="line" lang="python"> <span class="n" style="color: #333;">drug_out_df</span><span class="p">[</span><span class="s" style="color: #d14;">"Siginificant Interactions"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">drug_out_df</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="361" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
361
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC361" class="line" lang="python"> <span class="n" style="color: #333;">drug_out_df</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[(</span><span class="n" style="color: #333;">drug_out_df</span><span class="p">[</span><span class="s" style="color: #d14;">"qval concentration dependence"</span><span class="p">]</span><span class="o" style="font-weight: 600;"><</span><span class="mf" style="color: #099;">0.05</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">drug_out_df</span><span class="p">[</span><span class="s" style="color: #d14;">"Z"</span><span class="p">]</span><span class="o" style="font-weight: 600;"><-</span><span class="mi" style="color: #099;">2</span><span class="p">),</span><span class="s" style="color: #d14;">"Siginificant Interactions"</span><span class="p">]</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="362" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
362
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC362" class="line" lang="python"> <span class="n" style="color: #333;">drug_out_df</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[(</span><span class="n" style="color: #333;">drug_out_df</span><span class="p">[</span><span class="s" style="color: #d14;">"qval concentration dependence"</span><span class="p">]</span><span class="o" style="font-weight: 600;"><</span><span class="mf" style="color: #099;">0.05</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">drug_out_df</span><span class="p">[</span><span class="s" style="color: #d14;">"Z"</span><span class="p">]</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">2</span><span class="p">),</span><span class="s" style="color: #d14;">"Siginificant Interactions"</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="363" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
363
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC363" class="line" lang="python"> <span class="n" style="color: #333;">drug_out_df</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">insert</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">"Siginificant Interactions"</span><span class="p">,</span> <span class="n" style="color: #333;">drug_out_df</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">"Siginificant Interactions"</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="364" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
364
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC364" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="365" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
365
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC365" class="line" lang="python"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">drug_out_df</span><span class="p">[</span><span class="n" style="color: #333;">drug_out_df</span><span class="p">[</span><span class="s" style="color: #d14;">"Siginificant Interactions"</span><span class="p">]</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="366" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
366
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC366" class="line" lang="python"> <span class="n" style="color: #333;">depl_n</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">drug_out_df</span><span class="p">[</span><span class="n" style="color: #333;">drug_out_df</span><span class="p">[</span><span class="s" style="color: #d14;">"Siginificant Interactions"</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="367" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
367
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC367" class="line" lang="python"> <span class="n" style="color: #333;">enrich_n</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">drug_out_df</span><span class="p">[</span><span class="n" style="color: #333;">drug_out_df</span><span class="p">[</span><span class="s" style="color: #d14;">"Siginificant Interactions"</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="368" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
368
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC368" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"%d Total Siginificant Gene Interactions</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">n</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="369" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
369
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC369" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"%d Siginificant Gene Depletions</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">depl_n</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="370" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
370
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC370" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"%d Siginificant Gene Enrichments</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">enrich_n</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="371" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
371
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC371" class="line" lang="python"> </span>
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<td class="new_line diff-line-num new" data-linenumber="372" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
372
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC372" class="line" lang="python"> <span class="n" style="color: #333;">drug_out_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">drug_out_df</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">replace</span><span class="p">(</span><span class="sa">r</span><span class="s" style="color: #d14;">'\s+'</span><span class="p">,</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">nan</span><span class="p">,</span><span class="n" style="color: #333;">regex</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">).</span><span class="nf" style="color: #900; font-weight: 600;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">''</span><span class="p">,</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">nan</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="373" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
373
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC373" class="line" lang="python"> <span class="n" style="color: #333;">drug_out_txt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">drug_out_df</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_csv</span><span class="p">(</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="374" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
374
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC374" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">drug_out_txt</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="375" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
375
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC375" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="376" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
376
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC376" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">visualize</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span><span class="n" style="color: #333;">fractional_abundances_file</span><span class="p">,</span> <span class="n" style="color: #333;">gene</span><span class="p">,</span> <span class="n" style="color: #333;">fig_location</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="377" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
377
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC377" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">pandas</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pd</span></span>
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<td class="new_line diff-line-num new" data-linenumber="378" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
378
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC378" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">seaborn</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">sns</span></span>
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<td class="new_line diff-line-num new" data-linenumber="379" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
379
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC379" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">matplotlib.pyplot</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">plt</span></span>
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<td class="new_line diff-line-num new" data-linenumber="380" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
380
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC380" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">matplotlib</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">mpl</span></span>
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<td class="new_line diff-line-num new" data-linenumber="381" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
381
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC381" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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<td class="new_line diff-line-num new" data-linenumber="382" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
382
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC382" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">statsmodels.api</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">sm</span></span>
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<td class="new_line diff-line-num new" data-linenumber="383" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
383
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC383" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="384" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
384
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC384" class="line" lang="python"> <span class="n" style="color: #333;">abund_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">read_csv</span><span class="p">(</span><span class="n" style="color: #333;">fractional_abundances_file</span><span class="p">,</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">comment</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"#"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="385" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
385
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC385" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333;">fractional_abundances_file</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="386" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
386
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC386" class="line" lang="python"> <span class="n" style="color: #333;">first_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">readline</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="387" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
387
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC387" class="line" lang="python"> <span class="n" style="color: #333;">condition</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">first_line</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">" : "</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="388" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
388
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC388" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="389" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
389
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC389" class="line" lang="python"> <span class="n" style="color: #333;">abund_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">abund_df</span><span class="p">[(</span><span class="n" style="color: #333;">abund_df</span><span class="p">[</span><span class="s" style="color: #d14;">"gene"</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">gene</span><span class="p">)</span><span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="n" style="color: #333;">abund_df</span><span class="p">[</span><span class="s" style="color: #d14;">"orf"</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">gene</span><span class="p">)]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="390" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
390
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC390" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">abund_df</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="391" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
391
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC391" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Gene not found : %d </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">idx</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="392" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
392
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC392" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="393" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
393
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC393" class="line" lang="python"> <span class="n" style="color: #333;">abund_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">abund_df</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">reset_index</span><span class="p">(</span><span class="n" style="color: #333;">drop</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="394" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
394
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC394" class="line" lang="python"> <span class="n" style="color: #333;">all_slopes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="395" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
395
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC395" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="396" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
396
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC396" class="line" lang="python"> <span class="n" style="color: #333;">df_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="397" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
397
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC397" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idx</span><span class="p">,</span><span class="n" style="color: #333;">row</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">abund_df</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">iterrows</span><span class="p">():</span></span>
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<td class="new_line diff-line-num new" data-linenumber="398" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
398
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC398" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Fitting sgRNA # : %d </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">idx</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="399" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
399
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC399" class="line" lang="python"> <span class="n" style="color: #333;">raw_Y</span><span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">:].</span><span class="n" style="color: #333;">values</span></span>
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<td class="new_line diff-line-num new" data-linenumber="400" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
400
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC400" class="line" lang="python"> <span class="n" style="color: #333;">Y</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nf" style="color: #900; font-weight: 600;">max</span><span class="p">(</span><span class="mf" style="color: #099;">0.01</span><span class="p">,</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">raw_Y</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="401" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
401
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC401" class="line" lang="python"> <span class="n" style="color: #333;">Y</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">log10</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Y</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="402" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
402
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC402" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="403" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
403
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC403" class="line" lang="python"> <span class="n" style="color: #333;">X</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">abund_df</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">:]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="404" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
404
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC404" class="line" lang="python"> <span class="n" style="color: #333;">X</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nf" style="color: #900; font-weight: 600;">float</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">X</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="405" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
405
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC405" class="line" lang="python"> <span class="n" style="color: #333;">min_conc</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">min</span><span class="p">([</span><span class="n" style="color: #333;">i</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">X</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="406" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
406
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC406" class="line" lang="python"> <span class="n" style="color: #333;">X</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">min_conc</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">2</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">i</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">X</span> <span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="407" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
407
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC407" class="line" lang="python"> <span class="n" style="color: #333;">X</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">log2</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">float</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">X</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="408" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
408
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC408" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="409" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
409
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC409" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">DataFrame</span><span class="p">({</span><span class="s" style="color: #d14;">"Log (Concentration)"</span><span class="p">:</span><span class="n" style="color: #333;">X</span><span class="p">,</span> <span class="s" style="color: #d14;">"Log (Relative Abundance)"</span><span class="p">:</span><span class="n" style="color: #333;">Y</span><span class="p">})</span></span>
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<td class="new_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
410
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC410" class="line" lang="python"> <span class="n" style="color: #333;">X</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">DataFrame</span><span class="p">({</span><span class="s" style="color: #d14;">"log concentration"</span><span class="p">:</span><span class="n" style="color: #333;">X</span><span class="p">})</span></span>
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<td class="new_line diff-line-num new" data-linenumber="411" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
411
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC411" class="line" lang="python"> <span class="n" style="color: #333;">X_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sm</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">add_constant</span><span class="p">(</span><span class="n" style="color: #333;">X</span><span class="p">,</span> <span class="n" style="color: #333;">has_constant</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'add'</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="412" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
412
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC412" class="line" lang="python"> <span class="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sm</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">OLS</span><span class="p">(</span><span class="n" style="color: #333;">Y</span><span class="p">,</span><span class="n" style="color: #333;">X_in</span><span class="p">).</span><span class="nf" style="color: #900; font-weight: 600;">fit</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="413" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
413
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC413" class="line" lang="python"> <span class="n" style="color: #333;">all_slopes</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">results</span><span class="p">.</span><span class="n" style="color: #333;">params</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="414" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
414
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC414" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"sgRNA strength"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">"sgRNA strength"</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="415" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
415
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC415" class="line" lang="python"> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">"slope"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">results</span><span class="p">.</span><span class="n" style="color: #333;">params</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="416" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
416
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC416" class="line" lang="python"> <span class="n" style="color: #333;">df_list</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="417" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
417
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC417" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="418" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
418
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC418" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="419" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
419
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC419" class="line" lang="python"> <span class="n" style="color: #333;">plot_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">concat</span><span class="p">(</span><span class="n" style="color: #333;">df_list</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="420" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
420
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC420" class="line" lang="python"> <span class="n" style="color: #333;">plt</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">figure</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="421" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
421
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC421" class="line" lang="python"> <span class="n" style="color: #333;">cmap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mpl</span><span class="p">.</span><span class="n" style="color: #333;">colors</span><span class="p">.</span><span class="n" style="color: #333;">LinearSegmentedColormap</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">from_list</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"#8ecae6"</span><span class="p">,</span><span class="s" style="color: #d14;">"#219ebc"</span><span class="p">,</span><span class="s" style="color: #d14;">"#023047"</span><span class="p">,</span><span class="s" style="color: #d14;">"#ffb703"</span><span class="p">,</span><span class="s" style="color: #d14;">"#fb8500"</span><span class="p">],</span> <span class="n" style="color: #333;">N</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">abund_df</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="422" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
422
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC422" class="line" lang="python"> <span class="n" style="color: #333;">palette</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">mpl</span><span class="p">.</span><span class="n" style="color: #333;">colors</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">rgb2hex</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">cmap</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nf" style="color: #900; font-weight: 600;">range</span><span class="p">(</span><span class="n" style="color: #333;">cmap</span><span class="p">.</span><span class="n" style="color: #333;">N</span><span class="p">)]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="423" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
423
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC423" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print("-----------", bo_palette.as_hex())</span></span>
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<td class="new_line diff-line-num new" data-linenumber="424" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
424
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC424" class="line" lang="python"> <span class="n" style="color: #333;">g</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sns</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">lmplot</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">plot_df</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Log (Concentration)'</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Log (Relative Abundance)'</span><span class="p">,</span> <span class="n" style="color: #333;">hue</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"sgRNA strength"</span><span class="p">,</span> <span class="n" style="color: #333;">palette</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">palette</span><span class="p">,</span> <span class="n" style="color: #333;">legend</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span><span class="n" style="color: #333;">ci</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">scatter</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">line_kws</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">"lw"</span><span class="p">:</span><span class="mf" style="color: #099;">0.75</span><span class="p">})</span></span>
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<td class="new_line diff-line-num new" data-linenumber="425" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
425
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC425" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="426" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
426
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC426" class="line" lang="python"> <span class="n" style="color: #333;">sm1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mpl</span><span class="p">.</span><span class="n" style="color: #333;">cm</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">ScalarMappable</span><span class="p">(</span><span class="n" style="color: #333;">norm</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">mpl</span><span class="p">.</span><span class="n" style="color: #333;">colors</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">Normalize</span><span class="p">(</span><span class="n" style="color: #333;">vmin</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">plot_df</span><span class="p">[</span><span class="s" style="color: #d14;">'sgRNA strength'</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">min</span><span class="p">(),</span> <span class="n" style="color: #333;">vmax</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">clip</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">),</span> <span class="n" style="color: #333;">cmap</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cmap</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="427" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
427
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC427" class="line" lang="python"> <span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">figure</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">colorbar</span><span class="p">(</span><span class="n" style="color: #333;">sm1</span><span class="p">,</span> <span class="n" style="color: #333;">shrink</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.8</span><span class="p">,</span> <span class="n" style="color: #333;">aspect</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">50</span><span class="p">,</span> <span class="n" style="color: #333;">label</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"sgRNA strength"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="428" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
428
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC428" class="line" lang="python"> <span class="n" style="color: #333;">g</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">set</span><span class="p">(</span><span class="n" style="color: #333;">ylim</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">2.5</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="429" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
429
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC429" class="line" lang="python"> <span class="n" style="color: #333;">plt</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">gca</span><span class="p">().</span><span class="nf" style="color: #900; font-weight: 600;">set_title</span><span class="p">(</span><span class="n" style="color: #333;">gene</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">condition</span><span class="p">,</span> <span class="n" style="color: #333;">wrap</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="430" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
430
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC430" class="line" lang="python"> <span class="n" style="color: #333;">plt</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">tight_layout</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="431" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
431
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC431" class="line" lang="python"> <span class="n" style="color: #333;">plt</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">savefig</span><span class="p">(</span><span class="n" style="color: #333;">fig_location</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="432" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
432
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC432" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">################################</span></span>
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433
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC433" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="434" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
434
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC434" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"__main__"</span><span class="p">:</span></span>
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435
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC435" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="436" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
436
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC436" class="line" lang="python"> <span class="n" style="color: #333;">G</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CGI</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">fromargs</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:])</span></span>
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437
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC437" class="line" lang="python"> <span class="n" style="color: #333;">G</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">Run</span><span class="p">()</span></span>
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438
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC439" class="line" lang="python"></span></pre></td>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/compare/e7fcdb595572f7ea598ca27f80632375a9e0790d...898cc600b276228ce95ff463aa822e85dffdcaa1#0ffc91104acbadc1fba73c8b5711f169b29874db"><strong style="font-weight: bold;">src/pytransit/analysis/__init__.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="25" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="25" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -25,6 +25,7 @@ from pytransit.analysis import tnseq_stats</td>
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<td class="old_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="new_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">pytransit.analysis</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">corrplot</span></span>
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<td class="new_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC26" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">pytransit.analysis</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">heatmap</span></span>
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27
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<td class="new_line diff-line-num" data-linenumber="27" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC27" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">pytransit.analysis</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ttnfitness</span></span>
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<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
28
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC28" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">pytransit.analysis</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">CGI</span></span>
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<td class="new_line diff-line-num" data-linenumber="29" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
29
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC29" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="29" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
29
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<td class="new_line diff-line-num" data-linenumber="30" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC30" class="line" lang="python"><span class="n" style="color: #333;">methods</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC31" class="line" lang="python"><span class="n" style="color: #333;">methods</span><span class="p">[</span><span class="s" style="color: #d14;">"example"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">example</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">ExampleAnalysis</span><span class="p">()</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="48" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="49" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -48,6 +49,7 @@ methods["tnseq_stats"]=tnseq_stats.TnseqStats()</td>
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<td class="old_line diff-line-num" data-linenumber="48" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
48
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<td class="new_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
49
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC49" class="line" lang="python"><span class="n" style="color: #333;">methods</span><span class="p">[</span><span class="s" style="color: #d14;">"corrplot"</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">corrplot</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">Corrplot</span><span class="p">()</span></span>
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<td class="old_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
49
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<td class="new_line diff-line-num" data-linenumber="50" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
50
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC50" class="line" lang="python"><span class="n" style="color: #333;">methods</span><span class="p">[</span><span class="s" style="color: #d14;">"heatmap"</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">heatmap</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">Heatmap</span><span class="p">()</span></span>
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50
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<td class="new_line diff-line-num" data-linenumber="51" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
51
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC51" class="line" lang="python"><span class="n" style="color: #333;">methods</span><span class="p">[</span><span class="s" style="color: #d14;">"ttnfitness"</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ttnfitness</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">TTNFitnessAnalysis</span><span class="p">()</span></span>
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<td class="old_line diff-line-num new" data-linenumber="51" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="52" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
52
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC52" class="line" lang="python"><span class="n" style="color: #333;">methods</span><span class="p">[</span><span class="s" style="color: #d14;">"CGI"</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">CGI</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">CGI</span><span class="p">()</span></span>
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51
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<td class="new_line diff-line-num" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC53" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="52" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="new_line diff-line-num" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC54" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># EXPORT METHODS</span></span>
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<td class="new_line diff-line-num" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC55" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">pytransit.analysis</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">norm</span></span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/compare/e7fcdb595572f7ea598ca27f80632375a9e0790d...898cc600b276228ce95ff463aa822e85dffdcaa1#07ca99dc668f43ea2451861342e18d287151cf0c"><strong style="font-weight: bold;">src/pytransit/analysis/zinb.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="267" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="267" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -267,15 +267,20 @@ class ZinbMethod(base.MultiConditionMethod):</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC267" class="line" lang="python"> <span class="p">]</span></span>
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269
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269
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC269" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">def_r_zinb_signif</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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270
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<td class="new_line diff-line-num old" data-linenumber="270" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC270" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">r</span><span class="p">(</span><span class="s" style="color: #d14;">'''</span></span>
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<td class="old_line diff-line-num old" data-linenumber="271" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
271
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<td class="new_line diff-line-num old" data-linenumber="270" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC271" class="line" lang="python"><span class="s" style="color: #d14;"> zinb_signif = function(df,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="270" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
270
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC270" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">r</span><span class="p">(</span><span class="s" style="color: #d14;">"""</span></span>
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<td class="new_line diff-line-num new" data-linenumber="271" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
271
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC271" class="line" lang="python"><span class="s" style="color: #d14;"> zinb_signif = function(</span></span>
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<td class="new_line diff-line-num new" data-linenumber="272" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
272
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC272" class="line" lang="python"><span class="s" style="color: #d14;"> df,</span></span>
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272
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<td class="new_line diff-line-num" data-linenumber="273" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
273
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC273" class="line" lang="python"><span class="s" style="color: #d14;"> zinbMod1,</span></span>
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273
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<td class="new_line diff-line-num" data-linenumber="274" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
274
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC274" class="line" lang="python"><span class="s" style="color: #d14;"> zinbMod0,</span></span>
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274
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<td class="new_line diff-line-num" data-linenumber="275" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
275
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC275" class="line" lang="python"><span class="s" style="color: #d14;"> nbMod1,</span></span>
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275
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<td class="new_line diff-line-num old" data-linenumber="276" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC275" class="line" lang="python"><span class="s" style="color: #d14;"> nbMod0, DEBUG = F) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="276" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
276
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC276" class="line" lang="python"><span class="s" style="color: #d14;"> nbMod0,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="277" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
277
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC277" class="line" lang="python"><span class="s" style="color: #d14;"> DEBUG = F</span></span>
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<td class="new_line diff-line-num new" data-linenumber="278" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
278
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC278" class="line" lang="python"><span class="s" style="color: #d14;"> ) {</span></span>
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<td class="new_line diff-line-num new" data-linenumber="279" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
279
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC279" class="line" lang="python"><span class="s" style="color: #d14;"> print("Starting ZINB in R")</span></span>
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276
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<td class="new_line diff-line-num" data-linenumber="280" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
280
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC280" class="line" lang="python"><span class="s" style="color: #d14;"> suppressMessages(require(pscl))</span></span>
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277
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<td class="new_line diff-line-num" data-linenumber="281" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
281
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC281" class="line" lang="python"><span class="s" style="color: #d14;"> suppressMessages(require(MASS))</span></span>
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278
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<td class="new_line diff-line-num" data-linenumber="282" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
282
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC282" class="line" lang="python"><span class="s" style="color: #d14;"> melted = df</span></span>
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<td class="new_line diff-line-num new" data-linenumber="283" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
283
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC283" class="line" lang="python"><span class="s" style="color: #d14;"> #print(head(melted))</span></span>
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279
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284
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC284" class="line" lang="python"></span>
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280
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285
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC285" class="line" lang="python"><span class="s" style="color: #d14;"> # filter out genes that have low saturation across all conditions, since pscl sometimes does not fit params well (resulting in large negative intercepts and high std errors)</span></span>
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<td class="old_line diff-line-num" data-linenumber="281" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
281
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<td class="new_line diff-line-num" data-linenumber="286" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
286
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC286" class="line" lang="python"><span class="s" style="color: #d14;"> NZpercs = aggregate(melted$cnt,by=list(melted$cond),FUN=function(x) { sum(x>0)/length(x) })</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="288" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="293" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -288,7 +293,7 @@ class ZinbMethod(base.MultiConditionMethod):</td>
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288
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<td class="new_line diff-line-num" data-linenumber="293" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
293
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC293" class="line" lang="python"><span class="s" style="color: #d14;"> for (i in 1:length(sums[,1])) {</span></span>
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<td class="old_line diff-line-num" data-linenumber="289" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
289
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<td class="new_line diff-line-num" data-linenumber="294" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
294
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC294" class="line" lang="python"><span class="s" style="color: #d14;"> subset = melted[melted$cond==sums[i,1],]</span></span>
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<td class="old_line diff-line-num" data-linenumber="290" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
290
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<td class="new_line diff-line-num" data-linenumber="295" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
295
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC295" class="line" lang="python"><span class="s" style="color: #d14;"> newvec = subset[1,]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="291" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
291
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<td class="new_line diff-line-num old" data-linenumber="296" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC291" class="line" lang="python"><span class="s" style="color: #d14;"> newvec$cnt = 1 # note: <span class="idiff left right deletion" style="background-color: #fac5cd;">NZ</span>mean and NZperc are copied from last dataset in condition</span></span>
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<td class="old_line diff-line-num new" data-linenumber="292" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="296" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
296
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC296" class="line" lang="python"><span class="s" style="color: #d14;"> newvec$cnt = 1 # note: <span class="idiff left right addition" style="background-color: #c7f0d2;">non_zero_</span>mean and NZperc are copied from last dataset in condition</span></span>
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<td class="old_line diff-line-num" data-linenumber="292" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
292
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<td class="new_line diff-line-num" data-linenumber="297" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
297
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC297" class="line" lang="python"><span class="s" style="color: #d14;"> #newvec$cnt = as.integer(mean(subset$cnt))+1 # add the mean for each condition as a pseudocount</span></span>
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293
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<td class="new_line diff-line-num" data-linenumber="298" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
298
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC298" class="line" lang="python"><span class="s" style="color: #d14;"> melted = rbind(melted,newvec) }</span></span>
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299
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC299" class="line" lang="python"><span class="s" style="color: #d14;"> }</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="349" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="354" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -349,9 +354,10 @@ class ZinbMethod(base.MultiConditionMethod):</td>
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<td class="old_line diff-line-num" data-linenumber="349" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
349
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<td class="new_line diff-line-num" data-linenumber="354" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
354
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC354" class="line" lang="python"><span class="s" style="color: #d14;"> # this gives same answer, but I would need to extract the Pvalue...</span></span>
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350
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<td class="new_line diff-line-num" data-linenumber="355" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
355
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC355" class="line" lang="python"><span class="s" style="color: #d14;"> #require(lmtest)</span></span>
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351
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<td class="new_line diff-line-num" data-linenumber="356" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
356
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC356" class="line" lang="python"><span class="s" style="color: #d14;"> #print(lrtest(mod1,mod0))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="357" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
357
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC357" class="line" lang="python"><span class="s" style="color: #d14;"> print("Finished ZINB in R")</span></span>
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352
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<td class="new_line diff-line-num" data-linenumber="358" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
358
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC358" class="line" lang="python"><span class="s" style="color: #d14;"> return (c(pval, status))</span></span>
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353
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<td class="new_line diff-line-num" data-linenumber="359" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
359
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC359" class="line" lang="python"><span class="s" style="color: #d14;"> }</span></span>
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354
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<td class="new_line diff-line-num old" data-linenumber="360" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC354" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right deletion" style="background-color: #fac5cd;">'''</span></span><span class="p">)</span></span>
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360
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC360" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right addition" style="background-color: #c7f0d2;">"""</span></span><span class="p">)</span></span>
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361
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC361" class="line" lang="python"></span>
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356
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<td class="new_line diff-line-num" data-linenumber="362" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
362
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC362" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">globalenv</span><span class="p">[</span><span class="s" style="color: #d14;">'zinb_signif'</span><span class="p">]</span></span>
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357
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363
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC363" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="453" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="459" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -453,6 +459,12 @@ class ZinbMethod(base.MultiConditionMethod):</td>
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453
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<td class="new_line diff-line-num" data-linenumber="459" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
459
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC459" class="line" lang="python"> <span class="n" style="color: #333;">melted</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">DataFrame</span><span class="p">(</span><span class="n" style="color: #333;">df_args</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="454" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
454
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<td class="new_line diff-line-num" data-linenumber="460" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
460
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC460" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># r_args = [IntVector(readCounts), StrVector(condition), melted, map(lambda x: StrVector(x), covars), FloatVector(NZmean), FloatVector(logitZPerc)] + [True]</span></span>
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<td class="old_line diff-line-num" data-linenumber="455" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
455
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<td class="new_line diff-line-num" data-linenumber="461" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
461
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC461" class="line" lang="python"> <span class="n" style="color: #333;">debugFlag</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">DEBUG</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">GENE</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">False</span></span>
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<td class="old_line diff-line-num new" data-linenumber="456" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="462" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
462
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC462" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print(f'''melted =''', str(melted))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="456" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="463" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
463
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC463" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"zinbMod1"</span><span class="p">,</span> <span class="nf" style="color: #900; font-weight: 600;">str</span><span class="p">(</span><span class="n" style="color: #333;">zinbMod1</span><span class="p">))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="456" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="464" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
464
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC464" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"zinbMod0"</span><span class="p">,</span> <span class="nf" style="color: #900; font-weight: 600;">str</span><span class="p">(</span><span class="n" style="color: #333;">zinbMod0</span><span class="p">))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="456" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="465" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
465
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC465" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"nbMod1"</span><span class="p">,</span> <span class="nf" style="color: #900; font-weight: 600;">str</span><span class="p">(</span><span class="n" style="color: #333;">nbMod1</span><span class="p">))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="456" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="466" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
466
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC466" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"nbMod0"</span><span class="p">,</span> <span class="nf" style="color: #900; font-weight: 600;">str</span><span class="p">(</span><span class="n" style="color: #333;">nbMod0</span><span class="p">))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="456" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="467" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
467
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC467" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"debugFlag"</span><span class="p">,</span> <span class="nf" style="color: #900; font-weight: 600;">str</span><span class="p">(</span><span class="n" style="color: #333;">debugFlag</span><span class="p">))</span></span>
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<td class="old_line diff-line-num" data-linenumber="456" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
456
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<td class="new_line diff-line-num" data-linenumber="468" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
468
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC468" class="line" lang="python"> <span class="n" style="color: #333;">pval</span><span class="p">,</span> <span class="n" style="color: #333;">msg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">r_zinb_signif</span><span class="p">(</span><span class="n" style="color: #333;">melted</span><span class="p">,</span> <span class="n" style="color: #333;">zinbMod1</span><span class="p">,</span> <span class="n" style="color: #333;">zinbMod0</span><span class="p">,</span> <span class="n" style="color: #333;">nbMod1</span><span class="p">,</span> <span class="n" style="color: #333;">nbMod0</span><span class="p">,</span> <span class="n" style="color: #333;">debugFlag</span><span class="p">)</span></span>
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457
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<td class="new_line diff-line-num" data-linenumber="469" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
469
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC469" class="line" lang="python"> <span class="n" style="color: #333;">status</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">)</span></span>
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458
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<td class="new_line diff-line-num" data-linenumber="470" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
470
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC470" class="line" lang="python"> <span class="n" style="color: #333;">pvals</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">float</span><span class="p">(</span><span class="n" style="color: #333;">pval</span><span class="p">))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="525" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="537" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -525,8 +537,18 @@ class ZinbMethod(base.MultiConditionMethod):</td>
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<td class="old_line diff-line-num" data-linenumber="525" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
525
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<td class="new_line diff-line-num" data-linenumber="537" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
537
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC537" class="line" lang="python"> <span class="n" style="color: #333;">condition_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">condition</span></span>
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526
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538
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC538" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if a covar is not found, this crashes; check for it?</span></span>
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527
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<td class="new_line diff-line-num" data-linenumber="539" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
539
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC539" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># read it first with no condition specified, to get original Condition names</span></span>
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<td class="old_line diff-line-num old" data-linenumber="528" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
528
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<td class="new_line diff-line-num old" data-linenumber="540" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC528" class="line" lang="python"> <span class="n" style="color: #333;">conditionsByFile1</span><span class="p">,</span> <span class="n" style="color: #333;">covariatesByFileList1</span><span class="p">,</span> <span class="n" style="color: #333;">interactionsByFileList1</span><span class="p">,</span> <span class="n" style="color: #333;">orderingMetadata1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tnseq_tools</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">read_samples_metadata</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">covars</span><span class="p">,</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">interactions</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># without specifiying condition</span></span>
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529
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<td class="new_line diff-line-num old" data-linenumber="540" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC529" class="line" lang="python"> <span class="n" style="color: #333;">conditionsByFile</span><span class="p">,</span> <span class="n" style="color: #333;">covariatesByFileList</span><span class="p">,</span> <span class="n" style="color: #333;">interactionsByFileList</span><span class="p">,</span> <span class="n" style="color: #333;">orderingMetadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tnseq_tools</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">read_samples_metadata</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">covars</span><span class="p">,</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">interactions</span><span class="p">,</span> <span class="n" style="color: #333;">condition_name</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">condition_name</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="540" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
540
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC540" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># (</span></span>
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<td class="new_line diff-line-num new" data-linenumber="541" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
541
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC541" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># conditionsByFile1, # use this when the exclude condition arg</span></span>
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<td class="new_line diff-line-num new" data-linenumber="542" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
542
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC542" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># covariatesByFileList1,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="543" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
543
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC543" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># interactionsByFileList1,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="544" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
544
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC544" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># orderingMetadata1</span></span>
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<td class="old_line diff-line-num new" data-linenumber="530" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="545" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
545
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC545" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ) = tnseq_tools.read_samples_metadata(self.metadata, self.covars, self.interactions) # without specifiying condition</span></span>
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<td class="new_line diff-line-num new" data-linenumber="546" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
546
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC546" class="line" lang="python"> <span class="p">(</span></span>
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<td class="new_line diff-line-num new" data-linenumber="547" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
547
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC547" class="line" lang="python"> <span class="n" style="color: #333;">conditionsByFile</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="548" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
548
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC548" class="line" lang="python"> <span class="n" style="color: #333;">covariatesByFileList</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="549" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
549
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC549" class="line" lang="python"> <span class="n" style="color: #333;">interactionsByFileList</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="550" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
550
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC550" class="line" lang="python"> <span class="n" style="color: #333;">orderingMetadata</span></span>
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<td class="new_line diff-line-num new" data-linenumber="551" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
551
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC551" class="line" lang="python"> <span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tnseq_tools</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">read_samples_metadata</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">metadata</span><span class="p">,</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">covars</span><span class="p">,</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">interactions</span><span class="p">,</span> <span class="n" style="color: #333;">condition_name</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">condition_name</span><span class="p">)</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC552" class="line" lang="python"></span>
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531
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC553" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">## [Condition] in the order of files in combined wig</span></span>
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<td class="new_line diff-line-num" data-linenumber="554" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
554
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC554" class="line" lang="python"> <span class="n" style="color: #333;">conditions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">wigs_to_conditions</span><span class="p">(</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="597" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -575,6 +597,8 @@ class ZinbMethod(base.MultiConditionMethod):</td>
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575
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<td class="new_line diff-line-num" data-linenumber="597" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
597
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC597" class="line" lang="python"> <span class="n" style="color: #333;">pairs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="old_line diff-line-num" data-linenumber="576" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
576
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<td class="new_line diff-line-num" data-linenumber="598" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
598
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC598" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">samples in cross-product:"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="577" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
577
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<td class="new_line diff-line-num" data-linenumber="599" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
599
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC599" class="line" lang="python"> <span class="n" style="color: #333;">any_empty</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">expandVar</span><span class="p">([],</span><span class="nb" style="color: #0086b3;">vars</span><span class="p">,</span><span class="n" style="color: #333;">varsByFileList</span><span class="p">,</span><span class="n" style="color: #333;">vars2vals</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;">set</span><span class="p">(</span><span class="n" style="color: #333;">samples_used</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="600" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
600
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC600" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="sa">f</span><span class="s" style="color: #d14;">'''varsByFileList = </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">varsByFileList</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">'''</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="601" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
601
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC601" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="sa">f</span><span class="s" style="color: #d14;">'''vars2vals = </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">vars2vals</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">'''</span><span class="p">)</span></span>
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578
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<td class="new_line diff-line-num" data-linenumber="602" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
602
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC602" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">any_empty</span><span class="p">:</span> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"warning: ZINB requires samples in all combinations of conditions; the fact that one is empty could result in Model Errors"</span><span class="p">)</span></span>
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579
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<td class="new_line diff-line-num" data-linenumber="603" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
603
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC603" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="580" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
580
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<td class="new_line diff-line-num" data-linenumber="604" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
604
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC604" class="line" lang="python"> <span class="n" style="color: #333;">genes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tnseq_tools</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">read_genes</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">annotation_path</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/compare/e7fcdb595572f7ea598ca27f80632375a9e0790d...898cc600b276228ce95ff463aa822e85dffdcaa1#da7c215459bd208708ec6ca77c3ae6feca7c3d3a"><strong style="font-weight: bold;">src/pytransit/data.ignore/macrophages.comwig</strong></a>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/compare/e7fcdb595572f7ea598ca27f80632375a9e0790d...898cc600b276228ce95ff463aa822e85dffdcaa1#a3fb493f33fe187a3d0018b87497ffc8d0649bbc"><strong style="font-weight: bold;">src/pytransit/data.ignore/macrophages_metadata.txt</strong></a>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1" class="line" lang="plaintext">Id Condition Filename</span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/compare/e7fcdb595572f7ea598ca27f80632375a9e0790d...898cc600b276228ce95ff463aa822e85dffdcaa1#d70fa3621fe0a5c1985c073f2d2e131f0c4d4e8d"><strong style="font-weight: bold;">src/pytransit/data/CGI/IDs.H37Rv.CRISPRi.lib.txt</strong></a>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/compare/e7fcdb595572f7ea598ca27f80632375a9e0790d...898cc600b276228ce95ff463aa822e85dffdcaa1#df61716515a490346b9768764cd97f41dac21bea"><strong style="font-weight: bold;">src/pytransit/data/CGI/counts_metadata.txt</strong></a>
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5
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5" class="line" lang="plaintext">RIF_D1_Low_rep1 RIF 0.0625 1</span>
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6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6" class="line" lang="plaintext">RIF_D1_Low_rep2 RIF 0.0625 1</span>
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7
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7" class="line" lang="plaintext">RIF_D1_Low_rep3 RIF 0.0625 1</span>
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8
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC8" class="line" lang="plaintext">RIF_D1_Med_rep1 RIF 0.125 1</span>
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9
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC9" class="line" lang="plaintext">RIF_D1_Med_rep2 RIF 0.125 1</span>
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10
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10" class="line" lang="plaintext">RIF_D1_Med_rep3 RIF 0.125 1</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC11" class="line" lang="plaintext">RIF_D1_High_rep1 RIF 0.25 1</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC12" class="line" lang="plaintext">RIF_D1_High_rep2 RIF 0.25 1</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC13" class="line" lang="plaintext">RIF_D1_High_rep3 RIF 0.25 1</span></pre></td>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/compare/e7fcdb595572f7ea598ca27f80632375a9e0790d...898cc600b276228ce95ff463aa822e85dffdcaa1#c64ef9e062f0a088f8c3839b8d7fa181235d4d62"><strong style="font-weight: bold;">src/pytransit/data/CGI/sgRNA_metadata.txt</strong></a>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC8" class="line" lang="plaintext">CRISPRi-DR is designed to analyze CRISPRi libraries from CGI experiments and identify significant CGIs ie genes that affect sensitivity to the drug when depleted. </span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC13" class="line" lang="plaintext">--------</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC14" class="line" lang="plaintext">Starting with fastq files, barcode counts are extracted. The user creates their own metadata file, for the counts. Fractional abundances are and used to run the CRISPRi-DR model. The output of this model is a file that lists genes with their statistacal parameters and significance. Genes with significant interactions are those with qval of condetration dependence < 0.05 and \|Z score of concentration dpendence|>2 on the slope coefficient. However, genes can be ranked by depletion by sorting the coefficient of concentration dependence in ascending order</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC21" class="line" lang="plaintext">**Preprocessing: Fastq to Count Files**</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC23" class="line" lang="plaintext">This is a longer process, taking a few minutes each. However, the number of reads processed is printed to the console to indicate progress.</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC26" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC27" class="line" lang="plaintext"> > python3 ../src/transit.py CGI extract_counts <fastq_file> <ids_file> > <counts_file></span>
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<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
29
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC29" class="line" lang="plaintext">* ids_file : List of sgRNAs used in the experiment, where each row is one sgRNA id. </span>
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<td class="new_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC30" class="line" lang="plaintext"> * For H37Rv experiments, the ids file is available in : ``transit/src/pytransit/data/CGI/IDs.H37Rv.CRISPRi.lib.txt``</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC32" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC33" class="line" lang="plaintext">**Step 1: Combine Individual Counts File to a Combined Counts File**</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC34" class="line" lang="plaintext">This is a fairly fast process. It takes at most a minute for the combination of 12 files with 2 columns (sgRNA id and counts) to one large file of 13 columns (first column sgRNA id and remaining columns are counts from the files entered). </span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC38" class="line" lang="plaintext"> > python3 ../src/transit.py CGI combined_counts <comma seperated headers> <counts file 1> <counts file 2> ... <counts_file n> > <combined counts file></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC39" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC40" class="line" lang="plaintext">* counts files : sgRNA ids as their first column, and can have any number of columns.</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC41" class="line" lang="plaintext">* comma-separated headers: the column names of the combined counts file</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC42" class="line" lang="plaintext"> .. note::</span>
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<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC43" class="line" lang="plaintext"> the comma-seperated headers must be in order of the columns in the count files(s) provided</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC44" class="line" lang="plaintext"> </span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC45" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC46" class="line" lang="plaintext">**Step 2: Extract Fractional Abundances**</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC47" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC48" class="line" lang="plaintext"> This is a relatively quick process, taking less than a minute. This step is to turn the barcodes counts into relative normalized abundances. Counts are normalized within samples and calculated relative to the abundances in the uninduced ATC file, essentially fractions. The first few lines of the output file contains information about the counts files processed.</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC50" class="line" lang="plaintext">::</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC51" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="52" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC52" class="line" lang="plaintext"> > python3 ../src/transit.py CGI extract_abund <combined counts file> <counts metadata file> <control condition> <sgRNA strengths file> <uninduced ATC file> <drug> <days> > <fractional abundance file></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC53" class="line" lang="plaintext"></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC54" class="line" lang="plaintext">* counts metadata file (USER created):</span>
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<td class="new_line diff-line-num new" data-linenumber="56" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC56" class="line" lang="plaintext"> * The columns expected in this file: column_name, drug, conc_xMIC, days_predepletion</span>
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<td class="new_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
58
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC58" class="line" lang="plaintext"> * column_name: the corresponding header name(s) in the combined counts file</span>
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<td class="new_line diff-line-num new" data-linenumber="59" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
59
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC59" class="line" lang="plaintext"> * conc_xMIC is the concentration of the drug the sample is treated with </span>
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<td class="new_line diff-line-num new" data-linenumber="60" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
60
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC60" class="line" lang="plaintext"> .. warning::</span>
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<td class="new_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
61
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC61" class="line" lang="plaintext"> conc_xMIC must be a numerical value, ie. 0.5 and not a categorical value such as "low" or "high"</span>
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<td class="new_line diff-line-num new" data-linenumber="62" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
62
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC62" class="line" lang="plaintext"> * Equal number of replicates for all concentrations are not nessessary</span>
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<td class="new_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
63
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC63" class="line" lang="plaintext"> * see [Li, S et al. 2022, PMID: 35637331] for explanation of days_predepletion</span>
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64
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC64" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="65" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
65
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC65" class="line" lang="plaintext"> * Example metadata: ``transit/src/pytransit/data/CGI/counts_metadata.txt``</span>
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66
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC66" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="67" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
67
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC67" class="line" lang="plaintext">* control condition: The condition to to be considered the control for these set of experiments, as specificed in the "drug" column of the metadata file; typically an atc-induced (+ ATC) with 0 drug concentration condition.</span>
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<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
68
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC68" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
69
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC69" class="line" lang="plaintext">* sgRNA strengths file: A file that contains metadata for each sgRNA in the combined counts file, where the first column must be sgRNA id (as seen in the combined counts file) and the last column must be the strength measurement of the sgRNAs (in publication of this method, sgRNA strength is measurement as extrapolated LFCs calculated through a passaging experiment).</span>
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70
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC70" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
71
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC71" class="line" lang="plaintext">* uninduced ATC file: A two column file of sgRNAs and their counts in uninduced ATC (no ATC) with 0 drug concentration </span>
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72
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC72" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="73" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
73
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC73" class="line" lang="plaintext">* drug : Name of the drug in the "drug" column of the metadata file passed in to be fit in the model</span>
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74
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC74" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
75
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC75" class="line" lang="plaintext">* days: Sampled from predepletion day as listed in the "days_predepletion" column of the metadata file to be used in the analysis</span>
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78
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC78" class="line" lang="plaintext">**Step 3: Run the CRISPRi-DR model**</span>
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79
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC79" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="80" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
80
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC80" class="line" lang="plaintext">This is a relatively quick process, taking at most 3 minutes for a dataset of ~90,000 sgRNAs . This step fits the CRISPRi-DR model (statistical analysis of concentration dependence for each gene) to each gene in the file and prints each output to the <CRISPRi-DR results file> in a tab seperated file. </span>
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81
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82
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC82" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="83" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
83
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC83" class="line" lang="plaintext"> > python3 ../src/transit.py CGI run_model <fractional abundance file> > <CRISPRi-DR results file></span>
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84
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC84" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="85" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
85
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC85" class="line" lang="plaintext">* Siginificant interacting genes are those with adjusted P-val (Q-val) < 0.05 and \|Z slope\| > 2, these are indicated by a "-1" for depleted and "1" for enriched in in the "Significant Interactions" column</span>
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86
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<td class="new_line diff-line-num new" data-linenumber="87" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
87
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC87" class="line" lang="plaintext">.. note::</span>
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<td class="new_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
88
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC88" class="line" lang="plaintext"> When the file is sorted on the slope of concentration dependence, the user can rank the genes based on amount of depletion.</span>
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89
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90
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC90" class="line" lang="plaintext"></span>
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91
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC91" class="line" lang="plaintext">**Visualize Specific Genes**</span>
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92
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC92" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
93
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC93" class="line" lang="plaintext">This process is fairly quick, taking less than a minute to run. This figure visualizes the amount of depletion in a gene at the sgRNA level. If control concentration provided is 0, the lowest value on the x-axis in the plot refers to this concentration (due to taking log concentration, 0 concentration is treated as a teo fold lower than the lowest concentration.) The slope of relative abundance (fraction of abundance of counts in ATC induced vs. ATC uninduced) versus log2(concentration) for each sgRNA is calculated and plotted, colored by sgRNA strenght based on a blue-orange gradient (as seen here):</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC100" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="101" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
101
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC101" class="line" lang="plaintext"> > python3 ../src/transit.py CGI visualize <fractional abundance file> <gene> <output plot location></span>
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102
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC102" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="103" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
103
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC103" class="line" lang="plaintext">* fractional abundance file : Fractional abundance file as created in Step 2. </span>
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104
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105
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC105" class="line" lang="plaintext"> .. warning::</span>
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<td class="new_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
106
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC106" class="line" lang="plaintext"> This visualization assumes the columns are in increasing order of concentration, with the first three abundance columns (after the column "sgRNA strength"), as the control. This order depends on the order of columns during the creation of the combined counts file in Step 1.</span>
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107
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC107" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="108" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
108
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC108" class="line" lang="plaintext">* gene : select a gene to visualize. Use orf or gene name</span>
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109
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC109" class="line" lang="plaintext">* output plot location : The location where to save the generated plot.</span>
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110
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111
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC111" class="line" lang="plaintext">.. note::</span>
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112
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC112" class="line" lang="plaintext"> If comparing plots from different genes, note the scale of sgRNA strength shown in the plots.</span>
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113
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114
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115
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116
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC116" class="line" lang="plaintext">-------</span>
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<td class="new_line diff-line-num new" data-linenumber="117" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
117
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC117" class="line" lang="plaintext">**Data : Obtain FastQ files from NCBI using the following run numbers**</span>
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<td class="new_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
118
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC118" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
119
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC119" class="line" lang="plaintext">Fetch and process the following fastq files from NCBI using the SRA toolkit and place them in the ``transit/src/pytransit/data/CGI`` directory :</span>
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<td class="new_line diff-line-num new" data-linenumber="120" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
120
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC120" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="121" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
121
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC121" class="line" lang="plaintext">* FastQ files for the 3 replicates of control samples in this experiment. They are in a ATC-induced 0 drug concentration DMSO library with 1 day predepletion</span>
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<td class="new_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
122
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC122" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="123" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
123
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC123" class="line" lang="plaintext"> * SRR14827863 -> extracts SRR14827863_1.fastq</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="124" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
124
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC124" class="line" lang="plaintext"> * SRR14827862 -> extracts SRR14827862_1.fastq</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
125
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC125" class="line" lang="plaintext"> * SRR14827799 -> extracts SRR14827799_1.fastq </span>
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<td class="new_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
126
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC126" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
127
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC127" class="line" lang="plaintext">* FastQ files for 3 replicates of high concentration RIF in a 1 day pre-depletion library</span>
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<td class="new_line diff-line-num new" data-linenumber="128" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
128
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC128" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="129" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
129
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC129" class="line" lang="plaintext"> * SRR14827727 -> extracts SRR14827727_1.fastq</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="130" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
130
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC130" class="line" lang="plaintext"> * SRR14827861 -> extracts SRR14827861_1.fastq</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="131" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
131
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC131" class="line" lang="plaintext"> * SRR14827850 -> extracts SRR14827850_1.fastq</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
132
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC132" class="line" lang="plaintext">* FastQ files for 3 replicates of medium concentration RIF in a 1 day pre-depletion library</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="133" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
133
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC133" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="134" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
134
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC134" class="line" lang="plaintext"> * SRR14827760 -> extracts SRR14827760_1.fastq</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="135" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
135
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC135" class="line" lang="plaintext"> * SRR14827749 -> extracts SRR14827749_1.fastq</span>
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<td class="new_line diff-line-num new" data-linenumber="136" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
136
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC136" class="line" lang="plaintext"> * SRR14827738 -> extracts SRR14827738_1.fastq</span>
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<td class="new_line diff-line-num new" data-linenumber="137" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
137
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC137" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="138" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
138
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC138" class="line" lang="plaintext">* FastQ files for 3 replicates of low concentration RIF in a 1 day pre-depletion library</span>
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<td class="new_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
139
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC139" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="140" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
140
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC140" class="line" lang="plaintext"> * SRR14827769 -> extracts SRR14827769_1.fastq</span>
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<td class="new_line diff-line-num new" data-linenumber="141" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
141
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC141" class="line" lang="plaintext"> * SRR14827614 -> extracts SRR14827614_1.fastq</span>
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<td class="new_line diff-line-num new" data-linenumber="142" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
142
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC142" class="line" lang="plaintext"> * SRR14827870 -> extracts SRR14827870_1.fastq</span>
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<td class="new_line diff-line-num new" data-linenumber="143" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
143
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC143" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
144
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC144" class="line" lang="plaintext">This tutorial shows commands relative to this directory. Other files in the ``transit/src/pytransit/data/CGI`` directory are: </span>
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<td class="new_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
145
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC145" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="146" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
146
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC146" class="line" lang="plaintext">* counts_metadata.txt - describes the samples</span>
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<td class="new_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
147
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC147" class="line" lang="plaintext">* sgRNA_metadata.txt - contains extrapolated LFCs for each sgRNA</span>
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<td class="new_line diff-line-num new" data-linenumber="148" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
148
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC148" class="line" lang="plaintext">* uninduced_ATC_counts.txt - counts for uninduced ATC (no induction of target depletion) library</span>
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<td class="new_line diff-line-num new" data-linenumber="149" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
149
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC149" class="line" lang="plaintext">* IDs.H37Rv.CRISPRi.lib.txt - ids of the sgRNAs that target the genes in H37Rv used in these experiments </span>
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150
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC150" class="line" lang="plaintext"> </span>
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151
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC151" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="152" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
152
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC152" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="153" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
153
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC153" class="line" lang="plaintext">**Preprocessing: Fastq to Count Files**</span>
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<td class="new_line diff-line-num new" data-linenumber="154" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
154
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC154" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="155" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
155
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC155" class="line" lang="plaintext">Create file of barcode counts from fastq files. Each fastq files reflect one replicate of a drug concentration, thus each will be converted into a file with two columns, sgNRA id and barcode counts</span>
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156
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC156" class="line" lang="plaintext"></span>
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157
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC157" class="line" lang="plaintext">::</span>
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<td class="new_line diff-line-num new" data-linenumber="158" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
158
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC158" class="line" lang="plaintext"> </span>
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<td class="new_line diff-line-num new" data-linenumber="159" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
159
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC159" class="line" lang="plaintext"> > python3 ../../../transit.py CGI extract_counts RIF_fastq_files/SRR14827863_1.fastq IDs.H37Rv.CRISPRi.lib.txt > DMSO_D1_rep1.counts</span>
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<td class="new_line diff-line-num new" data-linenumber="160" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
160
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC160" class="line" lang="plaintext"> > python3 ../../../transit.py CGI extract_counts RIF_fastq_files/SRR14827862_1.fastq IDs.H37Rv.CRISPRi.lib.txt > DMSO_D1_rep2.counts</span>
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<td class="new_line diff-line-num new" data-linenumber="161" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
161
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC161" class="line" lang="plaintext"> > python3 ../../../transit.py CGI extract_counts RIF_fastq_files/SRR14827799_1.fastq IDs.H37Rv.CRISPRi.lib.txt > DMSO_D1_rep3.counts </span>
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<td class="new_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
162
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC162" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="163" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
163
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC163" class="line" lang="plaintext"> > python3 ../../../transit.py CGI extract_counts RIF_fastq_files/SRR14827769_1.fastq IDs.H37Rv.CRISPRi.lib.txt > RIF_D1_Low_rep1.counts</span>
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<td class="new_line diff-line-num new" data-linenumber="164" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
164
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC164" class="line" lang="plaintext"> > python3 ../../../transit.py CGI extract_counts RIF_fastq_files/SRR14827614_1.fastq IDs.H37Rv.CRISPRi.lib.txt > RIF_D1_Low_rep2.counts</span>
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<td class="new_line diff-line-num new" data-linenumber="165" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
165
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC165" class="line" lang="plaintext"> > python3 ../../../transit.py CGI extract_counts RIF_fastq_files/SRR14827870_1.fastq IDs.H37Rv.CRISPRi.lib.txt > RIF_D1_Low_rep3.counts </span>
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<td class="new_line diff-line-num new" data-linenumber="166" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
166
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC166" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="167" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
167
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC167" class="line" lang="plaintext"> > python3 ../../../transit.py CGI extract_counts RIF_fastq_files/SRR14827760_1.fastq IDs.H37Rv.CRISPRi.lib.txt > RIF_D1_Med_rep1.counts</span>
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<td class="new_line diff-line-num new" data-linenumber="168" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
168
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC168" class="line" lang="plaintext"> > python3 ../../../transit.py CGI extract_counts RIF_fastq_files/SRR14827749_1.fastq IDs.H37Rv.CRISPRi.lib.txt > RIF_D1_Med_rep2.counts</span>
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<td class="new_line diff-line-num new" data-linenumber="169" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
169
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC169" class="line" lang="plaintext"> > python3 ../../../transit.py CGI extract_counts RIF_fastq_files/SRR14827738_1.fastq IDs.H37Rv.CRISPRi.lib.txt > RIF_D1_Med_rep3.counts </span>
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<td class="new_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
170
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC170" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="171" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
171
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC171" class="line" lang="plaintext"> > python3 ../../../transit.py CGI extract_counts RIF_fastq_files/SRR14827727_1.fastq IDs.H37Rv.CRISPRi.lib.txt > RIF_D1_High_rep1.counts</span>
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<td class="new_line diff-line-num new" data-linenumber="172" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
172
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC172" class="line" lang="plaintext"> > python3 ../../../transit.py CGI extract_counts RIF_fastq_files/SRR14827861_1.fastq IDs.H37Rv.CRISPRi.lib.txt > RIF_D1_High_rep2.counts</span>
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<td class="new_line diff-line-num new" data-linenumber="173" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
173
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC173" class="line" lang="plaintext"> > python3 ../../../transit.py CGI extract_counts RIF_fastq_files/SRR14827850_1.fastq IDs.H37Rv.CRISPRi.lib.txt > RIF_D1_High_rep3.counts </span>
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174
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175
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176
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC176" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="177" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
177
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC177" class="line" lang="plaintext">**Step 1: Combine Counts Files to a Combined Counts File**</span>
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178
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<td class="new_line diff-line-num new" data-linenumber="179" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
179
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC179" class="line" lang="plaintext">Combine the 12 seperate counts files into one combined counts file. Here we put the control samples first (DMSO) and then the drug-treated libraries (RIF) in increasing concentration</span>
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180
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181
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182
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC182" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="183" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
183
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC183" class="line" lang="plaintext"> > python3 ../../../transit.py CGI create_combined_counts DMSO_D1_rep1,DMSO_D1_rep2,DMSO_D1_rep3,RIF_D1_Low_rep1,RIF_D1_Low_rep2,RIF_D1_Low_rep3,RIF_D1_Med_rep1,RIF_D1_Med_rep2,RIF_D1_Med_rep3,RIF_D1_High_rep1,RIF_D1_High_rep2,RIF_D1_High_rep3 DMSO_D1_rep1.counts DMSO_D1_rep2.counts DMSO_D1_rep3.counts RIF_D1_Low_rep1.counts RIF_D1_Low_rep2.counts RIF_D1_Low_rep3.counts RIF_D1_Med_rep1.counts RIF_D1_Med_rep2.counts RIF_D1_Med_rep3.counts RIF_D1_High_rep1.counts RIF_D1_High_rep2.counts RIF_D1_High_rep3.counts > RIF_D1_combined_counts.txt </span>
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184
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC184" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="185" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
185
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC185" class="line" lang="plaintext">The resulting file will have 13 columns, where the first column is sgRNA ids and the remaining are the counts for three replicates each for DMSO, RIF D1 Low Concentration, RIF D1 Med Concentration and RIF D1 High Concentration, respectively.</span>
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186
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<td class="new_line diff-line-num new" data-linenumber="187" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
187
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC187" class="line" lang="plaintext">**Step 2: Extract Fractional Abundances**</span>
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188
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189
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC189" class="line" lang="plaintext">.. note::</span>
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<td class="new_line diff-line-num new" data-linenumber="190" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
190
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC190" class="line" lang="plaintext"> As a part of this step, the *user must also generate a metadata file.* , ie. ``counts_metadata.txt``. Note the values in the conc_xMIC column is actual values (0.0625, 0.125, 0.25) and not categorical values ("low", "medium", "high") as seen in the counts file names. </span>
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191
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192
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193
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC193" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="194" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
194
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC194" class="line" lang="plaintext"> > python3 ../../../transit.py CGI extract_abund RIF_D1_combined_counts.txt counts_metadata.txt DMSO sgRNA_metadata.txt uninduced_ATC_counts.txt RIF 1 > RIF_D1_frac_abund.txt</span>
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<td class="new_line diff-line-num new" data-linenumber="195" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
195
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC195" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="196" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
196
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC196" class="line" lang="plaintext">The result of this command should be a file with a set of comments at the top, detailing the libraries used (DMSO and RIF). There should be a total of 17 columns, the last 12 of which are the calculated abundances, the first is the sgRNA ids followed by the orf/gene the sgRNA is targeting, uninduced ATC values, and sgRNA strength. </span>
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197
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC197" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="198" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
198
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC198" class="line" lang="plaintext">**Step 3: Run the CRISPRi-DR model**</span>
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<td class="new_line diff-line-num new" data-linenumber="199" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
199
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC199" class="line" lang="plaintext">::</span>
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200
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC200" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="201" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
201
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC201" class="line" lang="plaintext"> > python3 ../../../transit.py CGI run_model RIF_D1_frac_abund.txt > RIF_D1_CRISPRi-DR_results.txt</span>
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202
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC202" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="203" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
203
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC203" class="line" lang="plaintext">There should be a total of 184 significant gene interactions, where 111 are significant depletions and 73 are significantly enriched. </span>
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204
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC204" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="205" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
205
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC205" class="line" lang="plaintext">.. note::</span>
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<td class="new_line diff-line-num new" data-linenumber="206" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
206
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC206" class="line" lang="plaintext"> When the file is sorted on the slope of concentration dependence, the user can rank the genes based on amount of depletion.</span>
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207
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC207" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="208" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
208
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC208" class="line" lang="plaintext">**Visualize Specific Genes**</span>
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209
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC209" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
210
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC210" class="line" lang="plaintext">Here are a few samples of the interactions visualized at the sgRNA level for this experiment. Note the difference in sgRNA strength scales shown.</span>
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211
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC211" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="212" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
212
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC212" class="line" lang="plaintext">*Significantly depleted gene : RVBD3645*</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC214" class="line" lang="plaintext">*RVBD3645* is one of the significantly depleted genes in this experiment. In this plot, notice how most of the slopes are negative but the amount of depletion varies, where the more blue slopes (higher sgRNA strength) are steeper than orange sgRNA slopes (lower sgRNA strength)</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC222" class="line" lang="plaintext"> > python3 ../../../transit.py CGI visualize RIF_D1_frac_abund.txt RVBD3645 ./RVBD3645_lmplot.png</span>
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224
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC224" class="line" lang="plaintext">*Significantly enriched gene : ndh*</span>
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225
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC226" class="line" lang="plaintext">*ndh* is one of the signifincantly enriched genes in this experiment. In its plot, notice how sgRNAs of high strength (blue green ones) show a strong upwards trend but those will lower strength (the orange ones) do not. In fact there a few sgRNAs that show almost no change in fractional abundace as concentration increases.</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC234" class="line" lang="plaintext"> > python3 ../../../transit.py CGI visualize RIF_D1_frac_abund.txt ndh ./ndh_lmplot.png #enriched</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC238" class="line" lang="plaintext">*thiL* is an example on an non-interacting gene. It was found to be neither signifinicantly enriched nor depleted. Notice how in its plot, most of the slopes are fairly flat. As seen in the plots of *RVBD3645* and *ndh*, the bluer slopes show greater depletion than the orange slopes, but there is no overall trend present</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC247" class="line" lang="plaintext"> > python3 ../../../transit.py CGI visualize RIF_D1_frac_abund.txt thiL ./thiL_lmplot.png </span></pre></td>
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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -16,6 +16,15 @@ This page contains the documentation for TRANSIT. Below are a few</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC16" class="line" lang="plaintext">quick links to some of the most important sections of the</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC17" class="line" lang="plaintext">documentation, followed by a brief overview of TRANSIT's features.</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC19" class="line" lang="plaintext">.. NOTE::</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC20" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC21" class="line" lang="plaintext"> This documentation is for the original version of Transit. We</span>
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<td class="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
22
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC22" class="line" lang="plaintext"> recently released a new version of Transit called `TRANSIT2</span>
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<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
23
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC23" class="line" lang="plaintext"> <https://transit2.readthedocs.io/en/latest/>`_ (re-implementation</span>
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<td class="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
24
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC24" class="line" lang="plaintext"> from scratch), which has most of the same TnSeq analytical methods,</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC25" class="line" lang="plaintext"> but it has an enhanced GUI. Nonetheless, this original version of</span>
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<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
26
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC26" class="line" lang="plaintext"> TRANSIT is still being maintained for backwards-compatibility.</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC30" class="line" lang="plaintext">.. _quick-link:</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="79" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -70,10 +79,16 @@ TRANSIT offers a variety of features including:</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC79" class="line" lang="plaintext"> transit_install</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC80" class="line" lang="plaintext"> transit_running</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC81" class="line" lang="plaintext"> transit_features</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC82" class="line" lang="plaintext"> </span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC83" class="line" lang="plaintext">.. toctree::</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC84" class="line" lang="plaintext"> :maxdepth: 3</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC89" class="line" lang="plaintext">.. toctree::</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC90" class="line" lang="plaintext"> :maxdepth: 3</span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC76" class="line" lang="plaintext"> :caption: ANALYSIS METHODS</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC91" class="line" lang="plaintext"> :caption: <span class="idiff left right addition" style="background-color: #c7f0d2;">TnSeq </span>ANALYSIS METHODS</span>
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<a href="https://salsa.debian.org/med-team/tnseq-transit/-/compare/e7fcdb595572f7ea598ca27f80632375a9e0790d...898cc600b276228ce95ff463aa822e85dffdcaa1#ce4dd44a1a0db6bbc725cb081a9274ab0569c337"><strong style="font-weight: bold;">src/pytransit/doc/source/transit_install.rst</strong></a>
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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -35,6 +35,11 @@ Requirements</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC35" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC36" class="line" lang="plaintext">TRANSIT runs on both python2.7 and python3. But the dependencies vary slightly.</span>
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<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC38" class="line" lang="plaintext">Starting with release v3.0, TRANSIT now requires python3. </span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC40" class="line" lang="plaintext">To use TRANSIT with python2, use a TRANSIT release prior to 3.0 (e.g. v2.5.2)</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC43" class="line" lang="plaintext">Python 2.7:</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC44" class="line" lang="plaintext">-----------</span>
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