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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-cogent">Debian Med / python-cogent</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cogent/commit/975560e1e651f066b3846b15dc2950a05f8556ed">975560e1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-08T14:50:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cleanup test exceptions - test was totally rewritten by upstream
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cogent/commit/c851297cf6a3e328eaf0228a2b5d9a9e6481f13f">c851297c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-08T14:50:58+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove old patches from cogent 1.9
</pre>
</li>
</ul>
<h4>19 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#1687a440edf40221f475d315a08c43c2c9b4f3af">
<span class="deleted-file">
−
debian/patches/_series_
</span>
</a>
</li>
<li class="file-stats">
<a href="#6f160e43bccdd7bc16700f98b79ad2111615d129">
<span class="deleted-file">
−
debian/patches/accept_newer_cdhit.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#4c71915e422546ce6d427814c7e673af35b13adf">
<span class="deleted-file">
−
debian/patches/adapt_to_ncbi-data_201609.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bede03f038400f0164468023e3a643d25e728009">
<span class="deleted-file">
−
debian/patches/cd-hit-test.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#6105e11d6c7ef7d6ff4c6fca5ad448f6751f83d4">
<span class="deleted-file">
−
debian/patches/fasttree_not_in_caps.patch
</span>
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</li>
<li class="file-stats">
<a href="#a52eecc3ccf10fb6907f30a63bafbb742b2e939a">
<span class="deleted-file">
−
debian/patches/fix_python_shebang_line.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#f9ef23d9ffa9a1e60f7b065b61f85b8026e71baf">
<span class="deleted-file">
−
debian/patches/ignore_numpy_test_issue.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#2fbe13c6162cabd2c72dc9974d14642bb8674c5c">
<span class="deleted-file">
−
debian/patches/matplotlib-2.2.3.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#4d4f6ef83af2877362c82311d33e4ca3543d2238">
<span class="deleted-file">
−
debian/patches/numpy-doctests.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#25d9ba177293e2b5e1f5141ec899346c6ff76ec7">
<span class="deleted-file">
−
debian/patches/numpy_xor.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#de301967d761430006053b4513591cb30270b14f">
<span class="deleted-file">
−
debian/patches/parsinsert_not_in_caps.patch
</span>
</a>
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<li class="file-stats">
<a href="#b46d29336084baa469c9a38cc2012f37c6a81b88">
<span class="deleted-file">
−
debian/patches/privacy.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#461c8e5572730bd4125e5ab1bc91f8044d4262ea">
<span class="deleted-file">
−
debian/patches/raxml_unsupported_version.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#53a366e6fd78b87be2ab8cc6c261fc063f344a7d">
<span class="deleted-file">
−
debian/patches/rdp_classifier.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#feb5daf39635ac768fa3a18ca6bded0230a2e6f8">
<span class="deleted-file">
−
debian/patches/skip_weak_tests.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#198d5c00e2fa0be2217b15cd9a002e37bdf8a532">
<span class="deleted-file">
−
debian/patches/sphinx.ext.pngmath.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#0bba138a5eaaa1a94aa68148bc14ebf3112f1e0d">
<span class="deleted-file">
−
debian/patches/usr_bin_ls.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/python-cogent/compare/627ed619306bc8c8031f85bbc2a233f2628a7639...c851297cf6a3e328eaf0228a2b5d9a9e6481f13f#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 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">@@ -20,22 +20,6 @@ Build-Depends: debhelper-compat (= 12),</td>
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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
20
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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
20
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> python3-nbsphinx,</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
21
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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
21
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> python3-sphinxcontrib.bibtex,</span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="22" 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">
22
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<td class="diff-line-num new_line" data-linenumber="22" 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">
22
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> cython3,</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="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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> ncbi-blast+-legacy,</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="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="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">
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> bwa [any-amd64],</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="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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> cd-hit,</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="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">
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> cdbfasta,</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="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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> clearcut,</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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<td class="diff-line-num new_line old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> clustalw,</span>
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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="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">
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> dialign,</span>
</pre>
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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="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">
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> fasttree,</span>
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<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
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<td class="diff-line-num new_line old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> infernal [any-amd64 any-i386],</span>
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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
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<td class="diff-line-num new_line old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> mafft,</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">
33
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<td class="diff-line-num new_line old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> mothur [!s390x],</span>
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<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
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<td class="diff-line-num new_line old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"> muscle,</span>
</pre>
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<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
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<td class="diff-line-num new_line old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"> parsinsert,</span>
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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="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">
</td>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> raxml [any-amd64 any-i386],</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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<td class="diff-line-num new_line old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"> rdp-classifier,</span>
</pre>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext"> rtax,</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> pandoc</span>
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Standards-Version: 4.4.1</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/python-cogent</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -48,28 +32,14 @@ Depends: ${shlibs:Depends},</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> ${python3:Depends},</span>
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50
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> python3-matplotlib,</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"> python3-pandas</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> python3-pandas<span class="idiff left right">,</span></span>
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52
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> python3-plotly,</span>
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53
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> python3-scitrack,</span>
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54
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> python3-tqdm,</span>
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55
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> python3-tinydb</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">Recommends: ncbi-blast+-legacy,</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext"> bwa [any-amd64],</span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext"> cd-hit,</span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext"> clearcut,</span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext"> dialign,</span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext"> muscle</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> dialign</span>
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62
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">Suggests: python-cogent-doc,</span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext"> cdbfasta,</span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext"> clustalw,</span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext"> fasttree,</span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext"> infernal [any-amd64 any-i386],</span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext"> mafft,</span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext"> mothur [!s390x],</span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext"> parsinsert,</span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext"> raxml [any-amd64 any-i386],</span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext"> rdp-classifier,</span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext"> rtax</span>
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73
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">Description: framework for genomic biology</span>
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74
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44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> PyCogent is a software library for genomic biology. It is a fully</span>
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75
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45
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> integrated and thoroughly tested framework for:</span>
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<a href="https://salsa.debian.org/med-team/python-cogent/compare/627ed619306bc8c8031f85bbc2a233f2628a7639...c851297cf6a3e328eaf0228a2b5d9a9e6481f13f#1687a440edf40221f475d315a08c43c2c9b4f3af"><strong>debian/patches/_series_</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">accept_newer_cdhit.patch</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">fix_python_shebang_line.patch</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">parsinsert_not_in_caps.patch</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">fasttree_not_in_caps.patch</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">raxml_unsupported_version.patch</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">cd-hit-test.patch</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">rdp_classifier.patch</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">skip_weak_tests.patch</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">adapt_to_ncbi-data_201609.patch</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">ignore_numpy_test_issue.patch</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">usr_bin_ls.patch</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">numpy_xor.patch</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">numpy-doctests.patch</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">privacy.patch</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">matplotlib-2.2.3.patch</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">sphinx.ext.pngmath.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/python-cogent/compare/627ed619306bc8c8031f85bbc2a233f2628a7639...c851297cf6a3e328eaf0228a2b5d9a9e6481f13f#6f160e43bccdd7bc16700f98b79ad2111615d129"><strong>debian/patches/accept_newer_cdhit.patch</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Tim Booth <tbooth@ceh.ac.uk></span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Changed: Fri, 25 Apr 2014 17:27:42 +0100</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Description: Get Cogent to work with newer CD-HIT that doesn't leave</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> a temporary file sitting around. This patch has only been quickly tested and</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"> there may be deeper issues.</span>
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6
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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">--- PyCogent-1.5.3.orig/cogent/app/cd_hit.py</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ PyCogent-1.5.3/cogent/app/cd_hit.py</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="p">@@ -257,7 +257,10 @@</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> # perform cleanup</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> res.cleanUp()</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> shutil.rmtree(working_dir)</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;">- remove(params['-o'] + '.bak.clstr')</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;">+ try:</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;">+ remove(params['-o'] + '.bak.clstr')</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except OSError:</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;">+ pass #maybe there was no file</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> return remapped_clusters</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="p">@@ -299,7 +302,10 @@</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"> # perform cleanup</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"> res.cleanUp()</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> shutil.rmtree(working_dir)</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;">- remove(params['-o'] + '.bak.clstr')</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ try:</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ remove(params['-o'] + '.bak.clstr')</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except OSError:</span></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pass #maybe there was no file</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"> return SequenceCollection(new_seqs, MolType=moltype)</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"> </span></pre>
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<li id="4c71915e422546ce6d427814c7e673af35b13adf">
<a href="https://salsa.debian.org/med-team/python-cogent/compare/627ed619306bc8c8031f85bbc2a233f2628a7639...c851297cf6a3e328eaf0228a2b5d9a9e6481f13f#4c71915e422546ce6d427814c7e673af35b13adf"><strong>debian/patches/adapt_to_ncbi-data_201609.patch</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Description: Since ncbi-tools6 6.1.20160908-1 some blast relatet tests</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"> are failing at package Build time. These tests are deleted here.</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"> .</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> Without the patches in tests/test_app/test_blast.py the build hangs totally</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"> and needs to be interrupted by ^C.</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> .</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> The patches in tests/test_app/test_formatdb.py lead to regular test suite</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> failures with proper output of the problem.</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/847082</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="p">Last-Update: Mon, 05 Dec 2016 13:23:40 +0100</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff">--- a/tests/test_app/test_blast.py</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;">+++ b/tests/test_app/test_blast.py</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="p">@@ -174,71 +174,6 @@</span> MSGNIKKIVEPNSGIDYSLEKDFKIFTLSKELPITTYPSY</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> self.assertEqualItems(k, \</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> ['ece:Z4181','ecs:ECs3717','spt:SPA2730','cvi:CV2421','ece:Z4182'])</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> </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;">- def test_ids_from_seq_lower_threshold(self):</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;">- "ids_from_seq_lower_threshold returns psiblast hits, decreasing sens"</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;">- bdb_seqs = self.fasta_recs</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;">- f = open('test_bdb', 'w')</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;">- f.write(bdb_seqs)</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;">- f.close()</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;">- temp = popen('formatdb -i test_bdb -o T -p T')</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;">- params = {'-j':2,</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;">- '-d':'test_bdb'}</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- query = self.query_1.split('\n')</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- app = PsiBlast(params=params, </span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- InputHandler='_input_as_lines')</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #the command below should result in finding itself and 2554</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #it should run for max_iterations</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- result = ids_from_seq_lower_threshold(query, n=12, \</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- max_iterations=4, app=app, core_threshold=1e-50, \</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- lower_threshold=1e-20, step=10000)</span></span>
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36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(result[0],\</span></span>
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37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [('gi|100002553', '0.0'), ('gi|100002554', '0.0')])</span></span>
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38
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(result[1], 4)</span></span>
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39
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #if n=2, it should find the same sequences but only run for 1 iteration</span></span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #since it would hit n after the first blast search</span></span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- result = ids_from_seq_lower_threshold(query, n=2, \</span></span>
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42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- max_iterations=4, app=app, core_threshold=1e-50, \</span></span>
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43
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- lower_threshold=1e-20, step=10000)</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(result[0],\</span></span>
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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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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [('gi|100002553', '0.0'), ('gi|100002554', '0.0')])</span></span>
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46
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(result[1], 1)</span></span>
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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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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- query = self.query_2.split('\n')</span></span>
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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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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #query_2_s e-value for itself is 9e-47, it should not be found</span></span>
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49
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #with the lower_threshold set to 1e-48</span></span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- result = ids_from_seq_lower_threshold(query, n=12, \</span></span>
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51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- max_iterations=4, app=app, core_threshold=1e-50, \</span></span>
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52
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- lower_threshold=1e-48, step=10000)</span></span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(result[0], [])</span></span>
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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">
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #it also should not be found if the max_iterations is set to 1</span></span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- result = ids_from_seq_lower_threshold(query, n=12, \</span></span>
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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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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- max_iterations=1, app=app, core_threshold=1e-50, \</span></span>
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<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
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- lower_threshold=1e-20, step=10000)</span></span>
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58
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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.assertEqual(result[0], [])</span></span>
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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">
59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for fname in ['formatdb.log'] + glob('test_bdb*'):</span></span>
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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">
60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- remove(fname)</span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def test_psiblast_n_neighbors(self):</span></span>
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<td class="diff-line-num old old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "psiblast_n_neighbors psiblasts and stops when n neighbors are reached"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bdb_seqs = self.fasta_recs</span></span>
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<td class="diff-line-num old old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- f = open('test_bdb', 'w')</span></span>
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<td class="diff-line-num old old_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- f.write(bdb_seqs)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- f.close()</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- temp = popen('formatdb -i test_bdb -o T -p T')</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- params = {'-j':11}</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- lines = bdb_seqs.split('\n')</span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- results = psiblast_n_neighbors(lines, n=12, blast_db='test_bdb', \</span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- method='lower_threshold', params=params,\</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- core_threshold=1e-50, step=10000)</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #there should be 10 result entries since there were 10 queries</span></span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(len(results), 10)</span></span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in results:</span></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #each query should at least find itself</span></span>
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78
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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.failUnless(len(results[i][0]) >= 1)</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #each query should iterate 8 times since it can never reach max</span></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(results[i][1], 11)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for fname in ['formatdb.log'] + glob('test_bdb*'):</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- remove(fname)</span></span>
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83
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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>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="diff"> </span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="diff"> def wrap_qmes(qmes):</span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="diff"> """Converts qmes into a dict of {q:{m:e}}"""</span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/test_app/test_formatdb.py</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/test_app/test_formatdb.py</span></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="diff"><span class="p">@@ -76,120 +76,6 @@</span> class FormatDbTests(TestCase):</span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="diff"> self.assertFalse(exists(outpath),\</span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="diff"> "%s was not cleaned up." % outpath)</span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="diff"> </span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def test_blast_against_new_db(self):</span></span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- """Formatdb: blastall against a newly created DB functions as expected</span></span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- """</span></span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fdb = FormatDb(WorkingDir='/tmp')</span></span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- result = fdb(self.in_seqs1_fp)</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- blast_res = blastn(self.test_seq,blast_db=self.in_seqs1_fp)</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- result.cleanUp()</span></span>
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100
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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>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # Test that a blast result was returned</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue('s1' in blast_res,\</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "Not getting any blast results.")</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # Test that the sequence we expect was a good blast hit</span></span>
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<td class="diff-line-num old old_line" 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">
105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- subject_ids = [r['SUBJECT ID'] for r in blast_res['s1'][0]]</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue('11472384' in subject_ids,\</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "Not getting expected blast results.")</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def test_build_blast_db_from_seqs(self):</span></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- """build_blast_db_from_seqs convenience function works as expected</span></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- """</span></span>
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<td class="diff-line-num old old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- blast_db, db_files = build_blast_db_from_seqs(self.in_seqs1,output_dir='/tmp')</span></span>
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<td class="diff-line-num old old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
113
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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.assertTrue(blast_db.startswith('/tmp/Blast_tmp_db'))</span></span>
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<td class="diff-line-num old old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(blast_db.endswith('.fasta'))</span></span>
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<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
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- expected_db_files = set([blast_db + ext\</span></span>
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<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
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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="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for ext in ['.nhr','.nin','.nsq','.nsd','.nsi','.log']])</span></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(set(db_files),expected_db_files)</span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # result returned when blasting against new db</span></span>
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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(\</span></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- len(blastn(self.test_seq,blast_db=blast_db)),1)</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # Make sure all db_files exist</span></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for fp in db_files:</span></span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(exists(fp))</span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # Remove all db_files exist </span></span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- remove_files(db_files)</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # Make sure nothing weird happened in the remove</span></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for fp in db_files:</span></span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertFalse(exists(fp))</span></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def test_build_blast_db_from_fasta_path(self):</span></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- """build_blast_db_from_fasta_path convenience function works as expected</span></span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- """</span></span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- blast_db, db_files = \</span></span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- build_blast_db_from_fasta_path(self.in_seqs1_fp)</span></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(blast_db,self.in_seqs1_fp)</span></span>
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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="gd" style="color: #000; background-color: #fdd;">- expected_db_files = set([self.in_seqs1_fp + ext\</span></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for ext in ['.nhr','.nin','.nsq','.nsd','.nsi','.log']])</span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(set(db_files),expected_db_files)</span></span>
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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="gd" style="color: #000; background-color: #fdd;">-</span></span>
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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="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC144" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # result returned when blasting against new db</span></span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(\</span></span>
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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">
146
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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="LC146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- len(blastn(self.test_seq,blast_db=blast_db)),1)</span></span>
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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">
147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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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">
148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # Make sure all db_files exist</span></span>
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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">
149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for fp in db_files:</span></span>
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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">
150
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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="LC150" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(exists(fp))</span></span>
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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">
151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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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="gd" style="color: #000; background-color: #fdd;">- # Remove all db_files exist </span></span>
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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="gd" style="color: #000; background-color: #fdd;">- remove_files(db_files)</span></span>
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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="gd" style="color: #000; background-color: #fdd;">- </span></span>
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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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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC155" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # Make sure nothing weird happened in the remove</span></span>
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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="gd" style="color: #000; background-color: #fdd;">- for fp in db_files:</span></span>
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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="gd" style="color: #000; background-color: #fdd;">- self.assertFalse(exists(fp))</span></span>
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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">
158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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<td class="diff-line-num old old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def test_build_blast_db_from_fasta_path_aln(self):</span></span>
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<td class="diff-line-num old old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- """build_blast_db_from_fasta_path works with alignment as input</span></span>
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<td class="diff-line-num old old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- """</span></span>
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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">
162
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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="LC162" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- blast_db, db_files = build_blast_db_from_fasta_path(self.in_aln1_fp)</span></span>
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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">
163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(blast_db,self.in_aln1_fp)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- expected_db_files = set([blast_db + ext\</span></span>
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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">
165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for ext in ['.nhr','.nin','.nsq','.nsd','.nsi','.log']])</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(set(db_files),expected_db_files)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
167
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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="LC167" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # result returned when blasting against new db</span></span>
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<td class="diff-line-num old old_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(\</span></span>
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<td class="diff-line-num old old_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
169
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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="LC169" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- len(blastn(self.test_seq,blast_db=blast_db,e_value=0.0)),1)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
170
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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="LC170" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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<td class="diff-line-num old old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
171
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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="LC171" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # Make sure all db_files exist</span></span>
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<td class="diff-line-num old old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for fp in db_files:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
173
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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="LC173" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(exists(fp))</span></span>
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<td class="diff-line-num old old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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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">
175
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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="LC175" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # Remove all db_files exist </span></span>
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<td class="diff-line-num old old_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- remove_files(db_files)</span></span>
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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">
177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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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">
178
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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="LC178" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # Make sure nothing weird happened in the remove</span></span>
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<td class="diff-line-num old old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for fp in db_files:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertFalse(exists(fp))</span></span>
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<td class="diff-line-num old old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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<td class="diff-line-num old old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def test_build_blast_db_from_fasta_file(self):</span></span>
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<td class="diff-line-num old old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- """build_blast_db_from_fasta_file works with open files as input</span></span>
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<td class="diff-line-num old old_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- """</span></span>
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<td class="diff-line-num old old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- blast_db, db_files = \</span></span>
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<td class="diff-line-num old old_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- build_blast_db_from_fasta_file(open(self.in_aln1_fp),output_dir='/tmp/')</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
187
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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="LC187" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(blast_db.startswith('/tmp/BLAST_temp_db'))</span></span>
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<td class="diff-line-num old old_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
188
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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="LC188" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(blast_db.endswith('.fasta'))</span></span>
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<td class="diff-line-num old old_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
189
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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="LC189" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- expected_db_files = set([blast_db] + [blast_db + ext\</span></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for ext in ['.nhr','.nin','.nsq','.nsd','.nsi','.log']])</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(set(db_files),expected_db_files)</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # result returned when blasting against new db</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(\</span></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- len(blastn(self.test_seq,blast_db=blast_db,e_value=0.0)),1)</span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # Make sure all db_files exist</span></span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for fp in db_files:</span></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(exists(fp))</span></span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # Remove all db_files exist </span></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- remove_files(db_files)</span></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # Make sure nothing weird happened in the remove</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for fp in db_files:</span></span>
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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertFalse(exists(fp))</span></span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="diff"> </span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="diff"> in_seqs1 = """>11472286</span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="diff"> GATGAACGCTGGCGGCATGCTTAACACATGCAAGTCGAACGGAACACTTTGTGTTTTGAGTTAATAGTTCGATAGTAGATAGTAAATAGTGAACACTATGAACTAGTAAACTATTTAACTAGAAACTCTTAAACGCAGAGCGTTTAGTGGCGAACGGGTGAGTAATACATTGGTATCTACCTCGGAGAAGGACATAGCCTGCCGAAAGGTGGGGTAATTTCCTATAGTCCCCGCACATATTTGTTCTTAAATCTGTTAAAATGATTATATGTTTTATGTTTATTTGATAAAAAGCAGCAAGACAAATGAGTTTTATATTGGTTATACAGCAGATTTAAAAAATAGAATTAGGTCTCATAATCAGGGAGAAAACAAATCAACTAAATCTAAAATACCTTGGGAATTGGTTTACTATGAAGCCTACAAAAACCAAACATCAGCAAGGGTTAGAGAATCAAAGTTGAAACATTATGGGCAATCATTAACTAGACTTAAGAGAAGAATTGGTTTTTGAGAACAAATATGTGCGGGGTAAAGCAGCAATGCGCTCCGAGAGGAACCTCTGTCCTATCAGCTTGTTGGTAAGGTAATGGCTTACCAAGGCGACGACGGGTAGCTGGTGTGAGAGCACGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGAGGAATTTTCCACAATGGGCGCAAGCCTGATGGAGCAATGCCGCGTGAAGGATGAAGATTTTCGGATTGTAAACTTCTTTTAAGTAGGAAGATTATGACGGTACTACTTGAATAAGCATCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGATGCAAGCGTTATCCGGAATTACTGGGCGTAAAGCGTGTGTAGGTGGTTTATTAAGTTAAATGTTAAATTTTCAGGCTTAACTTGGAAACCGCATTTAATACTGGTAGACTTTGAGGACAAGAGAGGCAGGCGGAATTAGCGGAGTAGCGGTGAAATGCGTAGATATCGCTAAGAACACCAATGGCGAAGGCAGCCTGCTGGTTTGCACCTGACACTGAGATACGAAAGCGTGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCACGCCGTAAACGATGGTCACTAGCTGTTAGGGGCTCGACCCCTTTAGTAGCGAAGCTAACGCGTTAAGTGACCCGCCTGGGGAGTACGATCGCAAGATTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAACGTGAGGTTTAATTCGTCTCTAAGCGAAAAACCTTACCGAGGCTTGACATCTCCGGAAGACCTTAGAAATAAGGTTGTGCCCGAAAGGGAGCCGGATGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTCGGTTAAGTCCGTTAACGAGCGCAACCCTTGCTGTGTGTTGTATTTTTCACACAGGACTATCCTGGTCAACAGGGAGGAAGGTGGGGATGACGTCAAGTCAGCATGGCTCTTACGCCTCGGGCTACACTCGCGTTACAATGGCCGGTACAATGGGCTGCCAACTCGTAAGGGGGAGCTAATCCCATCAAAACCGGTCCCAGTTCGGATTGAGGGCTGCAATTCGCCCTCATGAAGTCGGAATCGCTAGTAACCGCGAATCAGCACGTCGCGGTGAATGCGTTCTCGGGTCTTGTACACACTGCCCGTCACACCACGAAAGTTAGTAACGCCCGAAGTGCCCTGTATGGGGTCCTAAGGTGGGGCTAGCGATTGGGGTG</span></pre>
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<li id="bede03f038400f0164468023e3a643d25e728009">
<a href="https://salsa.debian.org/med-team/python-cogent/compare/627ed619306bc8c8031f85bbc2a233f2628a7639...c851297cf6a3e328eaf0228a2b5d9a9e6481f13f#bede03f038400f0164468023e3a643d25e728009"><strong>debian/patches/cd-hit-test.patch</strong>
deleted
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Wed, 14 Sep 2016 16:43:40 +0200</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Description: Upstream confirmed that the app controller only supports</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> cd-hit 3.1.1.</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"> .</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> See https://github.com/pycogent/pycogent/issues/101</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> .</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> Exclude some tests for the moment since otherwise there is no chance</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> to get the new cogent version uploaded which in turn fixes lots of</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> other bugs</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff">--- a/tests/test_app/test_cd_hit.py</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/test_app/test_cd_hit.py</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="p">@@ -46,11 +46,6 @@</span> class CD_HIT_Tests(TestCase):</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> rmdir('/tmp/cdhit_test')</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> rmdir('/tmp/cdhit_test2')</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> </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;">- def test_cdhit_from_seqs(self):</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;">- """CD_HIT should return expected seqs"""</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;">- res = cdhit_from_seqs(protein_seqs, PROTEIN, {'-c':0.8})</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;">- self.assertEqual(res.toFasta(), protein_expected)</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"> class CD_HIT_EST_Tests(TestCase):</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> """Tests for the CD-HIT application controller"""</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="p">@@ -82,17 +77,6 @@</span> class CD_HIT_EST_Tests(TestCase):</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"> rmdir('/tmp/cdhitest_test')</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"> rmdir('/tmp/cdhitest_test2')</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def test_cdhit_from_seqs(self):</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- """CD_HIT should return expected seqs"""</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- res = cdhit_from_seqs(dna_seqs, DNA, {'-c':0.8})</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(res.toFasta(), dna_expected)</span></span>
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<pre style="margin: 0;">-<span id="LC34" 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="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def test_cdhit_from_seqs_synonym(self):</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- """CD_HIT should return expected seqs with -c synonym"""</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- res = cdhit_from_seqs(dna_seqs, DNA, {'Similarity':0.8})</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(res.toFasta(), dna_expected)</span></span>
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<pre style="margin: 0;">-<span id="LC39" 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="LC40" 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="LC41" class="line" lang="diff"> class CD_HIT_SupportMethodTests(TestCase):</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"> """Tests for supporting methods"""</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"> def test_clean_cluster_seq_id(self):</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"><span class="p">@@ -110,16 +94,6 @@</span> class CD_HIT_SupportMethodTests(TestCase</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"> obs = parse_cdhit_clstr_file(data)</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"> self.assertEqual(obs, exp)</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def test_cdhit_clusters_from_seqs(self):</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- """cdhit_clusters_from_seqs returns expected clusters"""</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- exp = [['cdhit_test_seqs_0'],['cdhit_test_seqs_1'],\</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;">- ['cdhit_test_seqs_2'],['cdhit_test_seqs_3'],\</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;">- ['cdhit_test_seqs_4'],['cdhit_test_seqs_5'],\</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ['cdhit_test_seqs_6','cdhit_test_seqs_8'],\</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;">- ['cdhit_test_seqs_7'],['cdhit_test_seqs_9']]</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;">- obs = cdhit_clusters_from_seqs(dna_seqs, DNA)</span></span>
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<pre style="margin: 0;">-<span id="LC56" 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="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"> dna_seqs = """>cdhit_test_seqs_0</span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"> AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCT</span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"> >cdhit_test_seqs_1</span></pre>
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<a href="https://salsa.debian.org/med-team/python-cogent/compare/627ed619306bc8c8031f85bbc2a233f2628a7639...c851297cf6a3e328eaf0228a2b5d9a9e6481f13f#6105e11d6c7ef7d6ff4c6fca5ad448f6751f83d4"><strong>debian/patches/fasttree_not_in_caps.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Fri, 25 Apr 2014 21:27:42 +0100</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Description: make script compatible with spelling of Debian's</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> fasttree package</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"> .</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> One test had to be excluded. This is reported upstream as issue #102</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">--- a/cogent/app/fasttree.py</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/cogent/app/fasttree.py</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="p">@@ -25,7 +25,7 @@</span> __status__ = "Development"</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> class FastTree(CommandLineApplication):</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> """FastTree application Controller"""</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"><span class="gd" style="color: #000; background-color: #fdd;">- _command = 'FastTree'</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;">+ _command = 'fasttree'</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> _input_handler = '_input_as_multiline_string'</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> _parameters = {</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> '-quiet':FlagParameter('-',Name='quiet'),</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;">--- a/cogent/app/fasttree_v1.py</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/cogent/app/fasttree_v1.py</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="p">@@ -20,7 +20,7 @@</span> __status__ = "Development"</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"> class FastTree(CommandLineApplication):</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"> """FastTree application Controller"""</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"><span class="gd" style="color: #000; background-color: #fdd;">- _command = 'FastTree'</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ _command = 'fasttree'</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"> _input_handler = '_input_as_multiline_string'</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"> _parameters = {</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> '-quiet':FlagParameter('-',Name='quiet'),</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/test_app/test_fasttree.py</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;">+++ b/tests/test_app/test_fasttree.py</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="p">@@ -27,15 +27,15 @@</span> class FastTreeTests(TestCase):</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"> def test_base_command(self):</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"> app = FastTree()</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"> self.assertEqual(app.BaseCommand, \</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ''.join(['cd "',getcwd(),'/"; ','FastTree']))</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;">+ ''.join(['cd "',getcwd(),'/"; ','fasttree']))</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"> app.Parameters['-nt'].on()</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"> self.assertEqual(app.BaseCommand, \</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ''.join(['cd "',getcwd(),'/"; ','FastTree -nt']))</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;">+ ''.join(['cd "',getcwd(),'/"; ','fasttree -nt']))</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"> def test_change_working_dir(self):</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"> app = FastTree(WorkingDir='/tmp/FastTreeTest')</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"> self.assertEqual(app.BaseCommand, \</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ''.join(['cd "','/tmp/FastTreeTest','/"; ','FastTree']))</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ''.join(['cd "','/tmp/FastTreeTest','/"; ','fasttree']))</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"> rmtree('/tmp/FastTreeTest')</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"> def test_build_tree_from_alignment(self):</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"><span class="p">@@ -47,8 +47,9 @@</span> class FastTreeTests(TestCase):</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"> self.assertFloatEqual(o.Length,e.Length)</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"> except AssertionError:</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"> for o,e in zip(tree.traverse(), DndParser(exp_tree_201).traverse()):</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.assertEqual(o.Name,e.Name)</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertFloatEqual(o.Length,e.Length)</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # self.assertEqual(o.Name,e.Name) # --> AssertionError: Got '0.409', but expected '0.466' see issue #102</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # self.assertFloatEqual(o.Length,e.Length) # --> AssertionError: Got 6e-09, but expected 0.00015 (diff was -0.00014999399999999997)</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pass</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"> test_seqs = """>test_set1_0</span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"> GGTAGATGGGACTACCTCATGACATGAAACTGCAGTCTGTTCTTTTATAGAAGCTTCATACTTGGAGATGTATACTATTA</span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"> CTTAGGACTATGGAGGTATA</span></pre>
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<li id="a52eecc3ccf10fb6907f30a63bafbb742b2e939a">
<a href="https://salsa.debian.org/med-team/python-cogent/compare/627ed619306bc8c8031f85bbc2a233f2628a7639...c851297cf6a3e328eaf0228a2b5d9a9e6481f13f#a52eecc3ccf10fb6907f30a63bafbb742b2e939a"><strong>debian/patches/fix_python_shebang_line.patch</strong>
deleted
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Steffen Moeller <moeller@debian.org></span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Description: fix path to python interpreter</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- PyCogent-1.5.3.orig/cogent/align/dp_calculation.py</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ PyCogent-1.5.3/cogent/align/dp_calculation.py</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env/python</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> </span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> from cogent.maths.markov import SiteClassTransitionMatrix</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> from cogent.recalculation.definition import PositiveParamDefn, \</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- PyCogent-1.5.3.orig/cogent/data/molecular_weight.py</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ PyCogent-1.5.3/cogent/data/molecular_weight.py</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env Python</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> """Data for molecular weight calculations on proteins and nucleotides."""</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> </span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> __author__ = "Rob Knight"</span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- PyCogent-1.5.3.orig/cogent/format/text_tree.py</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ PyCogent-1.5.3/cogent/format/text_tree.py</span></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/bin/env python</span></span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> # file text_tree.py</span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> """Simple base text representation of phylo tree."""</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> </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;">--- PyCogent-1.5.3.orig/cogent/recalculation/__init__.py</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ PyCogent-1.5.3/cogent/recalculation/__init__.py</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/envthon</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;">+#!/usr/bin/python</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"> __all__ = ['array', 'calculation', 'definition', 'scope', 'setting']</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"> __author__ = "Peter Maxwell"</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- PyCogent-1.5.3.orig/cogent/recalculation/setting.py</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ PyCogent-1.5.3/cogent/recalculation/setting.py</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python'</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"> """Instances of these classes are assigned to different parameter/scopes</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"> by a parameter controller"""</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- PyCogent-1.5.3.orig/cogent/phylo/maximum_likelihood.py</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ PyCogent-1.5.3/cogent/phylo/maximum_likelihood.py</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python'</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"> from tree_space import TreeEvaluator, ancestry2tree</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"> from least_squares import WLS</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"> from math import exp</span></pre>
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<li id="f9ef23d9ffa9a1e60f7b065b61f85b8026e71baf">
<a href="https://salsa.debian.org/med-team/python-cogent/compare/627ed619306bc8c8031f85bbc2a233f2628a7639...c851297cf6a3e328eaf0228a2b5d9a9e6481f13f#f9ef23d9ffa9a1e60f7b065b61f85b8026e71baf"><strong>debian/patches/ignore_numpy_test_issue.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Description: Skip test featuring wrong numpy usage</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"> Traceback (most recent call last):</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"> File "/<<PKGBUILDDIR>>/tests/test_util/test_array.py", line 596, in test_split_dimension</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> a = split_dimension(m, 0)</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"> File "/<<PKGBUILDDIR>>/cogent/util/array.py", line 504, in split_dimension</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> return reshape(m, new_dim)</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"> TypeError: 'numpy.float64' object cannot be interpreted as an index</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"> The issue occurred after upgrading from Numpy 1.11.2 to 1.12.0~b1 which</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> has cause also other packages test suites failures. Since this version</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> of Cogent is in low maintenance mode it will probably not be adapted to</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> any new Numpy versions so skipping two tests might be the most appropriate</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> step to deal with this issue</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/848746</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="p">Last-Update: Tue, 20 Dec 2016 09:36:34 +0100</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"></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;">--- a/tests/test_util/test_array.py</span></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;">+++ b/tests/test_util/test_array.py</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="p">@@ -591,12 +591,6 @@</span> class ArrayMathTests(TestCase):</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"> self.assertEqual(a.shape, (3,4,12,12))</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> #should fail with IndexError for invalid dimension</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> self.assertRaises(IndexError, split_dimension, m, 5, (3,4))</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;">- #should assume even split if not supplied</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;">- m = reshape(arange(16**3), (16,16,16))</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- a = split_dimension(m, 0)</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(a.shape, (4,4,16,16))</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- a = split_dimension(m, 1)</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(a.shape, (16,4,4,16))</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"> def test_non_diag(self):</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"> """non_diag should return non-diag elements from flattened matrices"""</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/test_draw/test_distribution_plots.py</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/test_draw/test_distribution_plots.py</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="p">@@ -233,12 +233,6 @@</span> class DistributionPlotsTests(TestCase):</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"> result = _plot_bar_data(ax, [], 'red', 0.5, 3.75, 1.5, 'sem')</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"> self.assertTrue(result is None)</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def test_plot_scatter_data(self):</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- """_plot_scatter_data() should return a Collection instance."""</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fig, ax = _create_plot()</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- result = _plot_scatter_data(ax, [1, 2, 3], '^', 0.77, 1, 1.5, 'stdv')</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertFloatEqual(result.get_sizes(), 20)</span></span>
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<pre style="margin: 0;">-<span id="LC46" 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="LC47" class="line" lang="diff"> def test_plot_scatter_data_empty(self):</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"> """_plot_scatter_data() should not error when given empty list of data,</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"> but should not plot anything."""</span></pre>
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<li id="2fbe13c6162cabd2c72dc9974d14642bb8674c5c">
<a href="https://salsa.debian.org/med-team/python-cogent/compare/627ed619306bc8c8031f85bbc2a233f2628a7639...c851297cf6a3e328eaf0228a2b5d9a9e6481f13f#2fbe13c6162cabd2c72dc9974d14642bb8674c5c"><strong>debian/patches/matplotlib-2.2.3.patch</strong>
deleted
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Description: Ignore test with matplotlib 2.2.3 where a warning message</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"> is different than expected</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/915908</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">Last-Update: Mon, 17 Dec 2018 08:21:47 +0100</span></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">--- a/tests/test_draw/test_distribution_plots.py</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/tests/test_draw/test_distribution_plots.py</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="p">@@ -507,12 +507,12 @@</span> class DistributionPlotsTests(TestCase):</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> _set_figure_size(fig, 3, 3)</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> self.assertFloatEqual(fig.get_size_inches(), (3, 3))</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> output = out.getvalue().strip()</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;">- self.assertEqual(output,</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;">- "Warning: could not automatically resize plot to make room for "</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;">- "axes labels and plot title. This can happen if the labels or "</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;">- "title are extremely long and the plot size is too small. Your "</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;">- "plot may have its labels and/or title cut-off. To fix this, "</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;">- "try increasing the plot's size (in inches) and try again.")</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# self.assertEqual(output,</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# "Warning: could not automatically resize plot to make room for "</span></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;">+# "axes labels and plot title. This can happen if the labels or "</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;">+# "title are extremely long and the plot size is too small. Your "</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;">+# "plot may have its labels and/or title cut-off. To fix this, "</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# "try increasing the plot's size (in inches) and try again.")</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> finally:</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> sys.stdout = saved_stdout</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/python-cogent/compare/627ed619306bc8c8031f85bbc2a233f2628a7639...c851297cf6a3e328eaf0228a2b5d9a9e6481f13f#4d4f6ef83af2877362c82311d33e4ca3543d2238"><strong>debian/patches/numpy-doctests.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Description: Ensure doctests pass with different numpy versions</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"> The numpy output format changed with numpy 1.14 and this causes doctests to</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"> fail if raw numerical output is compared. See</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> https://wiki.debian.org/ContinuousIntegration/TriagingTips/numpy-1.14-doctests</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">Author: Stuart Prescott <stuart@debian.org></span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="p">Last-Update: Tue, 05 Jun 2018 15:32:46 +0000 (UTC)</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">Origin: https://github.com/pycogent/pycogent/files/2072985/numpy-doctests.patch</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/899205</span></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">--- a/tests/alltests.py</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/alltests.py</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="p">@@ -6,6 +6,14 @@</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> import doctest, cogent.util.unit_test as unittest, sys, os</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> from cogent.util.misc import app_path</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"><span class="gi" style="color: #000; background-color: #dfd;">+# Whitespace changes between numpy 1.13 and 1.14 will cause the doctests</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;">+# to fail; when doctests are updated to 1.14 format, this can be removed.</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+try: # CRUFT</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ import numpy as np</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ np.set_printoptions(legacy='1.13')</span></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;">+except TypeError:</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;">+ pass</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;">+</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> __author__ = "Peter Maxwell and Gavin Huttley"</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> __copyright__ = "Copyright 2007-2016, The Cogent Project"</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> __credits__ = ["Peter Maxwell", "Gavin Huttley", "Rob Knight",</span></pre>
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<li id="25d9ba177293e2b5e1f5141ec899346c6ff76ec7">
<a href="https://salsa.debian.org/med-team/python-cogent/compare/627ed619306bc8c8031f85bbc2a233f2628a7639...c851297cf6a3e328eaf0228a2b5d9a9e6481f13f#25d9ba177293e2b5e1f5141ec899346c6ff76ec7"><strong>debian/patches/numpy_xor.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Description: Use xor rather than subtraction on booleans</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"> Numpy no longer accepts the ambiguous construction of a-b when a and b are bools.</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"> Normally, this can be replaced with XORs.</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Author: Stuart Prescott <stuart@debian.org></span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">Last-Update: Tue, 05 Jun 2018 15:32:46 +0000 (UTC)</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="p">Origin: https://github.com/pycogent/pycogent/files/2072984/numpy_xor.patch</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/899205</span></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">--- a/cogent/core/sequence.py</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/cogent/core/sequence.py</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="p">@@ -1248,7 +1248,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> gap_indices = map(self.Alphabet.index, self.MolType.Gaps)</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> valid_indices = self._data < len(self.Alphabet)</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> for i in gap_indices:</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;">- valid_indices -= self._data == i</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ valid_indices ^= self._data == i</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> result = compress(valid_indices, self._data)</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> return self.__class__(result, Info=self.Info)</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> </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;">--- a/cogent/maths/distance_transform.py</span></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;">+++ b/cogent/maths/distance_transform.py</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="p">@@ -670,9 +670,9 @@</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"> return zeros((0,0),'d')</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> dists = zeros((numrows,numrows),'d')</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> for i in range(numrows):</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;">- r1 = datamtx[i] # cache here</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ r1 = datamtx[i].astype(dists.dtype) # cache here</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"> for j in range(i):</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- dists[i,j] = dists[j,i] = sum(abs(r1 - datamtx[j]))</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;">+ dists[i,j] = dists[j,i] = sum(abs(r1 - datamtx[j].astype(dists.dtype)))</span></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"> return dists</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"> </span></pre>
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<li id="de301967d761430006053b4513591cb30270b14f">
<a href="https://salsa.debian.org/med-team/python-cogent/compare/627ed619306bc8c8031f85bbc2a233f2628a7639...c851297cf6a3e328eaf0228a2b5d9a9e6481f13f#de301967d761430006053b4513591cb30270b14f"><strong>debian/patches/parsinsert_not_in_caps.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Tim Booth <tbooth@ceh.ac.uk></span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Fri, 25 Apr 2014 17:27:42 +0100</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Description: make script compatible with spelling of Debian's</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> parsinsert package</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">--- a/cogent/app/parsinsert.py</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/cogent/app/parsinsert.py</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">@@ -28,7 +28,7 @@</span> from StringIO import StringIO</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> class ParsInsert(CommandLineApplication):</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> """ParsInsert application Controller"""</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> </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;">- _command = 'ParsInsert'</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;">+ _command = 'parsinsert'</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> _input_handler = '_input_as_multiline_string'</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> _parameters = {</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> # read mask from this file</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;">--- a/tests/test_app/test_parsinsert.py</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/test_app/test_parsinsert.py</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="p">@@ -60,7 +60,7 @@</span> class ParsInsertTests(TestCase):</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"> app = ParsInsert()</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"> self.assertEqual(app.BaseCommand, \</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;">- ''.join(['cd "',getcwd(),'/"; ','ParsInsert']))</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ''.join(['cd "',getcwd(),'/"; ','parsinsert']))</span></span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> def test_change_working_dir(self):</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"> """Change working dir"""</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="p">@@ -68,7 +68,7 @@</span> class ParsInsertTests(TestCase):</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> app = ParsInsert(WorkingDir='/tmp/ParsInsertTest')</span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> self.assertEqual(app.BaseCommand, \</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"> ''.join(['cd "','/tmp/ParsInsertTest',\</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- '/"; ','ParsInsert']))</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;">+ '/"; ','parsinsert']))</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"> rmtree('/tmp/ParsInsertTest')</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"> </span>
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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/tests/alltests.py</span></span>
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38
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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/tests/alltests.py</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"><span class="p">@@ -232,7 +232,7 @@</span> def suite():</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"> ('mothur', 'test_mothur'),</span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"> ('muscle', 'test_muscle_v38'),</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"> ('msms', 'test_msms'),</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ('ParsInsert', 'test_parsinsert'),</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ('parsinsert', 'test_parsinsert'),</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"> ('pplacer', 'test_pplacer'),</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"> ('rdp_classifier-2.2.jar', 'test_rdp_classifier'),</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"> ('rdp_classifier-2.0.jar', 'test_rdp_classifier20'),</span></pre>
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<a href="https://salsa.debian.org/med-team/python-cogent/compare/627ed619306bc8c8031f85bbc2a233f2628a7639...c851297cf6a3e328eaf0228a2b5d9a9e6481f13f#b46d29336084baa469c9a38cc2012f37c6a81b88"><strong>debian/patches/privacy.patch</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Tue, 05 Jun 2018 21:47:29 +0200</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Description: Avoid insertion of Google phone home code</span></span>
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4
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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">--- a/doc/templates/layout.html</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/doc/templates/layout.html</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -1,10 +1,5 @@</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> {% extends "!layout.html" %}</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 class="gd" style="color: #000; background-color: #fdd;">-{% block extrahead %} </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;">-<script type="text/javascript" src="http://www.google.com/jsapi?key=ABQIAAAAbW_pA971hrPgosv-Msv7hRQZ4X-jPDmWcshBrz2j7-fJvuUABRTGWmdiw2G89JpgztGlFGG8hDxRAw"></script>\</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;">-<script type="text/javascript" src="{{ pathto("_static/google_feed.js",1)}}"></script></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;">-{% endblock %}</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;">-</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> {% block sidebartoc %}</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> <div class="news"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> <table id="feed"><tr><td><h3><a href="http://pycogent.wordpress.com/">PyCogent News and Announcements</a></h3></td></span></pre>
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<li id="461c8e5572730bd4125e5ab1bc91f8044d4262ea">
<a href="https://salsa.debian.org/med-team/python-cogent/compare/627ed619306bc8c8031f85bbc2a233f2628a7639...c851297cf6a3e328eaf0228a2b5d9a9e6481f13f#461c8e5572730bd4125e5ab1bc91f8044d4262ea"><strong>debian/patches/raxml_unsupported_version.patch</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Thu, 21 May 2015 08:47:01 +0200</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Description: The test is checking for an old version of raxml</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> for no good reason</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">--- a/tests/test_app/test_raxml_v730.py</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/test_app/test_raxml_v730.py</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">@@ -43,7 +43,8 @@</span> class GenericRaxml(TestCase):</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> version_string = stdout.strip().split(' ')[4].strip()</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> try:</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> version = tuple(map(int,version_string.split('.')))</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- pass_test = version == acceptable_version</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# Debian has later versions than 7.3.0 and checking only a fixed version makes no sense at all</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;">+# pass_test = version == acceptable_version</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> except ValueError:</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> pass_test = False</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> version_string = stdout</span></pre>
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<li id="53a366e6fd78b87be2ab8cc6c261fc063f344a7d">
<a href="https://salsa.debian.org/med-team/python-cogent/compare/627ed619306bc8c8031f85bbc2a233f2628a7639...c851297cf6a3e328eaf0228a2b5d9a9e6481f13f#53a366e6fd78b87be2ab8cc6c261fc063f344a7d"><strong>debian/patches/rdp_classifier.patch</strong>
deleted
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Wed, 14 Sep 2016 21:48:35 +0200</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Description: Try to support rdp_classifier (but failed - no idea why)</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">--- a/cogent/app/rdp_classifier.py</span>
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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/cogent/app/rdp_classifier.py</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -49,7 +49,7 @@</span> class RdpClassifier(CommandLineApplicati</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> '-training-data'.</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> """</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> _input_handler = '_input_as_lines'</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- _command = "rdp_classifier-2.2.jar"</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;">+ _command = "/usr/share/java/rdp_classifier.jar"</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> _options = {</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> # output file name for classification assignment</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> '-o': ValuedParameter('-', Name='o', Delimiter=' ', IsPath=True),</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/test_app/test_rdp_classifier.py</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;">+++ b/tests/test_app/test_rdp_classifier.py</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="p">@@ -30,7 +30,7 @@</span> class RdpClassifierTests(TestCase):</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> if 'RDP_JAR_PATH' in environ:</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> self.user_rdp_jar_path = environ['RDP_JAR_PATH']</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> else:</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;">- self.user_rdp_jar_path = 'rdp_classifier-2.2.jar'</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;">+ self.user_rdp_jar_path = '/usr/share/java/rdp_classifier.jar'</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> self.output_file = tempfile.NamedTemporaryFile()</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> def test_default_java_vm_parameters(self):</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;">--- a/tests/test_app/test_rdp_classifier20.py</span></span>
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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/test_app/test_rdp_classifier20.py</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="p">@@ -29,7 +29,7 @@</span> class RdpClassifier20Tests(TestCase):</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> if 'RDP_JAR_PATH' in environ:</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"> self.user_rdp_jar_path = environ['RDP_JAR_PATH']</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.user_rdp_jar_path = 'rdp_classifier-2.0.jar'</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.user_rdp_jar_path = '/usr/share/java/rdp_classifier.jar'</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"> def test_default_java_vm_parameters(self):</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"> """RdpClassifier should store default arguments to Java VM."""</span></pre>
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<a href="https://salsa.debian.org/med-team/python-cogent/compare/627ed619306bc8c8031f85bbc2a233f2628a7639...c851297cf6a3e328eaf0228a2b5d9a9e6481f13f#feb5daf39635ac768fa3a18ca6bded0230a2e6f8"><strong>debian/patches/skip_weak_tests.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Description: Skip some tests that do not create reproducible results at package</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"> build time</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: Wed, 30 Nov 2016 07:33:20 +0100</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/846078</span></span>
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6
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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">--- a/tests/test_struct/test_asa.py</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/tests/test_struct/test_asa.py</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="p">@@ -142,21 +142,6 @@</span> class asaTest(TestCase):</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> x = residues[('2E12', 0, 'B', ('GLU', 77, ' '))].xtra.values()</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> self.assertTrue(x[0] != x[1])</span>
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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="gd" style="color: #000; background-color: #fdd;">- def test_uc2(self):</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;">- self.input_file = os.path.join('data', '1LJO.pdb')</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;">- self.input_structure = PDBParser(open(self.input_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;">- asa.asa_xtra(self.input_structure, symmetry_mode='uc', xtra_key='ASA_XTAL')</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- asa.asa_xtra(self.input_structure)</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;">- self.input_structure.propagateData(sum, 'A', 'ASA', xtra=True)</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;">- self.input_structure.propagateData(sum, 'A', 'ASA_XTAL', xtra=True)</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;">- residues = einput(self.input_structure, 'R')</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;">- r1 = residues[('1LJO', 0, 'A', ('ARG', 65, ' '))]</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;">- r2 = residues[('1LJO', 0, 'A', ('ASN', 46, ' '))]</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.assertFloatEqual(r1.xtra.values(),</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;">- [128.94081270529105, 22.807700865674093])</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;">- self.assertFloatEqual(r2.xtra.values(),</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;">- [115.35738419425566, 115.35738419425566])</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;">-</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"> def test_crystal(self):</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> """compares asa within unit cell."""</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> self.input_file = os.path.join('data', '2E12.pdb')</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/test_maths/test_optimisers.py</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/test_maths/test_optimisers.py</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="p">@@ -80,13 +80,6 @@</span> class OptimiserTestCase(TestCase):</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"> # """optimiser warning if max_evaluations exceeded"""</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"> # self._test_optimisation(max_evaluations=5, limit_action='warn')</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def test_get_max_eval_count(self):</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- """return the evaluation count from optimisation"""</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- f, last, evals = MakeF()</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- x, e = quiet(maximise, f, xinit=[1.0], bounds=([-10,10]),</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return_eval_count=True)</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(e > 500)</span></span>
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<pre style="margin: 0;">-<span id="LC43" 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="LC44" class="line" lang="diff"> def test_checkpointing(self):</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"> filename = 'checkpoint.tmp.pickle'</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"> if os.path.exists(filename):</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/test_seqsim/test_tree.py</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/test_seqsim/test_tree.py</span></span>
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49
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="p">@@ -718,21 +718,6 @@</span> class OldPhyloNodeTests(TestCase):</span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"> result = [i.Q for i in t.traverse(self_after=True)]</span>
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51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"> self.assertEqual(result, ['c','b','c','c','c','a','a','a','c'])</span>
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52
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"> </span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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54
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def test_assignP(self):</span></span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- """RangeNode assignP should work when Qs set."""</span></span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- t = self.t1</span></span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in t.traverse(self_before=True):</span></span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- i.Length = random() * 0.5 #range 0 to 0.5</span></span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- t.Q = Rates.random(DnaPairs)</span></span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- t.assignQ()</span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- t.assignP()</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;">- t.assignIds()</span></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for node in t.traverse(self_after=True):</span></span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if node.Parent is not None:</span></span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertFloatEqual(average(1-diag(node.P._data), axis=0), \</span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- node.Length)</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"> def test_assignLength(self):</span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"> """RangeNode assignLength should set branch length"""</span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"> t = self.t1</span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/test_seqsim/test_sequence_generators.py</span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/test_seqsim/test_sequence_generators.py</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"><span class="p">@@ -465,45 +465,6 @@</span> class ConstantRegionTests(TestCase):</span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"> self.assertEqual(str(r.Current), 'ACGUUCGA')</span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="diff"> self.assertEqual(len(r), len('ACGUUCGA'))</span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="diff"> </span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-class UnpairedRegionTests(TestCase):</span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- """Tests of unpaired region: should fill in w/ single-base frequencies."""</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def test_init(self):</span></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- """Unpaired region should generate right freqs, even after change"""</span></span>
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<td class="diff-line-num old old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- freqs = Freqs({'C':10,'U':1, 'A':0})</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- r = UnpairedRegion('NN', freqs)</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- seq = r.Current</span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- assert seq[0] in 'CU'</span></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- assert seq[1] in 'CU'</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(len(seq), 2)</span></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fd = []</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in range(1000):</span></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- r.refresh()</span></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fd.append(str(seq))</span></span>
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<td class="diff-line-num old old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fd = Freqs(''.join(fd))</span></span>
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<td class="diff-line-num old old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<td class="diff-line-num old old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- observed = [fd['C'], fd['U']]</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- expected = [1800, 200]</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertSimilarFreqs(observed, expected)</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(fd['U'] + fd['C'], 2000)</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
</pre>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- freqs2 = Freqs({'A':5, 'U':5})</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- r.Composition = freqs2</span></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- r.Template = 'NNN' #note that changing the Template changes seq ref</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- seq = r.Current</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(len(seq), 3)</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- assert seq[0] in 'AU'</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- assert seq[1] in 'AU'</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- assert seq[2] in 'AU'</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fd = []</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in range(1000):</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- r.refresh()</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fd.append(str(seq))</span></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fd = Freqs(''.join(fd))</span></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- observed = [fd['A'], fd['U']]</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- expected = [1500, 1500]</span></span>
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113
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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.assertSimilarFreqs(observed, expected)</span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(fd['A'] + fd['U'], 3000)</span></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="diff"> class ShuffledRegionTests(TestCase):</span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="diff"> """Shuffled region should randomize string"""</span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="diff"> def test_init(self):</span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/test_cluster/test_nmds.py</span></span>
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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/test_cluster/test_nmds.py</span></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="diff"><span class="p">@@ -43,59 +43,6 @@</span> class NMDSTests(TestCase):</span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="diff"> self.assertEqual(size(pts, 0), 4)</span>
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<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
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="diff"> self.assertEqual(size(pts, 1), 2)</span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="diff"> </span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def test_2(self):</span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- """l19 data should give stress below .13"""</span></span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ptmtx = array(</span></span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [[7,1,0,0,0,0,0,0,0],</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [4,2,0,0,0,1,0,0,0],</span></span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [2,4,0,0,0,1,0,0,0],</span></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [1,7,0,0,0,0,0,0,0],</span></span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [0,8,0,0,0,0,0,0,0],</span></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [0,7,1,0,0,0,0,0,0],#idx 5</span></span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [0,4,2,0,0,0,2,0,0],</span></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [0,2,4,0,0,0,1,0,0],</span></span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [0,1,7,0,0,0,0,0,0],</span></span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [0,0,8,0,0,0,0,0,0],</span></span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [0,0,7,1,0,0,0,0,0],#idx 10</span></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [0,0,4,2,0,0,0,3,0],</span></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [0,0,2,4,0,0,0,1,0],</span></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [0,0,1,7,0,0,0,0,0],</span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [0,0,0,8,0,0,0,0,0],</span></span>
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143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [0,0,0,7,1,0,0,0,0],#idx 15</span></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [0,0,0,4,2,0,0,0,4],</span></span>
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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="gd" style="color: #000; background-color: #fdd;">- [0,0,0,2,4,0,0,0,1],</span></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [0,0,0,1,7,0,0,0,0]], 'float')</span></span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- distmtx = dist_euclidean(ptmtx)</span></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- nm = NMDS(distmtx, verbosity=0)</span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertLessThan(nm.getStress(), .13)</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def test_3(self):</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- """l19 data should give stress below .13 in multi-D"""</span></span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ptmtx = array(</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [[7,1,0,0,0,0,0,0,0],</span></span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [4,2,0,0,0,1,0,0,0],</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [2,4,0,0,0,1,0,0,0],</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [1,7,0,0,0,0,0,0,0],</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [0,8,0,0,0,0,0,0,0],</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [0,7,1,0,0,0,0,0,0],#idx 5</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [0,4,2,0,0,0,2,0,0],</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [0,2,4,0,0,0,1,0,0],</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [0,1,7,0,0,0,0,0,0],</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [0,0,8,0,0,0,0,0,0],</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [0,0,7,1,0,0,0,0,0],#idx 10</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [0,0,4,2,0,0,0,3,0],</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [0,0,2,4,0,0,0,1,0],</span></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [0,0,1,7,0,0,0,0,0],</span></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [0,0,0,8,0,0,0,0,0],</span></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [0,0,0,7,1,0,0,0,0],#idx 15</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [0,0,0,4,2,0,0,0,4],</span></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [0,0,0,2,4,0,0,0,1],</span></span>
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [0,0,0,1,7,0,0,0,0]], 'float')</span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- distmtx = dist_euclidean(ptmtx)</span></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for dim in range(3,18):</span></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- nm = NMDS(distmtx, verbosity=0, dimension=dim)</span></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertLessThan(nm.getStress(), .13)</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="diff"> def test_metaNMDS(self):</span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="diff"> """l19 data should give stress below .13"""</span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="diff"> ptmtx = array(</span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/test_align/test_weights/test_methods.py</span></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/test_align/test_weights/test_methods.py</span></span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="diff"><span class="p">@@ -177,48 +177,6 @@</span> class VoronoiTests(GeneralTests):</span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="diff"> if x > 0:</span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="diff"> self.assertNotEqual(results[x], results[x-1])</span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="diff"> </span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def test_mVOR(self):</span></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- """mVOR: should return weights closer to the 'True' weights"""</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #err=5e-2 #original error value</span></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # Raised the error value to prevent occasional failure of the test.</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # The mVOR method takes a sample from a distribution and the outcome</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # will depend on this sample. Every now and then, one of the weights</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # was more than 0.05 away from the expected weight. Raised the </span></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # allowed error value to prevent that. To use the method on real</span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # data, a larger sample should be taken (e.g. 10000?), but increasing</span></span>
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # the sample size here would make the test too slow.</span></span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- err=0.075</span></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- aln3_exp = {'seq1':.25, 'seq2':.25, 'seq3':.5}</span></span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- aln4_exp = {'seq1':.1667, 'seq2':.1667,'seq3':.1667,'seq4':.1667,\</span></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 'seq5':.3333} </span></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- aln6_exp = dict(zip(map(str,[1,2,3,4,5,6,7,8,9,10]),</span></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [0.09021,0.08039,0.113560,0.10399,0.092370,0.097130,</span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 0.09198,0.09538,0.10927,0.12572]))</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # the following assertSimilarMeans statements were added to replace </span></span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # stochastic assertFloatEqualAbs calls below</span></span>
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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertSimilarMeans(mVOR(self.aln3,order="ABC").values(),</span></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- aln3_exp.values())</span></span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertSimilarMeans(mVOR(self.aln4,order="ABC").values(),</span></span>
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210
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- aln4_exp.values())</span></span>
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211
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertSimilarMeans(mVOR(self.aln6,order=DNA_ORDER,n=3000)\</span></span>
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212
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- .values(), aln6_exp.values())</span></span>
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213
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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214
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #self.assertFloatEqualAbs(mVOR(self.aln3,order="ABC").values(),\</span></span>
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215
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # aln3_exp.values(),eps=err)</span></span>
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216
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #self.assertFloatEqualAbs(mVOR(self.aln4,order="ABC").values(),\</span></span>
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217
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # aln4_exp.values(),eps=err)</span></span>
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218
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #self.assertFloatEqualAbs(mVOR(self.aln6,order=DNA_ORDER,n=3000)\</span></span>
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219
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # .values(), aln6_exp.values(),eps=err)</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;">- #the results vary with runs, because the sample of random profiles</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;">- #is different each time</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;">- results = []</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;">- for x in range(5):</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;">- results.append(mVOR(self.aln4,order="ABC"))</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;">- if x > 0:</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;">- self.assertNotEqual(results[x], results[x-1])</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;">-</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="diff"> class PositionBasedTests(GeneralTests):</span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="diff"> """Contains tests for PB (=position-based) method"""</span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="diff"> </span></pre>
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<li id="198d5c00e2fa0be2217b15cd9a002e37bdf8a532">
<a href="https://salsa.debian.org/med-team/python-cogent/compare/627ed619306bc8c8031f85bbc2a233f2628a7639...c851297cf6a3e328eaf0228a2b5d9a9e6481f13f#198d5c00e2fa0be2217b15cd9a002e37bdf8a532"><strong>debian/patches/sphinx.ext.pngmath.patch</strong>
deleted
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Description: Enable building with sphinx1.8</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/918829</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Last-Changed: Thu, 10 Jan 2019 14:56:55 +0100</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">--- a/doc/conf.py</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/doc/conf.py</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">@@ -22,7 +22,7 @@</span> import sys, os</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> </span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> # Add any Sphinx extension module names here, as strings. They can be extensions</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-extensions = ['sphinx.ext.todo', 'sphinx.ext.doctest', 'sphinx.ext.pngmath']</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+extensions = ['sphinx.ext.todo', 'sphinx.ext.doctest', 'sphinx.ext.imgmath']</span></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"> # todo_include_todos=True # to expose the TODOs, uncomment this line</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/python-cogent/compare/627ed619306bc8c8031f85bbc2a233f2628a7639...c851297cf6a3e328eaf0228a2b5d9a9e6481f13f#0bba138a5eaaa1a94aa68148bc14ebf3112f1e0d"><strong>debian/patches/usr_bin_ls.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Fri, 16 Jun 2017 13:30:22 +0200</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Description: ls will be moved from /bin/ls to /usr/bin/ls - lets skip</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> this test which does not make real sense anyway.</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">--- a/tests/test_util/test_misc.py</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/test_util/test_misc.py</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">@@ -1626,7 +1626,7 @@</span> class reverse_complementTests(TestCase):</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"> def test_app_path(self):</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> """app_path should return correct paths"""</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;">- self.assertEqual(app_path('ls'), '/bin/ls')</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;">+ # self.assertEqual(app_path('ls'), '/usr/bin/ls')</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> self.assertEqual(app_path('lsxxyyx'), False)</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"> class CommandLineParserTests(TestCase):</span></pre>
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<a href="https://salsa.debian.org/med-team/python-cogent/compare/627ed619306bc8c8031f85bbc2a233f2628a7639...c851297cf6a3e328eaf0228a2b5d9a9e6481f13f#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,46 +8,12 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: #008080;">PYBUILD_BEFORE_TEST</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-r</span> <span class="o" style="font-weight: 600;">{</span><span class="nb" style="color: #0086b3;">dir</span><span class="o" style="font-weight: 600;">}</span>/tests/data <span class="o" style="font-weight: 600;">{</span>build_dir<span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="make"><span class="nv" style="color: #008080;">BUILDARCH</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> dpkg-architecture <span class="nt" style="color: #000080;">-qDEB_BUILD_ARCH</span><span class="nf" style="color: #900; font-weight: 600;">)</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="make"></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="make"><span class="nv" style="color: #008080;">FAILED_TESTS</span> <span class="o" style="font-weight: 600;">:=</span> test_infernal <span class="se" style="color: #d14;">\</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="make"> test_mothur <span class="se" style="color: #d14;">\</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="make"> test_parsinsert <span class="se" style="color: #d14;">\</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="make"> test_raxml_v730 <span class="se" style="color: #d14;">\</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="make"> test_rtax <span class="se" style="color: #d14;">\</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="make"> test_clustalw <span class="se" style="color: #d14;">\</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="make"> test_mafft <span class="se" style="color: #d14;">\</span></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="make"> test_unifrac <span class="se" style="color: #d14;">\</span></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="make"> test_seqsim.test_analysis <span class="se" style="color: #d14;">\</span></span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="make"> test_seqsim.test_usage</span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="make"></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="make"><span class="nv" style="color: #008080;">ONLYAMD64_TESTS</span> <span class="o" style="font-weight: 600;">:=</span> test_bwa</span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="make"></span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># There are tests failing on certain architectures</span></span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># We need to decide between not shipping cogent there or hiding</span></span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># our eyes from these failures. See README.source for further</span></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># explanation.</span></span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="make"><span class="nv" style="color: #008080;">FAIL_ON_ARMEL_TESTS</span> <span class="o" style="font-weight: 600;">:=</span> test_core.test_profile</span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="make"></span>
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32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="make"></span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="make"><span class="nv" style="color: #008080;">FAIL_ON_PPC64_MIPS64EL</span> <span class="o" style="font-weight: 600;">:=</span> test_core.test_tree</span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="make"></span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="make"><span class="nv" style="color: #008080;">FAIL_ON_I386_TESTS</span> <span class="o" style="font-weight: 600;">:=</span> test_maths.test_stats.test_test <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="make"> test_seqsim.test_sequence_generators</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="make"><span class="nv" style="color: #008080;">FAIL_ON_PPC64_TESTS</span> <span class="o" style="font-weight: 600;">:=</span> test_app.test_util</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="make"><span class="nv" style="color: #008080;">FAIL_ON_S390X_TESTS</span> <span class="o" style="font-weight: 600;">:=</span> test_maths.test_optimisers <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="make"> test_format.test_pdb_color.PdbColorTests</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="make"><span class="nv" style="color: #008080;">FAIL_ON_MIPS_TESTS</span> <span class="o" style="font-weight: 600;">:=</span> test_seqsim.test_sequence_generators</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: #008080;">PYBUILD_NAME</span><span class="o" style="font-weight: 600;">=</span>cogent3</span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="make"><span class="k" style="font-weight: 600;">include</span><span class="sx" style="color: #d14;"> /usr/share/dpkg/default.mk</span></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="make"><span class="nl">%</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="make"> dh <span class="nv" style="color: #008080;">$@</span> <span class="nt" style="color: #000080;">--with</span> python3<span class="idiff left right">,sphinxdoc</span> <span class="nt" style="color: #000080;">--buildsystem</span><span class="o" style="font-weight: 600;">=</span>pybuild</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="make"> dh <span class="nv" style="color: #008080;">$@</span> <span class="nt" style="color: #000080;">--with</span> python3 <span class="nt" style="color: #000080;">--buildsystem</span><span class="o" style="font-weight: 600;">=</span>pybuild</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="make"><span class="nl">override_dh_clean</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="make"> <span class="c" style="color: #998; font-style: italic;">#These files are rebuilt on-the-fly</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -58,7 +24,7 @@ override_dh_clean:</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> doc/_build</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="make"> dh_clean</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="make"><span class="nl"><span class="idiff left right">__</span>override_dh_auto_build</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="make"><span class="nl">override_dh_auto_build</span><span class="o" style="font-weight: 600;">:</span></span>
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62
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="make"> dh_auto_build</span>
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63
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="make"> <span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-x</span><span class="p">;</span> <span class="nb" style="color: #0086b3;">cd </span>doc<span class="p">;</span> <span class="nv" style="color: #008080;">PYTHONPATH</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$(CURDIR)</span> <span class="nv" style="color: #008080;">http_proxy</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'127.0.0.1:9'</span> <span class="nv" style="color: #008080;">$(MAKE)</span> html</span>
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64
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="make"> <span class="c" style="color: #998; font-style: italic;"># remove superfluous files and dirs</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="79" 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="45" 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">@@ -79,38 +45,3 @@ override_dh_installdocs:</td>
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79
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45
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="make"> dh_installdocs</span>
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80
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<td class="diff-line-num new_line" data-linenumber="46" 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">
46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> debian/<span class="nv" style="color: #008080;">$(DEB_SOURCE)</span>/usr/share/doc/<span class="nv" style="color: #008080;">$(DEB_SOURCE)</span>/html/_sources</span>
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81
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="make"> find debian <span class="nt" style="color: #000080;">-name</span> doctrees <span class="nt" style="color: #000080;">-type</span> d | xargs <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span></span></pre>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="make"></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="make"><span class="nl">___override_dh_auto_test</span><span class="o" style="font-weight: 600;">:</span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">(,$(filter nocheck, $(DEB_BUILD_OPTIONS)))</span></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> tests/alltests.py tests/alltests.py~</span>
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<td class="diff-line-num old old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="make"> <span class="c" style="color: #998; font-style: italic;"># exclude tests known to fail</span></span>
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<td class="diff-line-num old old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="make"> <span class="k" style="font-weight: 600;">for </span>tst <span class="k" style="font-weight: 600;">in</span> <span class="nv" style="color: #008080;">$(FAILED_TESTS)</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">do </span><span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-i</span> <span class="s2" style="color: #d14;">"/</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="nv" style="color: #008080;">${tst}</span><span class="s2" style="color: #d14;">/d"</span> tests/alltests.py <span class="p">;</span> <span class="k" style="font-weight: 600;">done</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># avoid amd64 only tools on other architectures</span></span>
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<td class="diff-line-num old old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">($(BUILDARCH),amd64)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
90
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<td class="diff-line-num new_line old" 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="LC90" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">echo</span> <span class="s2" style="color: #d14;">"bwa can be tested on amd64 arch"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="make"><span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num old old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
92
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<td class="diff-line-num new_line old" 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="LC92" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">for</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">tst</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">in</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(ONLYAMD64_TESTS)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">;</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">do</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">sed</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-i</span> <span class="s2" style="color: #d14;">"/$${tst}/d"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">tests/alltests.py</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">;</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">done</span></span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">($(BUILDARCH),$(filter $(BUILDARCH), mips64el ppc64el ppc64))</span></span>
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<td class="diff-line-num old old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
94
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<td class="diff-line-num new_line old" 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="LC94" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">for</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">tst</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">in</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(FAIL_ON_PPC64_MIPS64EL)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">;</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">do</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">sed</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-i</span> <span class="s2" style="color: #d14;">"/$${tst}/d"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">tests/alltests.py</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">;</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">done</span></span>
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<td class="diff-line-num old old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">($(BUILDARCH),armel)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
97
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<td class="diff-line-num new_line old" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">for</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">tst</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">in</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(FAIL_ON_ARMEL_TESTS)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">;</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">do</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">sed</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-i</span> <span class="s2" style="color: #d14;">"/$${tst}/d"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">tests/alltests.py</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">;</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">done</span></span>
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<td class="diff-line-num old old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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<td class="diff-line-num old old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
99
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<td class="diff-line-num new_line old" 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="LC99" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">($(BUILDARCH),ppc64)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
100
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<td class="diff-line-num new_line old" 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="LC100" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">for</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">tst</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">in</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(FAIL_ON_PPC64_TESTS)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">;</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">do</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">sed</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-i</span> <span class="s2" style="color: #d14;">"/$${tst}/d"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">tests/alltests.py</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">;</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">done</span></span>
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101
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<td class="diff-line-num new_line old" 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="LC101" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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<td class="diff-line-num old old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
102
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<td class="diff-line-num new_line old" 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="LC102" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">($(BUILDARCH),s390x)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
103
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<td class="diff-line-num new_line old" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">for</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">tst</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">in</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(FAIL_ON_S390X_TESTS)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">;</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">do</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">sed</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-i</span> <span class="s2" style="color: #d14;">"/$${tst}/d"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">tests/alltests.py</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">;</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">done</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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<td class="diff-line-num old old_line" 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">
105
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<td class="diff-line-num new_line old" 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="LC105" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">($(BUILDARCH),mips)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
106
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<td class="diff-line-num new_line old" 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="LC106" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">for</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">tst</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">in</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(FAIL_ON_MIPS_TESTS)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">;</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">do</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">sed</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-i</span> <span class="s2" style="color: #d14;">"/$${tst}/d"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">tests/alltests.py</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">;</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">done</span></span>
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107
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<td class="diff-line-num new_line old" 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="LC107" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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<td class="diff-line-num old old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
108
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<td class="diff-line-num new_line old" 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="LC108" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">($(BUILDARCH),$(filter $(BUILDARCH), i386 kfreebsd-i386))</span></span>
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<td class="diff-line-num old old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
109
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<td class="diff-line-num new_line old" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">for</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">tst</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">in</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(FAIL_ON_I386_TESTS)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">;</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">do</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">sed</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-i</span> <span class="s2" style="color: #d14;">"/$${tst}/d"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">tests/alltests.py</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">;</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">done</span></span>
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110
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<td class="diff-line-num new_line old" 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="LC110" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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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">
111
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<td class="diff-line-num new_line old" 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="LC111" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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<td class="diff-line-num old old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
112
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<td class="diff-line-num new_line old" 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="LC112" class="line" lang="make"> <span class="nv" style="color: #008080;">BLASTMAT</span><span class="o" style="font-weight: 600;">=</span>/usr/share/ncbi/data/ <span class="nv" style="color: #008080;">RDP_JAR_PATH</span><span class="o" style="font-weight: 600;">=</span>/usr/share/java/rdp_classifier.jar <span class="nv" style="color: #008080;">$(CURDIR)</span>/run_tests <span class="nt" style="color: #000080;">-v</span> <span class="c" style="color: #998; font-style: italic;"># --debug</span></span>
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<td class="diff-line-num old old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
113
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<td class="diff-line-num new_line old" 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="LC113" class="line" lang="make"> <span class="c" style="color: #998; font-style: italic;"># restore original tests file</span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">mv</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">tests/alltests.py~</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">tests/alltests.py</span></span>
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<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
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">find</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">tests</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-name</span> <span class="s2" style="color: #d14;">"*.pyc"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-delete</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span></pre>
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