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Étienne Mollier pushed to branch master at <a href="https://salsa.debian.org/med-team/python-biopython" style="color: #1068bf;">Debian Med / python-biopython</a>
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Commits:
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<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/25c5fe429eb811b343fc6647b52d943f75443f90" style="color: #1068bf;">25c5fe42</a></strong>
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<span> by Étienne Mollier </span> <i> at 2022-11-24T19:25:37+01:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>muscle3.patch: fix my broken logic.
Gbp-Dch: ignore
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1 changed file:
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<a href="#32749c966355a96500c92d34ee01d73416f6757f" style="color: #1068bf;">
debian/patches/muscle3.patch
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Changes:
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<li id="32749c966355a96500c92d34ee01d73416f6757f">
<a href="https://salsa.debian.org/med-team/python-biopython/-/commit/25c5fe429eb811b343fc6647b52d943f75443f90#32749c966355a96500c92d34ee01d73416f6757f" style="color: #1068bf;"><strong style="font-weight: bold;">debian/patches/muscle3.patch</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -13,20 +13,19 @@ Last-Update: 2022-11-24</td>
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<td class="old_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
13
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<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC13" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span></span>
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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
14
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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
14
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-biopython.orig/Bio/Align/Applications/_Muscle.py</span></span>
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<td class="old_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
15
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<td class="new_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
15
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-biopython/Bio/Align/Applications/_Muscle.py</span></span>
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<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
16
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<td class="new_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); 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: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC16" class="line" lang="diff"><span class="p">@@ -10,6 +10,1<span class="idiff left right deletion" style="background-color: #fac5cd;">2</span> @@</span></span>
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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); 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="16" style="width: 35px; color: rgba(0,0,0,0.3); 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: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC16" class="line" lang="diff"><span class="p">@@ -10,6 +10,1<span class="idiff left right addition" style="background-color: #c7f0d2;">1</span> @@</span></span>
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<td class="old_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
17
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<td class="new_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
17
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC17" class="line" lang="diff"> from Bio.Application import _Option, _Switch, AbstractCommandline</span>
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<td class="old_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
18
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<td class="new_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
18
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC18" class="line" lang="diff"> from subprocess import getoutput</span>
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<td class="old_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
19
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<td class="new_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
19
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC19" class="line" lang="diff"> </span>
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<td class="old_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
20
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<td class="new_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
20
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# Prefer defaulting to muscle3, as can be installed alongside muscle version 5.</span></span>
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<td class="old_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
21
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<td class="new_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+default_muscle = "muscle3"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); 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: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+try:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); 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: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ _ = getoutput(default_muscle + " --version")</span></span>
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<td class="old_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); 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: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+except FileNotFoundError:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); 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="22" style="width: 35px; color: rgba(0,0,0,0.3); 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: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+output = getoutput(default_muscle + " --version")</span></span>
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<td class="old_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); 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="23" style="width: 35px; color: rgba(0,0,0,0.3); 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: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if "not found" in output or "not recognized" in output:</span></span>
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<td class="new_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ default_muscle = "muscle"</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC25" class="line" lang="diff"> </span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC26" class="line" lang="diff"> class MuscleCommandline(AbstractCommandline):</span>
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<td class="old_line diff-line-num" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
28
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<td class="new_line diff-line-num" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC27" class="line" lang="diff"> r"""Command line wrapper for the multiple alignment program MUSCLE.</span>
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<td class="new_line diff-line-num old" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); 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: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC29" class="line" lang="diff"><span class="p">@@ -43,7 +4<span class="idiff left right deletion" style="background-color: #fac5cd;">9</span>,7 @@</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC28" class="line" lang="diff"><span class="p">@@ -43,7 +4<span class="idiff left right addition" style="background-color: #c7f0d2;">8</span>,7 @@</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match" style="color: rgba(0,0,0,0.3); padding: inherit;" bgcolor="#fafafa">@@ -42,19 +41,15 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC41" class="line" lang="diff"> from subprocess import getoutput</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC42" class="line" lang="diff"> </span>
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<td class="new_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- output = getoutput("muscle -version")</span></span>
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<td class="old_line diff-line-num old" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
45
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<td class="new_line diff-line-num old" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); 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: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # Since "not found" may be in another language, try and be sure this is</span></span>
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46
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<td class="new_line diff-line-num old" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); 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: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # really the MUSCLE tool's output</span></span>
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47
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<td class="new_line diff-line-num old" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); 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: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if "not found" not in output and "not recognized" not in output:</span></span>
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48
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<td class="new_line diff-line-num old" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); 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: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if "MUSCLE" in output and "Edgar" in output:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); 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="44" style="width: 35px; color: rgba(0,0,0,0.3); 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: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ output = getoutput("muscle3 -version")</span></span>
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<td class="new_line diff-line-num new" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); 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: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC45" class="line" lang="diff"> # Since "not found" may be in another language, try and be sure this is</span>
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<td class="new_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); 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: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC46" class="line" lang="diff"> # really the MUSCLE tool's output</span>
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<td class="new_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); 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: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC47" class="line" lang="diff"> if "not found" not in output and "not recognized" not in output:</span>
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<td class="new_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); 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: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC48" class="line" lang="diff"> if "MUSCLE" in output and "Edgar" in output:</span>
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<td class="old_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
49
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<td class="new_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
49
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- muscle_exe = "muscle"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
50
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<td class="new_line diff-line-num old" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); 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: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ try:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
51
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<td class="new_line diff-line-num old" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); 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: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ output = getoutput("muscle3 -version")</span></span>
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<td class="old_line diff-line-num old" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
52
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<td class="new_line diff-line-num old" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); 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: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # Since "not found" may be in another language, try and be sure this is</span></span>
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<td class="old_line diff-line-num old" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
53
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<td class="new_line diff-line-num old" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); 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: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # really the MUSCLE tool's output</span></span>
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<td class="old_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
54
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<td class="new_line diff-line-num old" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); 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: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if "not found" not in output and "not recognized" not in output:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
55
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<td class="new_line diff-line-num old" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); 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: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if "MUSCLE" in output and "Edgar" in output:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
56
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<td class="new_line diff-line-num old" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); 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: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ muscle_exe = "muscle3"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
57
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<td class="new_line diff-line-num old" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); 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: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>-<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except FileNotFoundError:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); 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="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
50
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ muscle_exe = "muscle3"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); 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="51" style="width: 35px; color: rgba(0,0,0,0.3); 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: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); 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(0,0,0,0.3); 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: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'>+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # Maybe the unversionned version will still be muscle 3.</span></span>
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<td class="old_line diff-line-num" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
58
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<td class="new_line diff-line-num" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
53
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ output = getoutput("muscle -version")</span></span>
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<td class="old_line diff-line-num" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
59
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<td class="new_line diff-line-num" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
54
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if "not found" not in output and "not recognized" not in output:</span></span>
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<td class="old_line diff-line-num" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
60
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<td class="new_line diff-line-num" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fafafa">
55
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dbdbdb;'> <span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if "MUSCLE" in output and "Edgar" in output:</span></span>
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