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GitLab

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<h3>

Andreas Tille pushed to branch master

at <a href="https://salsa.debian.org/med-team/qiime">Debian Med / qiime</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/qiime/commit/b9552ff4c454f52e25a3f4528bcd87246072a440">b9552ff4</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-10-28T16:27:41Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">No doc package

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/qiime/commit/24733a1657340ec503db57452b150cd16ca30433">24733a16</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-10-28T16:28:34Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove remainings to get source package of qiime1

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/qiime/commit/f40b198fcebb9e83015e7f32a8e175b366da3e9f">f40b198f</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-10-28T16:30:19Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove qiime1 patches

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/qiime/commit/0bfafca41321240fddf49e7bb103f0dd8fbebb52">0bfafca4</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-10-28T16:40:31Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove old qiime config stuff

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/qiime/commit/7d6b53826988db773b76d73d5606098497efba53">7d6b5382</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-10-28T17:06:36Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop unused overrides

</pre>

</li>

</ul>

<h4>22 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#cf9802e192b48f765b1b5c8268d550d89c933053">

<span class="deleted-file">

−

debian/README.source

</span>

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

</li>

<li class="file-stats">

<a href="#fc932f0eaa389a4e2b93916f3995aae4019ea823">

<span class="deleted-file">

−

debian/get-orig-source

</span>

</a>

</li>

<li class="file-stats">

<a href="#51fbcd3634f989002acaeed72fd82779cb9adfa6">

<span class="deleted-file">

−

debian/patches/allow_empty_default_taxonomy.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#0bdf64c3863c393a2963d15271339d634ed0b6ac">

<span class="deleted-file">

−

debian/patches/call_renamed_seqprep_sortmerna.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#8cd9856906f375e3f6da0f598f79a30c0fb6f93e">

<span class="deleted-file">

−

debian/patches/check_config_file_in_new_location.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#1bae2a1e273ce6bd939db6796b58a556da834c67">

<span class="deleted-file">

−

debian/patches/detect_matplotlib_version.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#47ad2fb3c73990058d77dd8ec7bd2cb8b2857953">

<span class="deleted-file">

−

debian/patches/exclude_tests_that_need_to_fail.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#f7bf9619ee40c3284ec8034c645669b430e1738e">

<span class="deleted-file">

−

debian/patches/fix_binary_helper_location.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#3a7264d1c1519aba3fee5249c0aa903b55b94327">

<span class="deleted-file">

−

debian/patches/fix_path_for_support_files.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#2a358f77380ac0c6a1776bad65402a0aa7e75ad6">

<span class="deleted-file">

−

debian/patches/fix_script_usage_tests.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#0093db8a86c199cf12ec62807b212d92dfdedf55">

<span class="deleted-file">

−

debian/patches/make_qiime_accept_new_rdp_classifier.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#c45be83049c2ab6730e6e2647af109e8ab11c68b">

<span class="deleted-file">

−

debian/patches/prevent_download_on_builds.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#1036dc871db02015d583917a3b434053900dfdab">

<span class="deleted-file">

−

debian/patches/prevent_google_addsense.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#c219f8f308b3b9e77013e46607e5603631d9a0ea">

<span class="deleted-file">

−

debian/patches/relax_mothur_blast_raxml_versions.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

debian/patches/series

</a>

</li>

<li class="file-stats">

<a href="#24abe6a0133f788f204c33f7b28def90f2fb18a4">

<span class="deleted-file">

−

debian/qiime-doc.doc-base

</span>

</a>

</li>

<li class="file-stats">

<a href="#1e2e0f50a9779f424b876fbc8e0f98b049d2bd1c">

<span class="deleted-file">

−

debian/qiime-doc.links

</span>

</a>

</li>

<li class="file-stats">

<a href="#7e87233c9ee48d46f144c0134350e9a8b3a43dbd">

<span class="deleted-file">

−

debian/qiime_config

</span>

</a>

</li>

<li class="file-stats">

<a href="#280c3383888b855c650ea4a9360e393a4881752b">

<span class="deleted-file">

−

debian/scripts/print_qiime_config_all

</span>

</a>

</li>

<li class="file-stats">

<a href="#85ccdeeb03055211183e48520592d9a93592b330">

<span class="deleted-file">

−

debian/source/lintian-overrides

</span>

</a>

</li>

<li class="file-stats">

<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">

debian/watch

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="cf9802e192b48f765b1b5c8268d550d89c933053">

<a href="https://salsa.debian.org/med-team/qiime/compare/c4c1063f9ef9a29ea1c74344ab0d9e8a9e1cf98d...7d6b53826988db773b76d73d5606098497efba53#cf9802e192b48f765b1b5c8268d550d89c933053"><strong>debian/README.source</strong>

deleted

</a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num old old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">QIIME for Debian - source</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">=========================</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">.py endings and the qiime wrapper of Bio-Linux</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">----------------------------------------------</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

6

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

7

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Previous comment by Steffen:</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

8

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Lintian complains a lot about script-with-language-extension,</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

10

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">i.e. the .py endings for files ending up in /usr/bin.</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

11

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">What to do about this is not clear for the moment. For the</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">time speaking it seems like lintian is wrong here, too deeply</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">embedded is python in the project and Debian does not</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">want to become incompatible.</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

15

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

16

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">New comments by Tim:</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

17

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

18

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">I borrowed the Bio-Linux approach for QIIME which may or may not be the best idea.</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

19

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">Essentially, the Python scripts are not in the path and instead of running:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

20

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

21

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">% my_qiime_app.py</span>

</pre>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

22

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

23

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">You run:</span>

</pre>

</td>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

24

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

25

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">% qiime my_qiime_app.py</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

26

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

27

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">or equivalently just:</span>

</pre>

</td>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

28

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

29

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">% qiime my_qiime_app</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

30

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

31

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">The 'qiime' wrapper script adds the extension if needed and sets the path.  If run with</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

32

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext">no arguments it sets the path and drops to an interactive shell.</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

33

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

34

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext">The dependencies of QIIME essentially make it non-free despite the DFSG licence on the QIIME</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

35

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext">code itself.  Chief among these is UClust.  This package is supposed to handle the lack of UClust</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

36

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext">gracefully but it is still up to the user to fetch and install it.  </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

37

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

38

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext">Other dependencies/TODO:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

39

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext">------------------------</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

40

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

41

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">Everything else needed should be packaged, if not in Debian proper then in the SVN.  QIIME</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

42

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">keeps adding new deps so these need to be checked with each release.</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

43

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

44

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext">To package:</span>

</pre>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

45

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext"> * Emperor 1.8.0+</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

46

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext"> * python-burrito-fillings</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

47

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

48

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext">The</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

49

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext">   Build-Depends: bwa, infernal, raxml, sortmerna, swarm, vsearch</span>

</pre>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

50

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext">are just added to make sure the qiime package will build only on those architectures successfully</span>

</pre>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

51

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext">where all these dependencies exist.</span>

</pre>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

52

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

53

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext">QIIME data</span>

</pre>

</td>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

54

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext">----------</span>

</pre>

</td>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

55

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

56

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext">The QIIME installation instructions say that you need to download some core files from Greengenes.</span>

</pre>

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext">Since these barely change and are included in the upstream tarball I am now putting them into the</span>

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext">qiime-data package for easy access.  I have noted in copyright that these are CC licensed.</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext">See here for a discussion of what these are and why they don't change:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext">https://groups.google.com/forum/?hl=en-US#!searchin/qiime-forum/greengenes/qiime-forum/SvXFetaLNCM/HE6bsBY0yZIJ</span>

</pre>

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext"></span></pre>

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<br>

</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/qiime/compare/c4c1063f9ef9a29ea1c74344ab0d9e8a9e1cf98d...7d6b53826988db773b76d73d5606098497efba53#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -102,47 +102,6 @@ Description: Quantitative Insights Into Microbial Ecology</td>

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<td class="diff-line-num old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext"> PyCogent toolkit. It makes extensive use of unit tests, and is highly</span>

</pre>

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext"> modular to facilitate custom analyses.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC105" class="line" lang="plaintext">Package: qiime-doc</span>

</pre>

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<pre style="margin: 0;">-<span id="LC106" class="line" lang="plaintext">Architecture: all</span>

</pre>

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<pre style="margin: 0;">-<span id="LC107" class="line" lang="plaintext">Section: doc</span>

</pre>

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<pre style="margin: 0;">-<span id="LC108" class="line" lang="plaintext">Depends: ${misc:Depends},</span>

</pre>

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<pre style="margin: 0;">-<span id="LC109" class="line" lang="plaintext">         libjs-jquery,</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC110" class="line" lang="plaintext">         libjs-underscore</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC111" class="line" lang="plaintext">Description: Quantitative Insights Into Microbial Ecology (tutorial)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC112" class="line" lang="plaintext"> QIIME (canonically pronounced ‘Chime’) is a pipeline for performing</span>

</pre>

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<pre style="margin: 0;">-<span id="LC113" class="line" lang="plaintext"> microbial community analysis that integrates many third party tools which</span>

</pre>

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</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC114" class="line" lang="plaintext"> have become standard in the field. A standard QIIME analysis begins with</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

115

</td>

<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC115" class="line" lang="plaintext"> sequence data from one or more sequencing platforms, including</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

116

</td>

<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC116" class="line" lang="plaintext">  * Sanger,</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

117

</td>

<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC117" class="line" lang="plaintext">  * Roche/454, and</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

118

</td>

<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC118" class="line" lang="plaintext">  * Illumina GAIIx.</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

119

</td>

<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC119" class="line" lang="plaintext"> QIIME can perform:</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

120

</td>

<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC120" class="line" lang="plaintext">  * library de-multiplexing and quality filtering;</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

121

</td>

<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC121" class="line" lang="plaintext">  * denoising with PyroNoise;</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

122

</td>

<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC122" class="line" lang="plaintext">  * OTU and representative set picking with uclust, cdhit, mothur, BLAST,</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

123

</td>

<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC123" class="line" lang="plaintext">    or other tools;</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

124

</td>

<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC124" class="line" lang="plaintext">  * taxonomy assignment with BLAST or the RDP classifier;</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

125

</td>

<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC125" class="line" lang="plaintext">  * sequence alignment with PyNAST, muscle, infernal, or other tools;</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

126

</td>

<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC126" class="line" lang="plaintext">  * phylogeny reconstruction with FastTree, raxml, clearcut, or other tools;</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

127

</td>

<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC127" class="line" lang="plaintext">  * alpha diversity and rarefaction, including visualization of results,</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

128

</td>

<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC128" class="line" lang="plaintext">    using over 20 metrics including Phylogenetic Diversity, chao1, and</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

129

</td>

<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC129" class="line" lang="plaintext">    observed species;</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

130

</td>

<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC130" class="line" lang="plaintext">  * beta diversity and rarefaction, including visualization of results,</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

131

</td>

<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC131" class="line" lang="plaintext">    using over 25 metrics including weighted and unweighted UniFrac,</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

132

</td>

<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC132" class="line" lang="plaintext">    Euclidean distance, and Bray-Curtis;</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

133

</td>

<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC133" class="line" lang="plaintext">  * summarization and visualization of taxonomic composition of samples</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

134

</td>

<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC134" class="line" lang="plaintext">    using pie charts and histograms</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

135

</td>

<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC135" class="line" lang="plaintext"> and many other features.</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

136

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<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC136" class="line" lang="plaintext"> .</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

137

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<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC137" class="line" lang="plaintext"> QIIME includes parallelization capabilities for many of the</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

138

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<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC138" class="line" lang="plaintext"> computationally intensive steps. By default, these are configured to</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

139

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<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC139" class="line" lang="plaintext"> utilize a mutli-core environment, and are easily configured to run in</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

140

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<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC140" class="line" lang="plaintext"> a cluster environment. QIIME is built in Python using the open-source</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

141

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<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC141" class="line" lang="plaintext"> PyCogent toolkit. It makes extensive use of unit tests, and is highly</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

142

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<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC142" class="line" lang="plaintext"> modular to facilitate custom analyses.</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

143

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<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC143" class="line" lang="plaintext"> .</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

144

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<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC144" class="line" lang="plaintext"> This package contains the documentation and a tutorial.</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

145

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<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC145" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

146

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<td class="diff-line-num new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

105

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC105" class="line" lang="plaintext">Package: qiime-data</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

147

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<td class="diff-line-num new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

106

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC106" class="line" lang="plaintext">Architecture: all</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

148

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<td class="diff-line-num new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

107

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC107" class="line" lang="plaintext">Depends: ${misc:Depends}</span>

</pre>

</td>

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</table>

<br>

</li>

<li id="fc932f0eaa389a4e2b93916f3995aae4019ea823">

<a href="https://salsa.debian.org/med-team/qiime/compare/c4c1063f9ef9a29ea1c74344ab0d9e8a9e1cf98d...7d6b53826988db773b76d73d5606098497efba53#fc932f0eaa389a4e2b93916f3995aae4019ea823"><strong>debian/get-orig-source</strong>

deleted

</a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num old old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># strip binary JARs</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"><span class="nv" style="color: teal;">COMPRESSION</span><span class="o" style="font-weight: 600;">=</span>xz</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

6

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: navy;">-e</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

7

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"><span class="nv" style="color: teal;">NAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>dpkg-parsechangelog | <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'/^Source/ { print $2 }'</span><span class="sb" style="color: #d14;">`</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

8

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">!</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$@</span> | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-q</span> upstream-version <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

10

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;">    </span><span class="nv" style="color: teal;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>dpkg-parsechangelog | <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'/^Version:/ { print $2 }'</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/\([0-9\.]\+\)-[0-9]\+$/\1/'</span><span class="sb" style="color: #d14;">`</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

11

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"><span class="k" style="font-weight: 600;">    </span><span class="nv" style="color: teal;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$@</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="s2" style="color: #d14;">"s?^.*--upstream-version </span><span class="se" style="color: #d14;">\(</span><span class="s2" style="color: #d14;">[0-9.]</span><span class="se" style="color: #d14;">\+\)</span><span class="s2" style="color: #d14;"> .*</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">name</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">.*?</span><span class="se" style="color: #d14;">\1</span><span class="s2" style="color: #d14;">?"</span><span class="sb" style="color: #d14;">`</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell">    <span class="k" style="font-weight: 600;">if </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$VERSION</span><span class="s2" style="color: #d14;">"</span> | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-q</span> <span class="s2" style="color: #d14;">"upstream-version"</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="k" style="font-weight: 600;">        </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Unable to parse version number"</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

15

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell">        <span class="nb" style="color: #0086b3;">exit</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

16

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">    </span><span class="k" style="font-weight: 600;">fi</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

17

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

18

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

19

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Upstream tarball has upper case 'Q'</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

20

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell"><span class="nv" style="color: teal;">UPSTREAMNAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">echo</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">NAME</span><span class="k" style="font-weight: 600;">}</span> | <span class="nb" style="color: #0086b3;">tr</span> <span class="o" style="font-weight: 600;">[</span>q] <span class="o" style="font-weight: 600;">[</span>Q]<span class="sb" style="color: #d14;">`</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

21

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell"><span class="nv" style="color: teal;">TARDIR</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">UPSTREAMNAME</span><span class="k" style="font-weight: 600;">}</span>-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">VERSION</span><span class="k" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

22

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

23

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: navy;">-p</span> ../tarballs</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

24

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> ../tarballs</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

25

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">tar </span>xaf ../<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">UPSTREAMNAME</span><span class="k" style="font-weight: 600;">}</span>-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">VERSION</span><span class="k" style="font-weight: 600;">}</span>.tar.gz</span>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="shell"></span>

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Remove useless JAR and CLASS files</span></span>

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="shell">find <span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: navy;">-name</span> <span class="s2" style="color: #d14;">"*.jar"</span> <span class="nt" style="color: navy;">-delete</span></span>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="shell"></span>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="shell"><span class="nv" style="color: teal;">GZIP</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"--best --no-name"</span> <span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: navy;">--owner</span><span class="o" style="font-weight: 600;">=</span>root <span class="nt" style="color: navy;">--group</span><span class="o" style="font-weight: 600;">=</span>root <span class="nt" style="color: navy;">--mode</span><span class="o" style="font-weight: 600;">=</span>a+rX <span class="nt" style="color: navy;">-caf</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$NAME</span><span class="s2" style="color: #d14;">"</span>_<span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$VERSION</span><span class="s2" style="color: #d14;">"</span>.orig.tar.<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">COMPRESSION</span><span class="k" style="font-weight: 600;">}</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">TARDIR</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$TARDIR</span><span class="s2" style="color: #d14;">"</span></span></pre>

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<br>

</li>

<li id="51fbcd3634f989002acaeed72fd82779cb9adfa6">

<a href="https://salsa.debian.org/med-team/qiime/compare/c4c1063f9ef9a29ea1c74344ab0d9e8a9e1cf98d...7d6b53826988db773b76d73d5606098497efba53#51fbcd3634f989002acaeed72fd82779cb9adfa6"><strong>debian/patches/allow_empty_default_taxonomy.patch</strong>

deleted

</a>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">The behaviour in qiime/assign_taxonomy.py is that if the taxonomy file path is</span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">not set then the RDP classifier will not be retrained.</span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">But the script bin/assign_taxonomy.py detects if the parameter is set to None</span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff">and replaces it with the default value.</span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">So you always end up retraining the classifier, which is stupid.</span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">This is a nasty but effective workaround.</span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/assign_taxonomy.py</span></span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/assign_taxonomy.py</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -106,6 +106,13 @@</span></span>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> default_reference_seqs_fp = qiime_config['assign_taxonomy_reference_seqs_fp']</span>

</pre>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> default_id_to_taxonomy_fp = qiime_config['assign_taxonomy_id_to_taxonomy_fp']</span>

</pre>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# Setting a path that begins with '#' disables the option</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if default_reference_seqs_fp.lstrip().startswith('#'):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    default_reference_seqs_fp = None</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if default_id_to_taxonomy_fp.lstrip().startswith('#'):</span></span>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    default_id_to_taxonomy_fp = None</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> script_info['optional_options'] = [</span>

</pre>

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff">     make_option('-t', '--id_to_taxonomy_fp', type="existing_filepath",</span>

</pre>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff">                 help='Path to tab-delimited file mapping sequences to assigned '</span></pre>

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<br>

</li>

<li id="0bdf64c3863c393a2963d15271339d634ed0b6ac">

<a href="https://salsa.debian.org/med-team/qiime/compare/c4c1063f9ef9a29ea1c74344ab0d9e8a9e1cf98d...7d6b53826988db773b76d73d5606098497efba53#0bdf64c3863c393a2963d15271339d634ed0b6ac"><strong>debian/patches/call_renamed_seqprep_sortmerna.patch</strong>

deleted

</a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

</table>

<br>

</li>

<li id="8cd9856906f375e3f6da0f598f79a30c0fb6f93e">

<a href="https://salsa.debian.org/med-team/qiime/compare/c4c1063f9ef9a29ea1c74344ab0d9e8a9e1cf98d...7d6b53826988db773b76d73d5606098497efba53#8cd9856906f375e3f6da0f598f79a30c0fb6f93e"><strong>debian/patches/check_config_file_in_new_location.patch</strong>

deleted

</a>

<hr>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">We've moved the default config file, so tell this script to look in the new</span>

</pre>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">location.  See the next patch for other path fixes related to support_files</span>

</pre>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"></span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/print_qiime_config.py</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/print_qiime_config.py</span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -283,8 +283,7 @@</span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff">                               "config file as they will be ignored by QIIME.")</span>

</pre>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff">         qiime_project_dir = get_qiime_project_dir()</span>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        orig_config = parse_qiime_config_file(open(qiime_project_dir +</span></span>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                                   '/qiime/support_files/qiime_config'))</span></span>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        orig_config = parse_qiime_config_file(open('/etc/qiime/qiime_config'))</span></span>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff">         # check the env qiime_config</span>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff">         qiime_config_env_filepath = getenv('QIIME_CONFIG_FP')</span></pre>

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<br>

</li>

<li id="1bae2a1e273ce6bd939db6796b58a556da834c67">

<a href="https://salsa.debian.org/med-team/qiime/compare/c4c1063f9ef9a29ea1c74344ab0d9e8a9e1cf98d...7d6b53826988db773b76d73d5606098497efba53#1bae2a1e273ce6bd939db6796b58a556da834c67"><strong>debian/patches/detect_matplotlib_version.patch</strong>

deleted

</a>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Author: Tim Booth <tbooth@ceh.ac.uk></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Last-Update: Mon, 10 Mar 2014 14:20:08 +0000</span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">Description: Enable proper detection of mathplotlib</span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"></span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/print_qiime_config.py</span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/print_qiime_config.py</span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -306,7 +306,7 @@ class QIIMEDependencyBase(QIIMEConfig):</span></span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff">         max_acceptable_version = (1,3,1)</span>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff">         try:</span>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff">             from matplotlib import __version__ as matplotlib_lib_version</span>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            version = tuple(map(int,matplotlib_lib_version.split('.')))</span></span>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+     version = tuple(map(lambda x: int(x.replace("rc","")),matplotlib_lib_version.split('.')))</span></span>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff">             pass_test = (version >= min_acceptable_version and</span>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff">                          version <= max_acceptable_version)</span>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff">             version_string = str(matplotlib_lib_version)</span></pre>

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<br>

</li>

<li id="47ad2fb3c73990058d77dd8ec7bd2cb8b2857953">

<a href="https://salsa.debian.org/med-team/qiime/compare/c4c1063f9ef9a29ea1c74344ab0d9e8a9e1cf98d...7d6b53826988db773b76d73d5606098497efba53#47ad2fb3c73990058d77dd8ec7bd2cb8b2857953"><strong>debian/patches/exclude_tests_that_need_to_fail.patch</strong>

deleted

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Last-Update: Thu, 26 Dec 2013 07:39:57 +0100</span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">Description: Exclude tests that need to fail</span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> uclust is non-free and can not be packaged.  The QIIME package just contains</span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"> a wrapper telling this fact the user and thus the tests will fail.  To avoid</span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> useless failures these tests are excluded.</span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"></span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"></span>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/test_align_seqs.py</span></span>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/test_align_seqs.py</span></span>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -134,20 +134,20 @@ class InfernalAlignerTests(SharedSetupTe</span></span>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff">          LoadSeqs(data=infernal_test1_expected_alignment,aligned=Alignment,\</span>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff">             moltype=DNA)</span>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    def test_call_infernal_test1_file_output(self):</span></span>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """InfernalAligner writes correct output files for infernal_test1 seqs</span></span>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """</span></span>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # do not collect results; check output files instead</span></span>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        actual = self.infernal_test1_aligner(\</span></span>

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         self.infernal_test1_input_fp, result_path=self.result_fp,</span></span>

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         log_path=self.log_fp)</span></span>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         </span></span>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertTrue(actual == None,\</span></span>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         "Result should be None when result path provided.")</span></span>

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         </span></span>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        expected_aln = self.infernal_test1_expected_aln</span></span>

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        actual_aln = LoadSeqs(self.result_fp,aligned=Alignment)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(actual_aln,expected_aln)</span></span>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#    def test_call_infernal_test1_file_output(self):</span></span>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """InfernalAligner writes correct output files for infernal_test1 seqs</span></span>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # do not collect results; check output files instead</span></span>

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        actual = self.infernal_test1_aligner(\</span></span>

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         self.infernal_test1_input_fp, result_path=self.result_fp,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         log_path=self.log_fp)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         </span></span>

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertTrue(actual == None,\</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         "Result should be None when result path provided.")</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         </span></span>

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        expected_aln = self.infernal_test1_expected_aln</span></span>

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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        actual_aln = LoadSeqs(self.result_fp,aligned=Alignment)</span></span>

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(actual_aln,expected_aln)</span></span>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff">     def test_call_infernal_test1(self):</span>

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff">         """InfernalAligner: functions as expected when returing objects</span>

</pre>

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -221,84 +221,84 @@ class PyNastAlignerTests(SharedSetupTest</span></span>

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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff">         self.pynast_test1_expected_fail = \</span>

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff">          LoadSeqs(data=pynast_test1_expected_failure,aligned=False)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    def test_call_pynast_test1_file_output(self):</span></span>

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """PyNastAligner writes correct output files for pynast_test1 seqs</span></span>

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # do not collect results; check output files instead</span></span>

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        actual = self.pynast_test1_aligner(\</span></span>

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         self.pynast_test1_input_fp, result_path=self.result_fp,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         log_path=self.log_fp, failure_path=self.failure_fp)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         </span></span>

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertTrue(actual == None,\</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         "Result should be None when result path provided.")</span></span>

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        expected_aln = self.pynast_test1_expected_aln</span></span>

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        actual_aln = LoadSeqs(self.result_fp,aligned=DenseAlignment)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(actual_aln,expected_aln)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        actual_fail = LoadSeqs(self.failure_fp,aligned=False)</span></span>

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(actual_fail.toFasta(),\</span></span>

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         self.pynast_test1_expected_fail.toFasta())</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    def test_call_pynast_test1_file_output_alt_params(self):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """PyNastAligner writes correct output files when no seqs align</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """</span></span>

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        aligner = PyNastAligner({</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                'template_filepath': self.pynast_test1_template_fp,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                'min_len':1000})</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        actual = aligner(\</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         self.pynast_test1_input_fp, result_path=self.result_fp,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         log_path=self.log_fp, failure_path=self.failure_fp)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertTrue(actual == None,\</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         "Result should be None when result path provided.")</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(getsize(self.result_fp),0,\</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         "No alignable seqs should result in an empty file.")</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # all seqs reported to fail</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        actual_fail = LoadSeqs(self.failure_fp,aligned=False)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(actual_fail.getNumSeqs(),3)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    def test_call_pynast_test1(self):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """PyNastAligner: functions as expected when returing objects</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC93" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC94" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        actual_aln = self.pynast_test1_aligner(self.pynast_test1_input_fp)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC95" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        expected_aln = self.pynast_test1_expected_aln</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        expected_names = ['1 description field 1..23', '2 1..23']</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(actual_aln.Names, expected_names)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(actual_aln, expected_aln)</span></span>

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<pre style="margin: 0;">-<span id="LC100" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    def test_call_pynast_template_aln_with_dots(self):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """PyNastAligner: functions when template alignment contains dots</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        pynast_aligner = PyNastAligner({</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC105" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                'template_filepath': self.pynast_test_template_w_dots_fp,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC106" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                'min_len': 15,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                })</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        actual_aln = pynast_aligner(self.pynast_test1_input_fp)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        expected_aln = self.pynast_test1_expected_aln</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC111" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        expected_names = ['1 description field 1..23', '2 1..23']</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(actual_aln.Names, expected_names)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(actual_aln, expected_aln)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    def test_call_pynast_template_aln_with_lower(self):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """PyNastAligner: functions when template alignment contains lower case</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC117" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        pynast_aligner = PyNastAligner({</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC119" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                'template_filepath': self.pynast_test_template_w_lower_fp,</span></span>

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<pre style="margin: 0;">-<span id="LC120" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                'min_len': 15,</span></span>

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<pre style="margin: 0;">-<span id="LC121" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                })</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC122" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        actual_aln = pynast_aligner(self.pynast_test1_input_fp)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC123" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        expected_aln = self.pynast_test1_expected_aln</span></span>

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<pre style="margin: 0;">-<span id="LC124" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        expected_names = ['1 description field 1..23', '2 1..23']</span></span>

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<pre style="margin: 0;">-<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(actual_aln.Names, expected_names)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC127" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(actual_aln, expected_aln)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC128" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#    def test_call_pynast_test1_file_output(self):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC129" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """PyNastAligner writes correct output files for pynast_test1 seqs</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC130" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC131" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # do not collect results; check output files instead</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC132" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        actual = self.pynast_test1_aligner(\</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC133" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         self.pynast_test1_input_fp, result_path=self.result_fp,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC134" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         log_path=self.log_fp, failure_path=self.failure_fp)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC135" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         </span></span>

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<pre style="margin: 0;">-<span id="LC136" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertTrue(actual == None,\</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC137" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         "Result should be None when result path provided.")</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC138" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         </span></span>

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<pre style="margin: 0;">-<span id="LC139" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        expected_aln = self.pynast_test1_expected_aln</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

140

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<pre style="margin: 0;">-<span id="LC140" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        actual_aln = LoadSeqs(self.result_fp,aligned=DenseAlignment)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

141

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<pre style="margin: 0;">-<span id="LC141" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(actual_aln,expected_aln)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

142

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<pre style="margin: 0;">-<span id="LC142" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

143

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<pre style="margin: 0;">-<span id="LC143" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        actual_fail = LoadSeqs(self.failure_fp,aligned=False)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

144

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<pre style="margin: 0;">-<span id="LC144" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(actual_fail.toFasta(),\</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

145

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<pre style="margin: 0;">-<span id="LC145" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                         self.pynast_test1_expected_fail.toFasta())</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC146" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC147" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC148" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#    def test_call_pynast_test1_file_output_alt_params(self):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC149" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """PyNastAligner writes correct output files when no seqs align</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC150" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC151" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        aligner = PyNastAligner({</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

152

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<pre style="margin: 0;">-<span id="LC152" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                'template_filepath': self.pynast_test1_template_fp,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

153

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<pre style="margin: 0;">-<span id="LC153" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                'min_len':1000})</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

154

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<pre style="margin: 0;">-<span id="LC154" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

155

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<pre style="margin: 0;">-<span id="LC155" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        actual = aligner(\</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

156

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<pre style="margin: 0;">-<span id="LC156" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         self.pynast_test1_input_fp, result_path=self.result_fp,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

157

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<pre style="margin: 0;">-<span id="LC157" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         log_path=self.log_fp, failure_path=self.failure_fp)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC158" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC159" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertTrue(actual == None,\</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC160" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         "Result should be None when result path provided.")</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC161" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC162" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(getsize(self.result_fp),0,\</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC163" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         "No alignable seqs should result in an empty file.")</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC164" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC165" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # all seqs reported to fail</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC166" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        actual_fail = LoadSeqs(self.failure_fp,aligned=False)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC167" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(actual_fail.getNumSeqs(),3)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC168" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC169" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#    def test_call_pynast_test1(self):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC170" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """PyNastAligner: functions as expected when returing objects</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC171" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC172" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        actual_aln = self.pynast_test1_aligner(self.pynast_test1_input_fp)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC173" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        expected_aln = self.pynast_test1_expected_aln</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC174" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC175" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        expected_names = ['1 description field 1..23', '2 1..23']</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC176" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(actual_aln.Names, expected_names)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC177" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(actual_aln, expected_aln)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC178" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC179" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#    def test_call_pynast_template_aln_with_dots(self):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC180" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """PyNastAligner: functions when template alignment contains dots</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC181" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """</span></span>

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<pre style="margin: 0;">-<span id="LC182" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        pynast_aligner = PyNastAligner({</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC183" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                'template_filepath': self.pynast_test_template_w_dots_fp,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC184" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                'min_len': 15,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC185" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                })</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC186" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        actual_aln = pynast_aligner(self.pynast_test1_input_fp)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC187" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        expected_aln = self.pynast_test1_expected_aln</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC188" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC189" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        expected_names = ['1 description field 1..23', '2 1..23']</span></span>

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<pre style="margin: 0;">-<span id="LC190" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(actual_aln.Names, expected_names)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC191" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(actual_aln, expected_aln)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC192" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC193" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#    def test_call_pynast_template_aln_with_lower(self):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC194" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """PyNastAligner: functions when template alignment contains lower case</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC195" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC196" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        pynast_aligner = PyNastAligner({</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC197" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                'template_filepath': self.pynast_test_template_w_lower_fp,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC198" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                'min_len': 15,</span></span>

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<pre style="margin: 0;">-<span id="LC199" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                })</span></span>

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<pre style="margin: 0;">-<span id="LC200" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        actual_aln = pynast_aligner(self.pynast_test1_input_fp)</span></span>

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<pre style="margin: 0;">-<span id="LC201" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        expected_aln = self.pynast_test1_expected_aln</span></span>

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<pre style="margin: 0;">-<span id="LC202" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#</span></span>

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<pre style="margin: 0;">-<span id="LC203" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        expected_names = ['1 description field 1..23', '2 1..23']</span></span>

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<pre style="margin: 0;">-<span id="LC204" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(actual_aln.Names, expected_names)</span></span>

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<pre style="margin: 0;">-<span id="LC205" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(actual_aln, expected_aln)</span></span>

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<pre style="margin: 0;">-<span id="LC206" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC207" class="line" lang="diff">     def test_call_pynast_template_aln_with_U(self):</span>

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<pre style="margin: 0;">-<span id="LC208" class="line" lang="diff">         """PyNastAligner: error message when template contains bad char</span>

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<pre style="margin: 0;">-<span id="LC209" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -309,43 +309,43 @@ class PyNastAlignerTests(SharedSetupTest</span></span>

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<pre style="margin: 0;">-<span id="LC210" class="line" lang="diff">                 })</span>

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<pre style="margin: 0;">-<span id="LC211" class="line" lang="diff">         self.assertRaises(KeyError,pynast_aligner,self.pynast_test1_input_fp)</span>

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<pre style="margin: 0;">-<span id="LC212" class="line" lang="diff">         </span>

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<pre style="margin: 0;">-<span id="LC213" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    def test_call_pynast_alt_pairwise_method(self):</span></span>

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<pre style="margin: 0;">-<span id="LC214" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """PyNastAligner: alternate pairwise alignment method produces correct alignment</span></span>

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<pre style="margin: 0;">-<span id="LC215" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC216" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        aligner = PyNastAligner({</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC217" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                'pairwise_alignment_method': 'muscle',</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC218" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                'template_filepath': self.pynast_test1_template_fp,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC219" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                'min_len': 15,</span></span>

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<pre style="margin: 0;">-<span id="LC220" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                })</span></span>

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<pre style="margin: 0;">-<span id="LC221" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        actual_aln = aligner(self.pynast_test1_input_fp)</span></span>

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<pre style="margin: 0;">-<span id="LC222" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        expected_aln = self.pynast_test1_expected_aln</span></span>

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<pre style="margin: 0;">-<span id="LC223" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(actual_aln, expected_aln)</span></span>

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<pre style="margin: 0;">-<span id="LC224" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </span></span>

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<pre style="margin: 0;">-<span id="LC225" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    def test_call_pynast_test1_alt_min_len(self):</span></span>

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<pre style="margin: 0;">-<span id="LC226" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """PyNastAligner: returns no result when min_len too high</span></span>

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<pre style="margin: 0;">-<span id="LC227" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """</span></span>

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<pre style="margin: 0;">-<span id="LC228" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        aligner = PyNastAligner({</span></span>

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<pre style="margin: 0;">-<span id="LC229" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                'template_filepath': self.pynast_test1_template_fp,</span></span>

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<pre style="margin: 0;">-<span id="LC230" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                'min_len':1000})</span></span>

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<pre style="margin: 0;">-<span id="LC231" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </span></span>

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<pre style="margin: 0;">-<span id="LC232" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        actual_aln = aligner(\</span></span>

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<pre style="margin: 0;">-<span id="LC233" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         self.pynast_test1_input_fp)</span></span>

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<pre style="margin: 0;">-<span id="LC234" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        expected_aln = {}</span></span>

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<pre style="margin: 0;">-<span id="LC235" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;">-<span id="LC236" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(actual_aln, expected_aln)</span></span>

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<pre style="margin: 0;">-<span id="LC237" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </span></span>

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<pre style="margin: 0;">-<span id="LC238" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    def test_call_pynast_test1_alt_min_pct(self):</span></span>

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<pre style="margin: 0;">-<span id="LC239" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """PyNastAligner: returns no result when min_pct too high</span></span>

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<pre style="margin: 0;">-<span id="LC240" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC241" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        aligner = PyNastAligner({</span></span>

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<pre style="margin: 0;">-<span id="LC242" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                'template_filepath': self.pynast_test1_template_fp,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC243" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                'min_len':15,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC244" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                'min_pct':100.0})</span></span>

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<pre style="margin: 0;">-<span id="LC245" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </span></span>

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<pre style="margin: 0;">-<span id="LC246" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        actual_aln = aligner(self.pynast_test1_input_fp)</span></span>

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<pre style="margin: 0;">-<span id="LC247" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        expected_aln = {}</span></span>

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<pre style="margin: 0;">-<span id="LC248" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;">-<span id="LC249" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(actual_aln, expected_aln) </span></span>

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<pre style="margin: 0;">-<span id="LC250" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#    def test_call_pynast_alt_pairwise_method(self):</span></span>

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<pre style="margin: 0;">-<span id="LC251" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """PyNastAligner: alternate pairwise alignment method produces correct alignment</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC252" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """</span></span>

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<pre style="margin: 0;">-<span id="LC253" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        aligner = PyNastAligner({</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC254" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                'pairwise_alignment_method': 'muscle',</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC255" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                'template_filepath': self.pynast_test1_template_fp,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC256" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                'min_len': 15,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC257" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                })</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC258" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        actual_aln = aligner(self.pynast_test1_input_fp)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC259" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        expected_aln = self.pynast_test1_expected_aln</span></span>

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<pre style="margin: 0;">-<span id="LC260" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(actual_aln, expected_aln)</span></span>

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<pre style="margin: 0;">-<span id="LC261" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        </span></span>

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<pre style="margin: 0;">-<span id="LC262" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#    def test_call_pynast_test1_alt_min_len(self):</span></span>

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<pre style="margin: 0;">-<span id="LC263" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """PyNastAligner: returns no result when min_len too high</span></span>

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<pre style="margin: 0;">-<span id="LC264" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """</span></span>

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<pre style="margin: 0;">-<span id="LC265" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        aligner = PyNastAligner({</span></span>

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<pre style="margin: 0;">-<span id="LC266" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                'template_filepath': self.pynast_test1_template_fp,</span></span>

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<pre style="margin: 0;">-<span id="LC267" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                'min_len':1000})</span></span>

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<pre style="margin: 0;">-<span id="LC268" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        </span></span>

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<pre style="margin: 0;">-<span id="LC269" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        actual_aln = aligner(\</span></span>

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<pre style="margin: 0;">-<span id="LC270" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         self.pynast_test1_input_fp)</span></span>

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<pre style="margin: 0;">-<span id="LC271" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        expected_aln = {}</span></span>

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<pre style="margin: 0;">-<span id="LC272" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC273" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(actual_aln, expected_aln)</span></span>

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<pre style="margin: 0;">-<span id="LC274" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        </span></span>

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<pre style="margin: 0;">-<span id="LC275" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#    def test_call_pynast_test1_alt_min_pct(self):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC276" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """PyNastAligner: returns no result when min_pct too high</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC277" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC278" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        aligner = PyNastAligner({</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC279" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                'template_filepath': self.pynast_test1_template_fp,</span></span>

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<pre style="margin: 0;">-<span id="LC280" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                'min_len':15,</span></span>

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<pre style="margin: 0;">-<span id="LC281" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                'min_pct':100.0})</span></span>

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<pre style="margin: 0;">-<span id="LC282" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        </span></span>

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<pre style="margin: 0;">-<span id="LC283" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        actual_aln = aligner(self.pynast_test1_input_fp)</span></span>

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<pre style="margin: 0;">-<span id="LC284" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        expected_aln = {}</span></span>

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<pre style="margin: 0;">-<span id="LC285" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#</span></span>

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<pre style="margin: 0;">-<span id="LC286" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(actual_aln, expected_aln) </span></span>

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<pre style="margin: 0;">-<span id="LC287" class="line" lang="diff">         </span>

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<pre style="margin: 0;">-<span id="LC288" class="line" lang="diff">     def tearDown(self):</span>

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<pre style="margin: 0;">-<span id="LC289" class="line" lang="diff">         """</span>

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<pre style="margin: 0;">-<span id="LC290" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/test_assign_taxonomy.py</span></span>

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<pre style="margin: 0;">-<span id="LC291" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/test_assign_taxonomy.py</span></span>

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<pre style="margin: 0;">-<span id="LC292" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -134,53 +134,53 @@ class UclustConsensusTaxonAssignerTests(</span></span>

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<pre style="margin: 0;">-<span id="LC293" class="line" lang="diff">             if exists(d):</span>

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<pre style="margin: 0;">-<span id="LC294" class="line" lang="diff">                 rmtree(d)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC295" class="line" lang="diff">     </span>

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<pre style="margin: 0;">-<span id="LC296" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    def test_uclust_assigner_write_to_file(self):</span></span>

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<pre style="margin: 0;">-<span id="LC297" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """UclustConsensusTaxonAssigner returns without error, writing results</span></span>

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<pre style="margin: 0;">-<span id="LC298" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """</span></span>

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<pre style="margin: 0;">-<span id="LC299" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        params = {'id_to_taxonomy_fp':self.id_to_tax1_fp,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC300" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                  'reference_sequences_fp':self.refseqs1_fp}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC301" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC302" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        t = UclustConsensusTaxonAssigner(params)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC303" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        result = t(seq_path=self.inseqs1_fp,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC304" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                   result_path=self.output_txt_fp,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC305" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                   uc_path=self.output_uc_fp,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC306" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                   log_path=self.output_log_fp)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC307" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        del t</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC308" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # result files exist after the UclustConsensusTaxonAssigner</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC309" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # no longer exists</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC310" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertTrue(exists(self.output_txt_fp))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC311" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertTrue(exists(self.output_uc_fp))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC312" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertTrue(exists(self.output_log_fp))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC313" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC314" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # check that result has the expected lines</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC315" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        output_lines = list(open(self.output_txt_fp,'U'))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC316" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertTrue('q1\tA;F;G\t1.00\t1\n' in output_lines)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC317" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertTrue('q2\tA;H;I;J\t1.00\t1\n' in output_lines)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC318" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#    def test_uclust_assigner_write_to_file(self):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC319" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """UclustConsensusTaxonAssigner returns without error, writing results</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC320" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC321" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        params = {'id_to_taxonomy_fp':self.id_to_tax1_fp,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

322

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<pre style="margin: 0;">-<span id="LC322" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                  'reference_sequences_fp':self.refseqs1_fp}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC323" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC324" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        t = UclustConsensusTaxonAssigner(params)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC325" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        result = t(seq_path=self.inseqs1_fp,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC326" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                   result_path=self.output_txt_fp,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC327" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                   uc_path=self.output_uc_fp,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC328" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                   log_path=self.output_log_fp)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC329" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        del t</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC330" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # result files exist after the UclustConsensusTaxonAssigner</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC331" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # no longer exists</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC332" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertTrue(exists(self.output_txt_fp))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC333" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertTrue(exists(self.output_uc_fp))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC334" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertTrue(exists(self.output_log_fp))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC335" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC336" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # check that result has the expected lines</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC337" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        output_lines = list(open(self.output_txt_fp,'U'))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC338" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertTrue('q1\tA;F;G\t1.00\t1\n' in output_lines)</span></span>

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<pre style="margin: 0;">-<span id="LC339" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertTrue('q2\tA;H;I;J\t1.00\t1\n' in output_lines)</span></span>

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<pre style="margin: 0;">-<span id="LC340" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC341" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    def test_uclust_assigner(self):</span></span>

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<pre style="margin: 0;">-<span id="LC342" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """UclustConsensusTaxonAssigner returns without error, returning dict</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC343" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """</span></span>

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<pre style="margin: 0;">-<span id="LC344" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        params = {'id_to_taxonomy_fp':self.id_to_tax1_fp,</span></span>

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<pre style="margin: 0;">-<span id="LC345" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                  'reference_sequences_fp':self.refseqs1_fp}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC346" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </span></span>

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<pre style="margin: 0;">-<span id="LC347" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        t = UclustConsensusTaxonAssigner(params)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC348" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        result = t(seq_path=self.inseqs1_fp,</span></span>

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<pre style="margin: 0;">-<span id="LC349" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                   result_path=None,</span></span>

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<pre style="margin: 0;">-<span id="LC350" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                   uc_path=self.output_uc_fp,</span></span>

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<pre style="margin: 0;">-<span id="LC351" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                   log_path=self.output_log_fp)</span></span>

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<pre style="margin: 0;">-<span id="LC352" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                   </span></span>

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<pre style="margin: 0;">-<span id="LC353" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(result['q1'],(['A','F','G'],1.0,1))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC354" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(result['q2'],(['A','H','I','J'],1.0,1))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC355" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;">-<span id="LC356" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # no result paths provided</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC357" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        t = UclustConsensusTaxonAssigner(params)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC358" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        result = t(seq_path=self.inseqs1_fp,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC359" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                   result_path=None,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC360" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                   uc_path=None,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC361" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                   log_path=None)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC362" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                   </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC363" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(result['q1'],(['A','F','G'],1.0,1))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC364" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(result['q2'],(['A','H','I','J'],1.0,1))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC365" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#    def test_uclust_assigner(self):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC366" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """UclustConsensusTaxonAssigner returns without error, returning dict</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC367" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC368" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        params = {'id_to_taxonomy_fp':self.id_to_tax1_fp,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC369" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                  'reference_sequences_fp':self.refseqs1_fp}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC370" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC371" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        t = UclustConsensusTaxonAssigner(params)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC372" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        result = t(seq_path=self.inseqs1_fp,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC373" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                   result_path=None,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC374" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                   uc_path=self.output_uc_fp,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC375" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                   log_path=self.output_log_fp)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC376" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                   </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC377" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(result['q1'],(['A','F','G'],1.0,1))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC378" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(result['q2'],(['A','H','I','J'],1.0,1))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC379" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#</span></span>

</pre>

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380

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<pre style="margin: 0;">-<span id="LC380" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # no result paths provided</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC381" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        t = UclustConsensusTaxonAssigner(params)</span></span>

</pre>

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382

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<pre style="margin: 0;">-<span id="LC382" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        result = t(seq_path=self.inseqs1_fp,</span></span>

</pre>

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383

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<pre style="margin: 0;">-<span id="LC383" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                   result_path=None,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC384" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                   uc_path=None,</span></span>

</pre>

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385

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<pre style="margin: 0;">-<span id="LC385" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                   log_path=None)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC386" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                   </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC387" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(result['q1'],(['A','F','G'],1.0,1))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC388" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(result['q2'],(['A','H','I','J'],1.0,1))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC389" class="line" lang="diff">     </span>

</pre>

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<pre style="margin: 0;">-<span id="LC390" class="line" lang="diff">     def test_get_consensus_assignment(self):</span>

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<pre style="margin: 0;">-<span id="LC391" class="line" lang="diff">         """_get_consensus_assignment fuctions as expected """</span>

</pre>

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<pre style="margin: 0;">-<span id="LC392" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/test_pick_otus.py</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC393" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/test_pick_otus.py</span></span>

</pre>

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394

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<pre style="margin: 0;">-<span id="LC394" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2478,40 +2478,40 @@ class UclustOtuPickerTests(TestCase):</span></span>

</pre>

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395

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<pre style="margin: 0;">-<span id="LC395" class="line" lang="diff">         exp = {0:['s1','s4','s6','s2','s3','s5']}</span>

</pre>

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<pre style="margin: 0;">-<span id="LC396" class="line" lang="diff">         self.assertEqual(obs,exp)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC397" class="line" lang="diff">         </span>

</pre>

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<pre style="margin: 0;">-<span id="LC398" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    def test_abundance_sort(self):</span></span>

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<pre style="margin: 0;">-<span id="LC399" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """UclustOtuPicker: abundance sort functions as expected</span></span>

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<pre style="margin: 0;">-<span id="LC400" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """</span></span>

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<pre style="margin: 0;">-<span id="LC401" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        #enable abundance sorting with suppress sort = False (it gets</span></span>

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<pre style="margin: 0;">-<span id="LC402" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # set to True internally, otherwise uclust's length sort would</span></span>

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<pre style="margin: 0;">-<span id="LC403" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # override the abundance sorting)</span></span>

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<pre style="margin: 0;">-<span id="LC404" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        seqs = [('s1 comment1','ACCTTGTTACTTT'),  # three copies</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC405" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                ('s2 comment2','ACCTTGTTACTTTC'), # one copy</span></span>

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<pre style="margin: 0;">-<span id="LC406" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                ('s3 comment3','ACCTTGTTACTTTCC'),# two copies</span></span>

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<pre style="margin: 0;">-<span id="LC407" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                ('s4 comment4','ACCTTGTTACTTT'),</span></span>

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<pre style="margin: 0;">-<span id="LC408" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                ('s5 comment5','ACCTTGTTACTTTCC'),</span></span>

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<pre style="margin: 0;">-<span id="LC409" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                ('s6 comment6','ACCTTGTTACTTT')]</span></span>

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<pre style="margin: 0;">-<span id="LC410" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        seqs_fp = self.seqs_to_temp_fasta(seqs)</span></span>

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<pre style="margin: 0;">-<span id="LC411" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </span></span>

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<pre style="margin: 0;">-<span id="LC412" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # abundance sorting changes order </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC413" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        app = UclustOtuPicker(params={'Similarity':0.80,</span></span>

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<pre style="margin: 0;">-<span id="LC414" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                      'enable_rev_strand_matching':False,</span></span>

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<pre style="margin: 0;">-<span id="LC415" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                      'suppress_sort':False,</span></span>

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<pre style="margin: 0;">-<span id="LC416" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                      'presort_by_abundance':True,</span></span>

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<pre style="margin: 0;">-<span id="LC417" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                      'save_uc_files':False})</span></span>

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<pre style="margin: 0;">-<span id="LC418" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        obs = app(seqs_fp)</span></span>

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<pre style="margin: 0;">-<span id="LC419" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        exp = {0:['s1','s4','s6','s3','s5','s2']}</span></span>

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<pre style="margin: 0;">-<span id="LC420" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(obs,exp)</span></span>

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<pre style="margin: 0;">-<span id="LC421" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </span></span>

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<pre style="margin: 0;">-<span id="LC422" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # abundance sorting changes order -- same results with suppress_sort =</span></span>

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<pre style="margin: 0;">-<span id="LC423" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # True b/c (it gets set to True to when presorting by abundance)</span></span>

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<pre style="margin: 0;">-<span id="LC424" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        app = UclustOtuPicker(params={'Similarity':0.80,</span></span>

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<pre style="margin: 0;">-<span id="LC425" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                      'enable_rev_strand_matching':False,</span></span>

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<pre style="margin: 0;">-<span id="LC426" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                      'suppress_sort':True,</span></span>

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<pre style="margin: 0;">-<span id="LC427" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                      'presort_by_abundance':True,</span></span>

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<pre style="margin: 0;">-<span id="LC428" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                      'save_uc_files':False})</span></span>

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<pre style="margin: 0;">-<span id="LC429" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        obs = app(seqs_fp)</span></span>

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<pre style="margin: 0;">-<span id="LC430" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        exp = {0:['s1','s4','s6','s3','s5','s2']}</span></span>

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<pre style="margin: 0;">-<span id="LC431" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(obs,exp)</span></span>

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<pre style="margin: 0;">-<span id="LC432" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#    def test_abundance_sort(self):</span></span>

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<pre style="margin: 0;">-<span id="LC433" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """UclustOtuPicker: abundance sort functions as expected</span></span>

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<pre style="margin: 0;">-<span id="LC434" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """</span></span>

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<pre style="margin: 0;">-<span id="LC435" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        #enable abundance sorting with suppress sort = False (it gets</span></span>

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<pre style="margin: 0;">-<span id="LC436" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # set to True internally, otherwise uclust's length sort would</span></span>

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<pre style="margin: 0;">-<span id="LC437" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # override the abundance sorting)</span></span>

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<pre style="margin: 0;">-<span id="LC438" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        seqs = [('s1 comment1','ACCTTGTTACTTT'),  # three copies</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC439" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                ('s2 comment2','ACCTTGTTACTTTC'), # one copy</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC440" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                ('s3 comment3','ACCTTGTTACTTTCC'),# two copies</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC441" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                ('s4 comment4','ACCTTGTTACTTT'),</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC442" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                ('s5 comment5','ACCTTGTTACTTTCC'),</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC443" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                ('s6 comment6','ACCTTGTTACTTT')]</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC444" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        seqs_fp = self.seqs_to_temp_fasta(seqs)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC445" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC446" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # abundance sorting changes order </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC447" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        app = UclustOtuPicker(params={'Similarity':0.80,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC448" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                                      'enable_rev_strand_matching':False,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC449" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                                      'suppress_sort':False,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC450" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                                      'presort_by_abundance':True,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC451" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                                      'save_uc_files':False})</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC452" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        obs = app(seqs_fp)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC453" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        exp = {0:['s1','s4','s6','s3','s5','s2']}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC454" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(obs,exp)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC455" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC456" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # abundance sorting changes order -- same results with suppress_sort =</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC457" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # True b/c (it gets set to True to when presorting by abundance)</span></span>

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<pre style="margin: 0;">-<span id="LC458" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        app = UclustOtuPicker(params={'Similarity':0.80,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC459" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                                      'enable_rev_strand_matching':False,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC460" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                                      'suppress_sort':True,</span></span>

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<pre style="margin: 0;">-<span id="LC461" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                                      'presort_by_abundance':True,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC462" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                                      'save_uc_files':False})</span></span>

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<pre style="margin: 0;">-<span id="LC463" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        obs = app(seqs_fp)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC464" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        exp = {0:['s1','s4','s6','s3','s5','s2']}</span></span>

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<pre style="margin: 0;">-<span id="LC465" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(obs,exp)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC466" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC467" class="line" lang="diff">     def test_call_default_params(self):</span>

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<pre style="margin: 0;">-<span id="LC468" class="line" lang="diff">         """UclustOtuPicker.__call__ returns expected clusters default params"""</span>

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<pre style="margin: 0;">-<span id="LC469" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2542,35 +2542,35 @@ class UclustOtuPickerTests(TestCase):</span></span>

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<pre style="margin: 0;">-<span id="LC470" class="line" lang="diff">         self.assertEqual(obs_otu_ids, exp_otu_ids)</span>

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<pre style="margin: 0;">-<span id="LC471" class="line" lang="diff">         self.assertEqual(obs_clusters, exp_clusters)</span>

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<pre style="margin: 0;">-<span id="LC472" class="line" lang="diff">         </span>

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<pre style="margin: 0;">-<span id="LC473" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    def test_call_default_params_suppress_sort(self):</span></span>

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<pre style="margin: 0;">-<span id="LC474" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """UclustOtuPicker.__call__ returns expected clusters default params"""</span></span>

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<pre style="margin: 0;">-<span id="LC475" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;">-<span id="LC476" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # adapted from test_app.test_cd_hit.test_cdhit_clusters_from_seqs</span></span>

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<pre style="margin: 0;">-<span id="LC477" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </span></span>

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<pre style="margin: 0;">-<span id="LC478" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        exp_otu_ids = range(10)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC479" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        exp_clusters = [['uclust_test_seqs_0'],</span></span>

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<pre style="margin: 0;">-<span id="LC480" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_1'],</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC481" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_2'],</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC482" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_3'],</span></span>

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<pre style="margin: 0;">-<span id="LC483" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_4'],</span></span>

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<pre style="margin: 0;">-<span id="LC484" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_5'],</span></span>

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<pre style="margin: 0;">-<span id="LC485" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_6'],</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC486" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_7'],</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC487" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_8'],</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC488" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_9']]</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC489" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC490" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        app = UclustOtuPicker(params={'save_uc_files':False,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC491" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                      'suppress_sort':True})</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC492" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        obs = app(self.tmp_seq_filepath1)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC493" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        obs_otu_ids = obs.keys()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC494" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        obs_otu_ids.sort()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC495" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        obs_clusters = obs.values()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC496" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        obs_clusters.sort()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC497" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # The relation between otu ids and clusters is abitrary, and </span></span>

</pre>

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498

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<pre style="margin: 0;">-<span id="LC498" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # is not stable due to use of dicts when parsing clusters -- therefore</span></span>

</pre>

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499

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<pre style="margin: 0;">-<span id="LC499" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # just checks that we have the expected group of each</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

500

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<pre style="margin: 0;">-<span id="LC500" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(obs_otu_ids, exp_otu_ids)</span></span>

</pre>

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501

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<pre style="margin: 0;">-<span id="LC501" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(obs_clusters, exp_clusters)</span></span>

</pre>

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502

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<pre style="margin: 0;">-<span id="LC502" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#    def test_call_default_params_suppress_sort(self):</span></span>

</pre>

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503

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<pre style="margin: 0;">-<span id="LC503" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """UclustOtuPicker.__call__ returns expected clusters default params"""</span></span>

</pre>

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504

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<pre style="margin: 0;">-<span id="LC504" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

505

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<pre style="margin: 0;">-<span id="LC505" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # adapted from test_app.test_cd_hit.test_cdhit_clusters_from_seqs</span></span>

</pre>

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506

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<pre style="margin: 0;">-<span id="LC506" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        </span></span>

</pre>

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507

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<pre style="margin: 0;">-<span id="LC507" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        exp_otu_ids = range(10)</span></span>

</pre>

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508

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<pre style="margin: 0;">-<span id="LC508" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        exp_clusters = [['uclust_test_seqs_0'],</span></span>

</pre>

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509

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<pre style="margin: 0;">-<span id="LC509" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_1'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

510

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<pre style="margin: 0;">-<span id="LC510" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_2'],</span></span>

</pre>

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511

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<pre style="margin: 0;">-<span id="LC511" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_3'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

512

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<pre style="margin: 0;">-<span id="LC512" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_4'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

513

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC513" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_5'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

514

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC514" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_6'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

515

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC515" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_7'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

516

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<pre style="margin: 0;">-<span id="LC516" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_8'],</span></span>

</pre>

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517

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<pre style="margin: 0;">-<span id="LC517" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_9']]</span></span>

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518

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<pre style="margin: 0;">-<span id="LC518" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        </span></span>

</pre>

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519

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<pre style="margin: 0;">-<span id="LC519" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        app = UclustOtuPicker(params={'save_uc_files':False,</span></span>

</pre>

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520

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<pre style="margin: 0;">-<span id="LC520" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                                      'suppress_sort':True})</span></span>

</pre>

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521

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<pre style="margin: 0;">-<span id="LC521" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        obs = app(self.tmp_seq_filepath1)</span></span>

</pre>

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522

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<pre style="margin: 0;">-<span id="LC522" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        obs_otu_ids = obs.keys()</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC523" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        obs_otu_ids.sort()</span></span>

</pre>

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524

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<pre style="margin: 0;">-<span id="LC524" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        obs_clusters = obs.values()</span></span>

</pre>

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525

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<pre style="margin: 0;">-<span id="LC525" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        obs_clusters.sort()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

526

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<pre style="margin: 0;">-<span id="LC526" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # The relation between otu ids and clusters is abitrary, and </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

527

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<pre style="margin: 0;">-<span id="LC527" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # is not stable due to use of dicts when parsing clusters -- therefore</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC528" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # just checks that we have the expected group of each</span></span>

</pre>

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529

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<pre style="margin: 0;">-<span id="LC529" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(obs_otu_ids, exp_otu_ids)</span></span>

</pre>

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530

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<pre style="margin: 0;">-<span id="LC530" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(obs_clusters, exp_clusters)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC531" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC532" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC533" class="line" lang="diff">     def test_call_default_params_save_uc_file(self):</span>

</pre>

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<pre style="margin: 0;">-<span id="LC534" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2627,69 +2627,69 @@ class UclustOtuPickerTests(TestCase):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC535" class="line" lang="diff">         self.assertEqual(obs_otu_ids, exp_otu_ids)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC536" class="line" lang="diff">         self.assertEqual(obs_clusters, exp_clusters)</span>

</pre>

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537

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<pre style="margin: 0;">-<span id="LC537" class="line" lang="diff">         </span>

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<pre style="margin: 0;">-<span id="LC538" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    def test_call_alt_threshold(self):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

539

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<pre style="margin: 0;">-<span id="LC539" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """UclustOtuPicker.__call__ returns expected clusters with alt threshold</span></span>

</pre>

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540

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<pre style="margin: 0;">-<span id="LC540" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

541

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<pre style="margin: 0;">-<span id="LC541" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # adapted from test_app.test_cd_hit.test_cdhit_clusters_from_seqs</span></span>

</pre>

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542

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<pre style="margin: 0;">-<span id="LC542" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </span></span>

</pre>

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543

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<pre style="margin: 0;">-<span id="LC543" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        exp_otu_ids = range(9)</span></span>

</pre>

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544

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<pre style="margin: 0;">-<span id="LC544" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        exp_clusters = [['uclust_test_seqs_0'],</span></span>

</pre>

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545

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC545" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_1'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

546

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<pre style="margin: 0;">-<span id="LC546" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_2'],</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC547" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_3'],</span></span>

</pre>

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548

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<pre style="margin: 0;">-<span id="LC548" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_4'],</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC549" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_5'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC550" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_6','uclust_test_seqs_8'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

551

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC551" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_7'],</span></span>

</pre>

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552

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<pre style="margin: 0;">-<span id="LC552" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_9']]</span></span>

</pre>

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553

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<pre style="margin: 0;">-<span id="LC553" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

554

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC554" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        app = UclustOtuPicker(params={'Similarity':0.90,</span></span>

</pre>

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555

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<pre style="margin: 0;">-<span id="LC555" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                      'suppress_sort':False,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC556" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                      'presort_by_abundance':False,</span></span>

</pre>

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557

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC557" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                      'save_uc_files':False})</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC558" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        obs = app(self.tmp_seq_filepath1)</span></span>

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<pre style="margin: 0;">-<span id="LC559" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        obs_otu_ids = obs.keys()</span></span>

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<pre style="margin: 0;">-<span id="LC560" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        obs_otu_ids.sort()</span></span>

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<pre style="margin: 0;">-<span id="LC561" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        obs_clusters = obs.values()</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC562" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        obs_clusters.sort()</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC563" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # The relation between otu ids and clusters is abitrary, and </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC564" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # is not stable due to use of dicts when parsing clusters -- therefore</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC565" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # just checks that we have the expected group of each</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC566" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(obs_otu_ids, exp_otu_ids)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC567" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(obs_clusters, exp_clusters)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC568" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </span></span>

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<pre style="margin: 0;">-<span id="LC569" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </span></span>

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<pre style="margin: 0;">-<span id="LC570" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    def test_call_otu_id_prefix(self):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC571" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """UclustOtuPicker.__call__ returns expected clusters with alt threshold</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC572" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC573" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # adapted from test_app.test_cd_hit.test_cdhit_clusters_from_seqs</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC574" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </span></span>

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<pre style="margin: 0;">-<span id="LC575" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        exp_otu_ids = ['my_otu_%d' % i for i in range(9)]</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC576" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        exp_clusters = [['uclust_test_seqs_0'],</span></span>

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<pre style="margin: 0;">-<span id="LC577" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_1'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

578

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<pre style="margin: 0;">-<span id="LC578" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_2'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

579

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<pre style="margin: 0;">-<span id="LC579" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_3'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

580

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC580" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_4'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

581

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC581" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_5'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

582

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC582" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_6','uclust_test_seqs_8'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

583

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC583" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_7'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

584

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<pre style="margin: 0;">-<span id="LC584" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_9']]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

585

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<pre style="margin: 0;">-<span id="LC585" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

586

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<pre style="margin: 0;">-<span id="LC586" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        app = UclustOtuPicker(params={'Similarity':0.90,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC587" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                      'suppress_sort':False,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

588

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<pre style="margin: 0;">-<span id="LC588" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                      'presort_by_abundance':False,</span></span>

</pre>

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589

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<pre style="margin: 0;">-<span id="LC589" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                      'new_cluster_identifier':'my_otu_',</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC590" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                      'save_uc_files':False})</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

591

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<pre style="margin: 0;">-<span id="LC591" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        obs = app(self.tmp_seq_filepath1)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

592

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<pre style="margin: 0;">-<span id="LC592" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        obs_otu_ids = obs.keys()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

593

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<pre style="margin: 0;">-<span id="LC593" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        obs_otu_ids.sort()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC594" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        obs_clusters = obs.values()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC595" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        obs_clusters.sort()</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC596" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # The relation between otu ids and clusters is abitrary, and </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC597" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # is not stable due to use of dicts when parsing clusters -- therefore</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

598

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<pre style="margin: 0;">-<span id="LC598" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # just checks that we have the expected group of each</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

599

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<pre style="margin: 0;">-<span id="LC599" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(obs_otu_ids, exp_otu_ids)</span></span>

</pre>

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600

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<pre style="margin: 0;">-<span id="LC600" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(obs_clusters, exp_clusters)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

601

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<pre style="margin: 0;">-<span id="LC601" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#    def test_call_alt_threshold(self):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

602

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<pre style="margin: 0;">-<span id="LC602" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """UclustOtuPicker.__call__ returns expected clusters with alt threshold</span></span>

</pre>

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603

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<pre style="margin: 0;">-<span id="LC603" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

604

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<pre style="margin: 0;">-<span id="LC604" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # adapted from test_app.test_cd_hit.test_cdhit_clusters_from_seqs</span></span>

</pre>

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605

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<pre style="margin: 0;">-<span id="LC605" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

606

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<pre style="margin: 0;">-<span id="LC606" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        exp_otu_ids = range(9)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

607

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<pre style="margin: 0;">-<span id="LC607" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        exp_clusters = [['uclust_test_seqs_0'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

608

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<pre style="margin: 0;">-<span id="LC608" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_1'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

609

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC609" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_2'],</span></span>

</pre>

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610

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC610" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_3'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

611

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC611" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_4'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

612

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC612" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_5'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

613

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC613" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_6','uclust_test_seqs_8'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

614

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC614" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_7'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

615

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC615" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_9']]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

616

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<pre style="margin: 0;">-<span id="LC616" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

617

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC617" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        app = UclustOtuPicker(params={'Similarity':0.90,</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

618

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC618" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                                      'suppress_sort':False,</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

619

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC619" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                                      'presort_by_abundance':False,</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

620

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC620" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                                      'save_uc_files':False})</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

621

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC621" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        obs = app(self.tmp_seq_filepath1)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

622

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC622" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        obs_otu_ids = obs.keys()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

623

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC623" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        obs_otu_ids.sort()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

624

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC624" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        obs_clusters = obs.values()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

625

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC625" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        obs_clusters.sort()</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

626

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC626" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # The relation between otu ids and clusters is abitrary, and </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

627

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC627" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # is not stable due to use of dicts when parsing clusters -- therefore</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

628

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC628" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # just checks that we have the expected group of each</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

629

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC629" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(obs_otu_ids, exp_otu_ids)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

630

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC630" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(obs_clusters, exp_clusters)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

631

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC631" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        </span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

632

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC632" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        </span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

633

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC633" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#    def test_call_otu_id_prefix(self):</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

634

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC634" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """UclustOtuPicker.__call__ returns expected clusters with alt threshold</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

635

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC635" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

636

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC636" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # adapted from test_app.test_cd_hit.test_cdhit_clusters_from_seqs</span></span>

</pre>

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637

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC637" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

638

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC638" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        exp_otu_ids = ['my_otu_%d' % i for i in range(9)]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

639

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC639" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        exp_clusters = [['uclust_test_seqs_0'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

640

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC640" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_1'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

641

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC641" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_2'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

642

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC642" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_3'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

643

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC643" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_4'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

644

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC644" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_5'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

645

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC645" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_6','uclust_test_seqs_8'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

646

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC646" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_7'],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

647

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC647" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_9']]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

648

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC648" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

649

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC649" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        app = UclustOtuPicker(params={'Similarity':0.90,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

650

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC650" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                                      'suppress_sort':False,</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

651

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC651" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                                      'presort_by_abundance':False,</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

652

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC652" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                                      'new_cluster_identifier':'my_otu_',</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

653

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC653" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                                      'save_uc_files':False})</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

654

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC654" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        obs = app(self.tmp_seq_filepath1)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

655

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC655" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        obs_otu_ids = obs.keys()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC656" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        obs_otu_ids.sort()</span></span>

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<pre style="margin: 0;">-<span id="LC657" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        obs_clusters = obs.values()</span></span>

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<pre style="margin: 0;">-<span id="LC658" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        obs_clusters.sort()</span></span>

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<pre style="margin: 0;">-<span id="LC659" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # The relation between otu ids and clusters is abitrary, and </span></span>

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<pre style="margin: 0;">-<span id="LC660" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # is not stable due to use of dicts when parsing clusters -- therefore</span></span>

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<pre style="margin: 0;">-<span id="LC661" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # just checks that we have the expected group of each</span></span>

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<pre style="margin: 0;">-<span id="LC662" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(obs_otu_ids, exp_otu_ids)</span></span>

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<pre style="margin: 0;">-<span id="LC663" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(obs_clusters, exp_clusters)</span></span>

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<pre style="margin: 0;">-<span id="LC664" class="line" lang="diff">         </span>

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<pre style="margin: 0;">-<span id="LC665" class="line" lang="diff">     def test_call_suppress_sort(self):</span>

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<pre style="margin: 0;">-<span id="LC666" class="line" lang="diff">         """UclustOtuPicker.__call__ handles suppress sort</span>

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<pre style="margin: 0;">-<span id="LC667" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2716,131 +2716,131 @@ class UclustOtuPickerTests(TestCase):</span></span>

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<pre style="margin: 0;">-<span id="LC668" class="line" lang="diff">         self.assertEqual(obs_otu_ids, exp_otu_ids)</span>

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<pre style="margin: 0;">-<span id="LC669" class="line" lang="diff">         self.assertEqual(obs_clusters, exp_clusters)</span>

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<pre style="margin: 0;">-<span id="LC670" class="line" lang="diff">         </span>

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<pre style="margin: 0;">-<span id="LC671" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    def test_call_rev_matching(self):</span></span>

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<pre style="margin: 0;">-<span id="LC672" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """UclustOtuPicker.__call__ handles reverse strand matching</span></span>

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<pre style="margin: 0;">-<span id="LC673" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """</span></span>

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<pre style="margin: 0;">-<span id="LC674" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        exp_otu_ids = range(2)</span></span>

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<pre style="margin: 0;">-<span id="LC675" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        exp_clusters = [['uclust_test_seqs_0'],['uclust_test_seqs_0_rc']]</span></span>

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<pre style="margin: 0;">-<span id="LC676" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        app = UclustOtuPicker(params={'Similarity':0.90,</span></span>

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<pre style="margin: 0;">-<span id="LC677" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                      'enable_rev_strand_matching':False,</span></span>

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<pre style="margin: 0;">-<span id="LC678" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                      'suppress_sort':False,</span></span>

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<pre style="margin: 0;">-<span id="LC679" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                      'presort_by_abundance':False,</span></span>

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<pre style="margin: 0;">-<span id="LC680" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                      'save_uc_files':False})</span></span>

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<pre style="margin: 0;">-<span id="LC681" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        obs = app(self.tmp_seq_filepath3)</span></span>

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<pre style="margin: 0;">-<span id="LC682" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        obs_otu_ids = obs.keys()</span></span>

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<pre style="margin: 0;">-<span id="LC683" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        obs_otu_ids.sort()</span></span>

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<pre style="margin: 0;">-<span id="LC684" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        obs_clusters = obs.values()</span></span>

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<pre style="margin: 0;">-<span id="LC685" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        obs_clusters.sort()</span></span>

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<pre style="margin: 0;">-<span id="LC686" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # The relation between otu ids and clusters is abitrary, and </span></span>

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<pre style="margin: 0;">-<span id="LC687" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # is not stable due to use of dicts when parsing clusters -- therefore</span></span>

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<pre style="margin: 0;">-<span id="LC688" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # just checks that we have the expected group of each</span></span>

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<pre style="margin: 0;">-<span id="LC689" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(obs_otu_ids, exp_otu_ids)</span></span>

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<pre style="margin: 0;">-<span id="LC690" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(obs_clusters, exp_clusters)</span></span>

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<pre style="margin: 0;">-<span id="LC691" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </span></span>

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<pre style="margin: 0;">-<span id="LC692" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        exp = {0: ['uclust_test_seqs_0','uclust_test_seqs_0_rc']}</span></span>

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<pre style="margin: 0;">-<span id="LC693" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        app = UclustOtuPicker(params={'Similarity':0.90,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC694" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                      'enable_rev_strand_matching':True,</span></span>

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<pre style="margin: 0;">-<span id="LC695" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                      'suppress_sort':False,</span></span>

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<pre style="margin: 0;">-<span id="LC696" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                      'presort_by_abundance':False,</span></span>

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<pre style="margin: 0;">-<span id="LC697" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                      'save_uc_files':False})</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC698" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        obs = app(self.tmp_seq_filepath3)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC699" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(obs, exp)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC700" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </span></span>

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<pre style="margin: 0;">-<span id="LC701" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    def test_call_output_to_file(self):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC702" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """UclustHitOtuPicker.__call__ output to file functions as expected</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC703" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC704" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC705" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        tmp_result_filepath = get_tmp_filename(\</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC706" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         prefix='UclustOtuPickerTest.test_call_output_to_file_',\</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC707" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         suffix='.txt')</span></span>

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<pre style="margin: 0;">-<span id="LC708" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC709" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        app = UclustOtuPicker(params={'Similarity':0.90,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC710" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                      'suppress_sort':False,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC711" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                      'presort_by_abundance':False,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC712" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                      'save_uc_files':False})</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC713" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        obs = app(self.tmp_seq_filepath1,result_path=tmp_result_filepath)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC714" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC715" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        result_file = open(tmp_result_filepath)</span></span>

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716

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC716" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        result_file_str = result_file.read()</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

717

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC717" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        result_file.close()</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

718

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC718" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # remove the result file before running the test, so in </span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

719

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC719" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # case it fails the temp file is still cleaned up</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

720

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC720" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        remove(tmp_result_filepath)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

721

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC721" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

722

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC722" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        exp_otu_ids = map(str,range(9))</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

723

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC723" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        exp_clusters = [['uclust_test_seqs_0'],</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

724

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC724" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_1'],</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

725

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC725" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_2'],</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

726

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC726" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_3'],</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

727

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC727" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_4'],</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

728

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC728" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_5'],</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

729

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC729" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_6','uclust_test_seqs_8'],</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

730

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC730" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_7'],</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

731

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC731" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        ['uclust_test_seqs_9']]</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

732

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC732" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        obs_otu_ids = []</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

733

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC733" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        obs_clusters = []</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

734

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC734" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        for line in result_file_str.split('\n'):</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

735

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC735" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            if line:</span></span>

</pre>

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736

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<pre style="margin: 0;">-<span id="LC736" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                fields = line.split('\t')</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

737

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC737" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                obs_otu_ids.append(fields[0])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

738

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC738" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                obs_clusters.append(fields[1:])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

739

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC739" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        obs_otu_ids.sort()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

740

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC740" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        obs_clusters.sort()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

741

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC741" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # The relation between otu ids and clusters is abitrary, and </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

742

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC742" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # is not stable due to use of dicts when parsing clusters -- therefore</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

743

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC743" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # just checks that we have the expected group of each</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

744

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC744" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(obs_otu_ids, exp_otu_ids)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

745

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<pre style="margin: 0;">-<span id="LC745" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(obs_clusters, exp_clusters)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

746

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC746" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # confirm that nothing is returned when result_path is specified</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

747

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC747" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqual(obs,None)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

748

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC748" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

749

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC749" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    def test_call_log_file(self):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

750

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC750" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """UclustOtuPicker.__call__ writes log when expected</span></span>

</pre>

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751

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC751" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        """</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

752

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC752" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

753

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<pre style="margin: 0;">-<span id="LC753" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        tmp_log_filepath = get_tmp_filename(\</span></span>

</pre>

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754

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<pre style="margin: 0;">-<span id="LC754" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         prefix='UclustOtuPickerTest.test_call_output_to_file_l_',\</span></span>

</pre>

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755

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<pre style="margin: 0;">-<span id="LC755" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         suffix='.txt')</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC756" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        tmp_result_filepath = get_tmp_filename(\</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC757" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         prefix='UclustOtuPickerTest.test_call_output_to_file_r_',\</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC758" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         suffix='.txt')</span></span>

</pre>

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759

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<pre style="margin: 0;">-<span id="LC759" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

760

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<pre style="margin: 0;">-<span id="LC760" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        app = UclustOtuPicker(params={'Similarity':0.99,</span></span>

</pre>

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761

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<pre style="margin: 0;">-<span id="LC761" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                      'save_uc_files':False})</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC762" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        obs = app(self.tmp_seq_filepath1,\</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC763" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         result_path=tmp_result_filepath,log_path=tmp_log_filepath)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

764

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<pre style="margin: 0;">-<span id="LC764" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC765" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        log_file = open(tmp_log_filepath)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

766

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<pre style="margin: 0;">-<span id="LC766" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        log_file_str = log_file.read()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

767

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<pre style="margin: 0;">-<span id="LC767" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        log_file.close()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

768

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC768" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # remove the temp files before running the test, so in </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

769

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC769" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # case it fails the temp file is still cleaned up</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC770" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        remove(tmp_log_filepath)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC771" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        remove(tmp_result_filepath)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

772

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<pre style="margin: 0;">-<span id="LC772" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC773" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        log_file_99_exp = ["UclustOtuPicker parameters:",</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC774" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         "Similarity:0.99","Application:uclust",</span></span>

</pre>

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775

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC775" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         "enable_rev_strand_matching:False",</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

776

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC776" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         "suppress_sort:True",</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

777

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC777" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         "optimal:False",</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

778

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC778" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         'max_accepts:20',</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

779

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC779" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         'max_rejects:500',</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

780

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC780" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         'stepwords:20',</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

781

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC781" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         'word_length:12',</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

782

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC782" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         "exact:False",</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

783

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC783" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         "Num OTUs:10",</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

784

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC784" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         "new_cluster_identifier:None",</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

785

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC785" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         "presort_by_abundance:True",</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

786

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC786" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         "stable_sort:True",</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

787

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC787" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         "output_dir:.",</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

788

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC788" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         "save_uc_files:False",</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

789

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC789" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         "prefilter_identical_sequences:True",</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

790

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC790" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-         "Result path: %s" % tmp_result_filepath]</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

791

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC791" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # compare data in log file to fake expected log file</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

792

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC792" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # NOTE: Since app.params is a dict, the order of lines is not</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

793

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC793" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # guaranteed, so testing is performed to make sure that </span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

794

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC794" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        # the equal unordered lists of lines is present in actual and expected</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

795

</td>

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<pre style="margin: 0;">-<span id="LC795" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        self.assertEqualItems(log_file_str.split('\n'), log_file_99_exp)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

796

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC796" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#    def test_call_rev_matching(self):</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

797

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC797" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """UclustOtuPicker.__call__ handles reverse strand matching</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

798

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC798" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

799

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC799" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        exp_otu_ids = range(2)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

800

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC800" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        exp_clusters = [['uclust_test_seqs_0'],['uclust_test_seqs_0_rc']]</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

801

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC801" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        app = UclustOtuPicker(params={'Similarity':0.90,</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

802

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC802" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                                      'enable_rev_strand_matching':False,</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

803

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC803" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                                      'suppress_sort':False,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

804

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC804" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                                      'presort_by_abundance':False,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

805

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC805" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                                      'save_uc_files':False})</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

806

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC806" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        obs = app(self.tmp_seq_filepath3)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

807

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC807" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        obs_otu_ids = obs.keys()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

808

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC808" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        obs_otu_ids.sort()</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

809

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC809" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        obs_clusters = obs.values()</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

810

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC810" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        obs_clusters.sort()</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

811

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC811" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # The relation between otu ids and clusters is abitrary, and </span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

812

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC812" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # is not stable due to use of dicts when parsing clusters -- therefore</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

813

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC813" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # just checks that we have the expected group of each</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

814

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC814" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(obs_otu_ids, exp_otu_ids)</span></span>

</pre>

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</tr>

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<td class="diff-line-num old old_line" data-linenumber="815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

815

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC815" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(obs_clusters, exp_clusters)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

816

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC816" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        </span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

817

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC817" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        exp = {0: ['uclust_test_seqs_0','uclust_test_seqs_0_rc']}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

818

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC818" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        app = UclustOtuPicker(params={'Similarity':0.90,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

819

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC819" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                                      'enable_rev_strand_matching':True,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

820

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC820" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                                      'suppress_sort':False,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

821

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC821" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                                      'presort_by_abundance':False,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

822

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC822" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                                      'save_uc_files':False})</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

823

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC823" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        obs = app(self.tmp_seq_filepath3)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

824

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC824" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(obs, exp)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

825

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC825" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        </span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

826

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC826" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#    def test_call_output_to_file(self):</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

827

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC827" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """UclustHitOtuPicker.__call__ output to file functions as expected</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

828

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC828" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

829

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC829" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        </span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

830

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC830" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        tmp_result_filepath = get_tmp_filename(\</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

831

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC831" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         prefix='UclustOtuPickerTest.test_call_output_to_file_',\</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

832

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC832" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         suffix='.txt')</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

833

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC833" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        </span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

834

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC834" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        app = UclustOtuPicker(params={'Similarity':0.90,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

835

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC835" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                                      'suppress_sort':False,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

836

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC836" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                                      'presort_by_abundance':False,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

837

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC837" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                                      'save_uc_files':False})</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

838

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC838" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        obs = app(self.tmp_seq_filepath1,result_path=tmp_result_filepath)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

839

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC839" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        </span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

840

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC840" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        result_file = open(tmp_result_filepath)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

841

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC841" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        result_file_str = result_file.read()</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

842

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC842" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        result_file.close()</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

843

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC843" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # remove the result file before running the test, so in </span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

844

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC844" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # case it fails the temp file is still cleaned up</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

845

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC845" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        remove(tmp_result_filepath)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

846

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC846" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

847

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC847" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        exp_otu_ids = map(str,range(9))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

848

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC848" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        exp_clusters = [['uclust_test_seqs_0'],</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

849

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC849" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_1'],</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

850

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC850" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_2'],</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

851

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC851" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_3'],</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

852

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC852" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_4'],</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

853

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC853" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_5'],</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

854

</td>

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<pre style="margin: 0;">-<span id="LC854" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_6','uclust_test_seqs_8'],</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

855

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC855" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_7'],</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

856

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC856" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                        ['uclust_test_seqs_9']]</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

857

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC857" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        obs_otu_ids = []</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

858

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC858" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        obs_clusters = []</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

859

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC859" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        for line in result_file_str.split('\n'):</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

860

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC860" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#            if line:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

861

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC861" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                fields = line.split('\t')</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

862

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC862" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                obs_otu_ids.append(fields[0])</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

863

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC863" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                obs_clusters.append(fields[1:])</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

864

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC864" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        obs_otu_ids.sort()</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

865

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC865" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        obs_clusters.sort()</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

866

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC866" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # The relation between otu ids and clusters is abitrary, and </span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

867

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC867" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # is not stable due to use of dicts when parsing clusters -- therefore</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

868

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC868" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # just checks that we have the expected group of each</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

869

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC869" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(obs_otu_ids, exp_otu_ids)</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

870

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC870" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(obs_clusters, exp_clusters)</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

871

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC871" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # confirm that nothing is returned when result_path is specified</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

872

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC872" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqual(obs,None)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

873

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC873" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        </span></span>

</pre>

</td>

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874

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<pre style="margin: 0;">-<span id="LC874" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#    def test_call_log_file(self):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

875

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC875" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """UclustOtuPicker.__call__ writes log when expected</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

876

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<pre style="margin: 0;">-<span id="LC876" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        """</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

877

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<pre style="margin: 0;">-<span id="LC877" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        </span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

878

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC878" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        tmp_log_filepath = get_tmp_filename(\</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

879

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC879" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         prefix='UclustOtuPickerTest.test_call_output_to_file_l_',\</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

880

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<pre style="margin: 0;">-<span id="LC880" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         suffix='.txt')</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

881

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC881" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        tmp_result_filepath = get_tmp_filename(\</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

882

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC882" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         prefix='UclustOtuPickerTest.test_call_output_to_file_r_',\</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

883

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<pre style="margin: 0;">-<span id="LC883" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         suffix='.txt')</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

884

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<pre style="margin: 0;">-<span id="LC884" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

885

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC885" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        app = UclustOtuPicker(params={'Similarity':0.99,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

886

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC886" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#                                      'save_uc_files':False})</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

887

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC887" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        obs = app(self.tmp_seq_filepath1,\</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

888

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC888" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         result_path=tmp_result_filepath,log_path=tmp_log_filepath)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

889

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC889" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        </span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

890

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC890" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        log_file = open(tmp_log_filepath)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

891

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC891" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        log_file_str = log_file.read()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

892

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC892" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        log_file.close()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

893

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC893" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # remove the temp files before running the test, so in </span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

894

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC894" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # case it fails the temp file is still cleaned up</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

895

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC895" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        remove(tmp_log_filepath)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

896

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC896" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        remove(tmp_result_filepath)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

897

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC897" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        </span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

898

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC898" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        log_file_99_exp = ["UclustOtuPicker parameters:",</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

899

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC899" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         "Similarity:0.99","Application:uclust",</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

900

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC900" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         "enable_rev_strand_matching:False",</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

901

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC901" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         "suppress_sort:True",</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

902

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC902" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         "optimal:False",</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

903

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC903" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         'max_accepts:20',</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

904

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC904" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         'max_rejects:500',</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

905

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC905" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         'stepwords:20',</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

906

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC906" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         'word_length:12',</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

907

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC907" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         "exact:False",</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

908

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC908" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         "Num OTUs:10",</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

909

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC909" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         "new_cluster_identifier:None",</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

910

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC910" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         "presort_by_abundance:True",</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

911

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC911" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         "stable_sort:True",</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

912

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC912" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         "output_dir:.",</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

913

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC913" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         "save_uc_files:False",</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

914

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC914" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         "prefilter_identical_sequences:True",</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

915

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC915" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#         "Result path: %s" % tmp_result_filepath]</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

916

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC916" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # compare data in log file to fake expected log file</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

917

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC917" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # NOTE: Since app.params is a dict, the order of lines is not</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

918

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC918" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # guaranteed, so testing is performed to make sure that </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

919

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC919" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        # the equal unordered lists of lines is present in actual and expected</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

920

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC920" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        self.assertEqualItems(log_file_str.split('\n'), log_file_99_exp)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

921

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC921" class="line" lang="diff">         </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

922

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC922" class="line" lang="diff">         </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

923

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<pre style="margin: 0;">-<span id="LC923" class="line" lang="diff">     def test_map_filtered_clusters_to_full_clusters(self):</span></pre>

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<br>

</li>

<li id="f7bf9619ee40c3284ec8034c645669b430e1738e">

<a href="https://salsa.debian.org/med-team/qiime/compare/c4c1063f9ef9a29ea1c74344ab0d9e8a9e1cf98d...7d6b53826988db773b76d73d5606098497efba53#f7bf9619ee40c3284ec8034c645669b430e1738e"><strong>debian/patches/fix_binary_helper_location.patch</strong>

deleted

</a>

<hr>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Last-Update: Mon, 06 Aug 2012 09:22:42 +0200</span>

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2

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Description: Fix path to binary helper for denoiser</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/qiime/denoiser/utils.py</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/qiime/denoiser/utils.py</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

6

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -60,8 +60,9 @@ def get_denoiser_data_dir():</span></span>

</pre>

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7

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> def get_flowgram_ali_exe():</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

8

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff">     """Return the path to the flowgram alignment prog</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff">     """</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

10

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    fp = get_qiime_scripts_dir() + "/FlowgramAli_4frame"</span></span>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    return fp</span></span>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #fp = get_qiime_scripts_dir() + "/FlowgramAli_4frame"</span></span>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #return fp</span></span>

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14

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    return "/usr/lib/qiime/support_files/denoiser/bin/FlowgramAli_4frame"</span></span>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> def check_flowgram_ali_exe():</span>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff">    """Check if we have a working FlowgramAligner"""</span></pre>

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<br>

</li>

<li id="3a7264d1c1519aba3fee5249c0aa903b55b94327">

<a href="https://salsa.debian.org/med-team/qiime/compare/c4c1063f9ef9a29ea1c74344ab0d9e8a9e1cf98d...7d6b53826988db773b76d73d5606098497efba53#3a7264d1c1519aba3fee5249c0aa903b55b94327"><strong>debian/patches/fix_path_for_support_files.patch</strong>

deleted

</a>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Author: Tim Booth <tbooth@ceh.ac.uk></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Last-Update: Mon, 10 Mar 2014 14:20:08 +0000</span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">Description: This may be a much simpler fix than patching every single mention</span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> of support_files, but I'm not sure what else this function is used</span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"> to find?</span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/qiime/util.py</span></span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/qiime/util.py</span></span>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -268,14 +268,10 @@</span></span>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> def get_qiime_project_dir():</span>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff">     """ Returns the top-level QIIME directory</span>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    """</span></span>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    # Get the full path of util.py</span></span>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    current_file_path = abspath(__file__)</span></span>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    # Get the directory containing util.py</span></span>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    current_dir_path = dirname(current_file_path)</span></span>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    # Return the directory containing the directory containing util.py</span></span>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    return dirname(current_dir_path)</span></span>

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    In Debian we know this is always /usr/lib/[qiime]</span></span>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    """</span></span>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    return "/usr/lib"</span></span>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> def get_qiime_scripts_dir():</span>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff">     """Return the directory containing QIIME scripts.</span></pre>

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<br>

</li>

<li id="2a358f77380ac0c6a1776bad65402a0aa7e75ad6">

<a href="https://salsa.debian.org/med-team/qiime/compare/c4c1063f9ef9a29ea1c74344ab0d9e8a9e1cf98d...7d6b53826988db773b76d73d5606098497efba53#2a358f77380ac0c6a1776bad65402a0aa7e75ad6"><strong>debian/patches/fix_script_usage_tests.patch</strong>

deleted

</a>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Author: Tim Booth <tbooth@ceh.ac.uk></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Last-Update: Mon, 10 Mar 2014 14:20:08 +0000</span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">Description: Enhancing unit tests</span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"></span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/qiime/test.py</span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/qiime/test.py</span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -15,7 +15,7 @@</span></span>

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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

8

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> from os import chdir, getcwd</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> from shutil import copytree, rmtree</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

10

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> from glob import glob</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

11

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from site import addsitedir</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import sys</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> from tempfile import NamedTemporaryFile</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> from traceback import format_exc</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

15

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> from skbio.util import remove_files</span>

</pre>

</td>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

16

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -806,7 +806,9 @@</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

17

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff">         self._log('Scripts to test:\n %s' % ' '.join(scripts))</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

18

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff">         self._log('')</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

19

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> </span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

20

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        addsitedir(scripts_dir)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

21

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        #addsitedir(scripts_dir)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

22

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        # This is not strong enough.  The scripts-dir must be the first thing in the PATH</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

23

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        sys.path = [ scripts_dir ] + sys.path</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

24

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

25

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff">         for script_name in scripts:</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

26

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff">             self.total_scripts += 1</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

27

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/all_tests.py</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

28

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/all_tests.py</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -96,6 +96,9 @@</span></span>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff">                     bad_tests.append(unittest_name)</span>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff">     qiime_test_data_dir = join(get_qiime_project_dir(), 'qiime_test_data')</span>

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #Allow tests to be run without installing test data to system dir</span></span>

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    if exists("../qiime_test_data"):</span></span>

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ qiime_test_data_dir = "../qiime_test_data"</span></span>

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff">     qiime_test_data_dir_exists = exists(qiime_test_data_dir)</span>

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff">     if not opts.suppress_script_usage_tests and qiime_test_data_dir_exists:</span>

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff">         if opts.script_usage_tests is not None:</span></pre>

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<br>

</li>

<li id="0093db8a86c199cf12ec62807b212d92dfdedf55">

<a href="https://salsa.debian.org/med-team/qiime/compare/c4c1063f9ef9a29ea1c74344ab0d9e8a9e1cf98d...7d6b53826988db773b76d73d5606098497efba53#0093db8a86c199cf12ec62807b212d92dfdedf55"><strong>debian/patches/make_qiime_accept_new_rdp_classifier.patch</strong>

deleted

</a>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Author: Tim Booth <tbooth@ceh.ac.uk></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Last-Update: Tue, 11 Jun 2013 16:49:19 +0100</span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">Description: This patch twists QIIME's arm to accept running a newer version</span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> of the RDP classifier by setting RDP_JAR_VERSION_OK, which is done</span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"> by the QIIME wrapper.</span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> This is a nasty hack and hopefully the patch can be dropped for QIIME 1.6</span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"></span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/qiime/assign_taxonomy.py</span></span>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/qiime/assign_taxonomy.py</span></span>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -54,14 +54,19 @@</span></span>

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11

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff">             "http://qiime.org/install/install.html#rdp-install"</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff">         )</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    rdp_jarname = os.path.basename(rdp_jarpath)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

15

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    version_match = re.search("\d\.\d", rdp_jarname)</span></span>

</pre>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

16

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    if version_match is None:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

17

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        raise RuntimeError(</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

18

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            "Unable to detect RDP Classifier version in file %s" % rdp_jarname</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

19

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        )</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

20

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #Patch for Bio-Linux/Debian.  Allow us to reassure QIIME about the version</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

21

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #of RDP Classifier using an environment variable.</span></span>

</pre>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

22

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    if os.getenv('RDP_JAR_VERSION_OK') is not None :</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

23

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ version = os.getenv('RDP_JAR_VERSION_OK')</span></span>

</pre>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

24

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    else :</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

25

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rdp_jarname = os.path.basename(rdp_jarpath)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

26

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ version_match = re.search("\d\.\d", rdp_jarname)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

27

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if version_match is None:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

28

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+     raise RuntimeError(</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

29

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+         "Unable to detect RDP Classifier version in file %s" % rdp_jarname</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

30

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+         )</span></span>

</pre>

</td>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        version = float(version_match.group())</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    version = float(version_match.group())</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff">     if version < 2.1:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff">         raise RuntimeError(</span>

</pre>

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff">             "RDP Classifier does not look like version 2.2 or greater."</span>

</pre>

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/assign_taxonomy.py</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/assign_taxonomy.py</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -366,6 +366,11 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff">             'training_data_properties_fp'] = opts.training_data_properties_fp</span>

</pre>

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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff">         params['max_memory'] = "%sM" % opts.rdp_max_memory</span>

</pre>

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #Record actual RDP version.  This shouldn't fail as it was called once</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #already.</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ params['real_rdp_version'] = str(validate_rdp_version())</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff">     elif assignment_method == 'rtax':</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff">         params['id_to_taxonomy_fp'] = opts.id_to_taxonomy_fp</span>

</pre>

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff">         params['reference_sequences_fp'] = opts.reference_seqs_fp</span></pre>

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<br>

</li>

<li id="c45be83049c2ab6730e6e2647af109e8ab11c68b">

<a href="https://salsa.debian.org/med-team/qiime/compare/c4c1063f9ef9a29ea1c74344ab0d9e8a9e1cf98d...7d6b53826988db773b76d73d5606098497efba53#c45be83049c2ab6730e6e2647af109e8ab11c68b"><strong>debian/patches/prevent_download_on_builds.patch</strong>

deleted

</a>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Author: Tim Booth <tbooth@ceh.ac.uk>, Andreas Tille <tille@debian.org></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Last-Update: Wed, 22 Jan 2014 08:51:45 +0100</span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">Description: Do not try to download uclust at build time</span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"></span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/setup.py</span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/setup.py</span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -358,9 +358,8 @@</span></span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff">         chdir(cwd)</span>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# don't build any of the non-Python dependencies if the following modes are</span></span>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# invoked</span></span>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if all([e not in sys.argv for e in 'egg_info', 'sdist', 'register']):</span></span>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# don't build any of the non-Python dependencies - let DPKG handle it</span></span>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if False:</span></span>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff">     catch_install_errors(build_denoiser, 'denoiser')</span>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff">     catch_install_errors(download_UCLUST, 'UCLUST')</span>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff">     catch_install_errors(build_FastTree, 'FastTree')</span></pre>

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</li>

<li id="1036dc871db02015d583917a3b434053900dfdab">

<a href="https://salsa.debian.org/med-team/qiime/compare/c4c1063f9ef9a29ea1c74344ab0d9e8a9e1cf98d...7d6b53826988db773b76d73d5606098497efba53#1036dc871db02015d583917a3b434053900dfdab"><strong>debian/patches/prevent_google_addsense.patch</strong>

deleted

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Last-Update: Sat, 21 Dec 2013 08:50:20 +0100</span>

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<td class="diff-line-num old old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">Description: Remove Google Addsense from user documentation</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> to save user privacy</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

6

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

7

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/doc/_templates/layout.html</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

8

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/doc/_templates/layout.html</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2,8 +2,6 @@</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

10

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> </span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

11

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> {% block extrahead %}</span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> <meta http-equiv="Content-Style-Type" content="text/css" /></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-<script type="text/javascript" src="http://www.google.com/jsapi?key=ABQIAAAAbW_pA971hrPgosv-Msv7hRRE2viNBUPuU405tK6p2cguOFmlFBQSwZMG6_q_v6Z42nkdo9ejT1aHmA"></script></span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-<script type="text/javascript" src="{{ pathto("_static/google_feed.js",1)}}"></script></span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

15

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> {% endblock %}</span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

16

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

17

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> {% block relbar1 %}</span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

18

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -47,10 +45,6 @@</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

19

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> <br /></div></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

20

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> {{ super() }}</span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

21

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> <script type="text/javascript"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

22

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

23

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));</span></span>

</pre>

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24

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</script></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

25

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-<script type="text/javascript"></span></span>

</pre>

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26

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> try {</span>

</pre>

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27

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"> var pageTracker = _gat._getTracker("UA-6636235-4");</span>

</pre>

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28

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"> pageTracker._trackPageview();</span></pre>

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<br>

</li>

<li id="c219f8f308b3b9e77013e46607e5603631d9a0ea">

<a href="https://salsa.debian.org/med-team/qiime/compare/c4c1063f9ef9a29ea1c74344ab0d9e8a9e1cf98d...7d6b53826988db773b76d73d5606098497efba53#c219f8f308b3b9e77013e46607e5603631d9a0ea"><strong>debian/patches/relax_mothur_blast_raxml_versions.patch</strong>

deleted

</a>

<hr>

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1

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Author: Tim Booth <tbooth@ceh.ac.uk></span>

</pre>

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2

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Last-Update: Mon, 10 Mar 2014 14:20:08 +0000</span>

</pre>

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3

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">Description: Enable running more tests successfully by relaxing version number</span>

</pre>

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4

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"></span>

</pre>

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5

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/print_qiime_config.py</span></span>

</pre>

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6

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/print_qiime_config.py</span></span>

</pre>

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7

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -326,7 +326,7 @@</span></span>

</pre>

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8

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff">         version_string = stdout.strip().split('v')[-1].strip('q')</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff">         try:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

10

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff">             version = tuple(map(int, version_string.split('.')))</span>

</pre>

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11

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            pass_test = version == acceptable_version</span></span>

</pre>

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12

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            pass_test = version >= acceptable_version</span></span>

</pre>

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13

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff">         except ValueError:</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff">             pass_test = False</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

15

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff">             version_string = stdout</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

16

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -360,7 +360,7 @@</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

17

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

18

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff">         try:</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

19

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff">             version = tuple(map(int, version_str.split('.')))</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

20

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            pass_test = version == acceptable_version</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

21

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            pass_test = version >= acceptable_version</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

22

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff">         except ValueError:</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

23

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff">             pass_test = False</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

24

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

25

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -460,7 +460,7 @@</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

26

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff">         version_string = stdout.strip().split(' ')[1].strip()</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

27

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff">         try:</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

28

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff">             version = tuple(map(int, version_string.split('.')))</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

29

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            pass_test = version == acceptable_version</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

30

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            pass_test = version >= acceptable_version</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

31

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff">         except ValueError:</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

32

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff">             pass_test = False</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

33

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff">             version_string = stdout</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

34

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -481,7 +481,7 @@</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

35

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff">         version_string = stdout.strip().split(' ')[2].strip()</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

36

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff">         try:</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

37

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff">             version = tuple(map(int, version_string.split('.')))</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

38

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            pass_test = version == acceptable_version</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

39

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            pass_test = version >= acceptable_version</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

40

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff">         except ValueError:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

41

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff">             pass_test = False</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

42

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff">             version_string = stdout</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

43

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -548,7 +548,7 @@</span></span>

</pre>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

44

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff">         version_string = stdout.strip().split(' ')[1].strip('v.')</span>

</pre>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

45

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff">         try:</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

46

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff">             version = tuple(map(int, version_string.split('.')))</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

47

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            pass_test = version == acceptable_version</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

48

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            pass_test = version >= acceptable_version</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

49

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff">         except ValueError:</span>

</pre>

</td>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

50

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff">             pass_test = False</span>

</pre>

</td>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

51

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff">             version_string = stdout</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

52

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -573,7 +573,7 @@</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

53

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

54

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff">     def test_raxmlHPC_supported_version(self):</span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

55

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff">         """raxmlHPC is in path and version is supported """</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

56

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        acceptable_version = [(7, 3, 0), (7, 3, 0)]</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

57

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        acceptable_version = [(7, 3, 0), (7, 3, 5)]</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff">         self.assertTrue(which('raxmlHPC'),</span>

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff">                         "raxmlHPC not found. This may or may not be a problem depending on " +</span>

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff">                         "which components of QIIME you plan to use.")</span></pre>

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</li>

<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<a href="https://salsa.debian.org/med-team/qiime/compare/c4c1063f9ef9a29ea1c74344ab0d9e8a9e1cf98d...7d6b53826988db773b76d73d5606098497efba53#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">#allow_empty_default_taxonomy.patch</span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">#check_config_file_in_new_location.patch</span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">#make_qiime_accept_new_rdp_classifier.patch</span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">#fix_path_for_support_files.patch</span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">#relax_mothur_blast_raxml_versions.patch</span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">#prevent_google_addsense.patch</span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">#fix_script_usage_tests.patch</span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">#prevent_download_on_builds.patch</span>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">##exclude_tests_that_need_to_fail.patch</span>

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">0000_fixme_hack_around_UnicodeDecodeError_in_bibtex.patch</span></pre>

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<li id="24abe6a0133f788f204c33f7b28def90f2fb18a4">

<a href="https://salsa.debian.org/med-team/qiime/compare/c4c1063f9ef9a29ea1c74344ab0d9e8a9e1cf98d...7d6b53826988db773b76d73d5606098497efba53#24abe6a0133f788f204c33f7b28def90f2fb18a4"><strong>debian/qiime-doc.doc-base</strong>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Document: qiime</span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Title: QIIME: Quantitative Insights Into Microbial Ecology</span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Author: Greg Caporaso <gregcaporaso@gmail.com></span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">Abstract: Quantitative Insights Into Microbial Ecology</span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> QIIME (canonically pronounced ‘Chime’) is a pipeline for performing</span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> microbial community analysis that integrates many third party tools</span>

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7

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> which have become standard in the field. </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

8

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> .</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> Rather than reimplementing commonly used algorithms, QIIME wraps popular</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

10

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> implementations of those algorithms. This allows us to make use of the</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

11

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> many excellent tools available in this area, and allows faster</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> integration of new tools. If you use tools that you think would be</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> useful additions to QIIME, consider submitting a feature request.</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> .</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

15

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> A standard QIIME analysis begins with sequence data from one or more</span>

</pre>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

16

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> sequencing platforms, including Sanger, Roche/454, and Illumina GAIIx.</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

17

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> QIIME can perform library de-multiplexing and quality filtering;</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

18

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> denoising with AmpliconNoise or the QIIME Denoiser; OTU and</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

19

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> representative set picking with uclust, cdhit, mothur, BLAST, or other</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

20

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> tools; taxonomy assignment with BLAST or the RDP classifier; sequence</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

21

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> alignment with PyNAST, muscle, infernal, or other tools; phylogeny</span>

</pre>

</td>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

22

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> reconstruction with FastTree, raxml, clearcut, or other tools; alpha</span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

23

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> diversity and rarefaction, including visualization of results, using</span>

</pre>

</td>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

24

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> over 20 metrics including Phylogenetic Diversity, chao1, and observed</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

25

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> species; beta diversity and rarefaction, including visualization of</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

26

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> results, using over 25 metrics including weighted and unweighted</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

27

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> UniFrac, Euclidean distance, and Bray-Curtis; summarization and</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

28

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> visualization of taxonomic composition of samples using area, bar and</span>

</pre>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> pie charts along with distance histograms; and many other features.</span>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> While QIIME is primarily used for analysis of amplicon data, many of the</span>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> downstream analysis pipeline (such as alpha rarefaction and jackknifed</span>

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> beta diversity) can be performed on any type of sample x observation</span>

</pre>

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> tables if they are formatted correctly.</span>

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext">Section: Science/Biology</span>

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext">Format: html</span>

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext">Files: /usr/share/doc/qiime/html/*</span>

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext">Index: /usr/share/doc/qiime/html/index.html</span></pre>

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<br>

</li>

<li id="1e2e0f50a9779f424b876fbc8e0f98b049d2bd1c">

<a href="https://salsa.debian.org/med-team/qiime/compare/c4c1063f9ef9a29ea1c74344ab0d9e8a9e1cf98d...7d6b53826988db773b76d73d5606098497efba53#1e2e0f50a9779f424b876fbc8e0f98b049d2bd1c"><strong>debian/qiime-doc.links</strong>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">usr/share/javascript/jquery/jquery.js         usr/share/doc/qiime/html/_static/jquery.js</span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">usr/share/javascript/underscore/underscore.js usr/share/doc/qiime/html/_static/underscore.js</span></pre>

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<br>

</li>

<li id="7e87233c9ee48d46f144c0134350e9a8b3a43dbd">

<a href="https://salsa.debian.org/med-team/qiime/compare/c4c1063f9ef9a29ea1c74344ab0d9e8a9e1cf98d...7d6b53826988db773b76d73d5606098497efba53#7e87233c9ee48d46f144c0134350e9a8b3a43dbd"><strong>debian/qiime_config</strong>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"># qiime_config</span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"># WARNING: DO NOT EDIT OR DELETE /etc/qiime/qiime_config</span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"># To overwrite defaults, copy this file to $HOME/.qiime_config or a path</span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"># specified by $QIIME_CONFIG_FP and edit that copy of the file.</span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"># This file refers to default GreenGenes data files installed by the qiime-data</span>

</pre>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"># package.</span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">cluster_jobs_fp</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

10

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">python_exe_fp            python</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

11

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">working_dir      .</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">blastmat_dir     /usr/share/ncbi/data</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">blastall_fp      blastall</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">pynast_template_alignment_fp /usr/share/qiime/data/core_set_aligned.fasta.imputed</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

15

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">#template_alignment_lanemask_fp      /usr/share/qiime/data/lanemask_in_1s_and_0s</span>

</pre>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

16

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">pynast_template_alignment_blastdb</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

17

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">jobs_to_start            1</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

18

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">seconds_to_sleep    60</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

19

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">qiime_scripts_dir   /usr/lib/qiime/bin/</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

20

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">temp_dir         /tmp</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

21

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

22

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"># Uncomment these to enable always re-training the RDP classifier, which is the</span>

</pre>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

23

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"># default behaviour for QIIME 1.9.  This takes a lot of time and RAM, so</span>

</pre>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

24

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"># for Bio-Linux the default behaviour is to quickly use the built-in index.</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

25

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"># If you are using another assignment method you may need to specify these settings</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

26

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"># in all cases.</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

27

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">assign_taxonomy_id_to_taxonomy_fp  # /usr/share/qiime/data/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt</span>

</pre>

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<td class="diff-line-num old old_line" 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: 0 5px;" align="right" bgcolor="#f9d7dc">

28

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext">assign_taxonomy_reference_seqs_fp  # /usr/share/qiime/data/gg_13_8_otus/rep_set/97_otus.fasta</span></pre>

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</li>

<li id="280c3383888b855c650ea4a9360e393a4881752b">

<a href="https://salsa.debian.org/med-team/qiime/compare/c4c1063f9ef9a29ea1c74344ab0d9e8a9e1cf98d...7d6b53826988db773b76d73d5606098497efba53#280c3383888b855c650ea4a9360e393a4881752b"><strong>debian/scripts/print_qiime_config_all</strong>

deleted

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>

</pre>

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2

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="shell"></span>

</pre>

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3

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell">print_qiime_config.py <span class="nt" style="color: navy;">-t</span></span>

</pre>

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4

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"></span>

</pre>

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5

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

6

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

7

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Here are the versions of the packages that QIIME depends on as reported by"</span></span>

</pre>

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8

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"the system package manager:"</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>

</pre>

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10

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

11

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell">dpkg <span class="nt" style="color: navy;">-s</span> qiime | perl <span class="nt" style="color: navy;">-ne</span> <span class="s1" style="color: #d14;">'/^Depends: (.*)/ &&</span></span>

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12

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"><span class="s1" style="color: #d14;">  map {s/[ :].*//;</span></span>

</pre>

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13

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell"><span class="s1" style="color: #d14;">       printf "%-26s: %s", $_, `dpkg -s "$_" | sed -n "/Version:/s/.* //p"`</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="s1" style="color: #d14;">   }</span></span>

</pre>

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15

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"><span class="s1" style="color: #d14;">   grep {! /^lib/}</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell"><span class="s1" style="color: #d14;">   sort</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

17

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"><span class="s1" style="color: #d14;">   split(/, /,"$1, mothur")'</span> | <span class="nb" style="color: #0086b3;">uniq</span> <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

18

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"><span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">{</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="p">;</span> <span class="nb" style="color: #0086b3;">echo </span>OK <span class="p">;</span> <span class="o" style="font-weight: 600;">}</span></span></pre>

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<br>

</li>

<li id="85ccdeeb03055211183e48520592d9a93592b330">

<a href="https://salsa.debian.org/med-team/qiime/compare/c4c1063f9ef9a29ea1c74344ab0d9e8a9e1cf98d...7d6b53826988db773b76d73d5606098497efba53#85ccdeeb03055211183e48520592d9a93592b330"><strong>debian/source/lintian-overrides</strong>

deleted

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"># These files are actually editable JS source files and the lintian error is a false positive</span>

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2

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">qiime source: source-is-missing qiime/support_files/js/overlib.js*</span>

</pre>

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3

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">qiime source: source-is-missing qiime/support_files/js/otu_count_display.js*</span>

</pre>

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4

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">qiime source: source-is-missing qiime_test_data/make_2d_plots/js/overlib.js*</span></pre>

</td>

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</table>

<br>

</li>

<li id="68ef9f98c01c7eecd4c605cc26048a06f3304b79">

<a href="https://salsa.debian.org/med-team/qiime/compare/c4c1063f9ef9a29ea1c74344ab0d9e8a9e1cf98d...7d6b53826988db773b76d73d5606098497efba53#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>

<hr>

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1

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<td class="diff-line-num new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=4</span>

</pre>

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2

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2

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>

</pre>

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3

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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">##opts="repacksuffix=+dfsg,dversionmangle=auto,repack,compression=xz" \</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">https://github.com/qiime2/qiime2/releases .*/archive/(\d[\d.]+)@ARCHIVE_EXT@</span></pre>

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