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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/conservation-code">Debian Med / conservation-code</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/conservation-code/commit/24188a3d15453d55d04caf3288fd2b4373a62cff">24188a3d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-15T14:56:32Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Rename test dir in autopktest from ADTTMP to AUTOPKGTEST_TMP
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/conservation-code/commit/30e20fe1f08ec7edff13b0738723e68d7cc8542d">30e20fe1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-15T14:59:52Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use 2to3 to port from Python2 to Python3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/conservation-code/commit/2af1513a649b485fb6ce3181a240c678e114a4ad">2af1513a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-15T15:00:08Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/conservation-code/commit/80774d294f8950c9fedbdfa5ec742507754a0af2">80774d29</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-15T15:00:12Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.4.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/conservation-code/commit/7b46d429b17c4f3155c5a1623fac3182d2f4f962">7b46d429</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-15T15:00:13Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">R-U: Trailing whitespace in debian/changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/conservation-code/commit/b739ec2be69ccfc3e24cc0b8644f305f5290b45e">b739ec2b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-15T15:14:00Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Do not parse d/changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/conservation-code/commit/305f4b2f00da91e58a305068e274524f7c4a81cf">305f4b2f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-15T15:14:00Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Trim trailing whitespace.
Fixes lintian: file-contains-trailing-whitespace
See https://lintian.debian.org/tags/file-contains-trailing-whitespace.html for more details.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/conservation-code/commit/c4bddda20e8c47f6cfeabcc9592ddc4abb950385">c4bddda2</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-15T15:14:08Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use secure URI in Homepage field.
Fixes lintian: homepage-field-uses-insecure-uri
See https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html for more details.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/conservation-code/commit/de30ec55a1a0dd1ae5bd52d98474145a94ad9d15">de30ec55</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-15T15:14:30Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove obsolete fields Contact, Name from debian/upstream/metadata.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/conservation-code/commit/a386694488ead6088d7a6211a89d4c821e7a1c2c">a3866944</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-15T15:14:30Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove unnecessary get-orig-source-target.
Fixes lintian: debian-rules-contains-unnecessary-get-orig-source-target
See https://lintian.debian.org/tags/debian-rules-contains-unnecessary-get-orig-source-target.html for more details.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/conservation-code/commit/944a149e99d17932f55a83f9e0c53045aaca0d73">944a149e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-15T15:15:30Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Python3 in packaging
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/conservation-code/commit/ecb87e5dc1ee9c65015c668f01afd10cffc538b7">ecb87e5d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-15T15:23:55Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Replace tab by spaces since Python3 is picky about spacing errors
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/conservation-code/commit/f83e1fd4e55bf279d5ee76bf46a9451ca5522861">f83e1fd4</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-15T15:26:37Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>9 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="deleted-file">
−
debian/compat
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
<span class="new-file">
+
debian/patches/2to3.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#17d8869115f55e024a85a6d17443302815985358">
debian/tests/installation-test
</a>
</li>
<li class="file-stats">
<a href="#cdcfe09f6e63c35ce29bc1d25e7958efb82eef69">
debian/tests/non-default-params-test
</a>
</li>
<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/conservation-code/compare/b7176bea5f3d9c048e9f041adb86b26f376afa56...f83e1fd4e55bf279d5ee76bf46a9451ca5522861#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">conservation-code (20110309.0-8) unstable; urgency=medium</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Rename test dir in autopktest from ADTTMP to AUTOPKGTEST_TMP</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Use 2to3 to port from Python2 to Python3</span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Closes: #942925</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * debhelper-compat 12</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Standards-Version: 4.4.1</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Remove trailing whitespace in debian/changelog</span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Do not parse d/changelog</span>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Trim trailing whitespace.</span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * Use secure URI in Homepage field.</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Remove obsolete fields Contact, Name from debian/upstream/metadata.</span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * Remove unnecessary get-orig-source-target.</span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Sun, 15 Dec 2019 16:24:28 +0100</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">conservation-code (20110309.0-7) unstable; urgency=medium</span>
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2
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> * debhelper 11</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">@@ -25,10 +41,10 @@ conservation-code (20110309.0-5) unstable; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"> * upstream fix - to load identity matrix without error when no alignment</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"> matrix is found</span>
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27
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"> * add hardening</span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> * allow-stderr for testsuite to allow test pass instead of fail when matrix<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> * allow-stderr for testsuite to allow test pass instead of fail when matrix</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> file is not found</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"> * verbose output in test + check distributions usage</span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> * simplified debian/tests/non-default-params-test, but made more verbose<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> * simplified debian/tests/non-default-params-test, but made more verbose</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"> debian/README.test</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"> * cme fix dpkg-copyright</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/conservation-code/compare/b7176bea5f3d9c048e9f041adb86b26f376afa56...f83e1fd4e55bf279d5ee76bf46a9451ca5522861#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">11</span></pre>
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<a href="https://salsa.debian.org/med-team/conservation-code/compare/b7176bea5f3d9c048e9f041adb86b26f376afa56...f83e1fd4e55bf279d5ee76bf46a9451ca5522861#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -4,19 +4,19 @@ Uploaders: Laszlo Kajan <lkajan@rostlab.org>,</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right"> (>= 11~</span>),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right">-compat (= 12</span>),</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> dh-python,</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> python</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2</span>.1</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> python<span class="idiff left right">3</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4</span>.1</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/conservation-code</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/conservation-code.git</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">Homepage: http://compbio.cs.princeton.edu/conservation/</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Homepage: http<span class="idiff left right">s</span>://compbio.cs.princeton.edu/conservation/</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Package: conservation-code</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> ${python:Depends},</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> python-numpy</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> ${python<span class="idiff left right">3</span>:Depends},</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> python<span class="idiff left right">3</span>-numpy</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Enhances: concavity</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Description: protein sequence conservation scoring tool</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> This package provides score_conservation(1), a tool to score protein sequence</span>
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<li id="555c85016bd79aa8bbb523506af81b69d9c69534">
<a href="https://salsa.debian.org/med-team/conservation-code/compare/b7176bea5f3d9c048e9f041adb86b26f376afa56...f83e1fd4e55bf279d5ee76bf46a9451ca5522861#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Use 2to3 to port from Python2 to Python3</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/942925</span></span>
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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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: Sun, 15 Dec 2019 15:56:03 +0100</span></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/score_conservation.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/score_conservation.py</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></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>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> # score_conservation.py - Copyright Tony Capra 2007 - Last Update: 03/09/11</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">@@ -83,7 +83,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> ################################################################################</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;">-from __future__ import print_function</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;">+</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> import math, sys, getopt</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> import re</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> # numarray imported below</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="p">@@ -126,21 +126,21 @@</span> def weighted_freq_count_pseudocount(col,</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"> # if the weights do not match, use equal weight</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> if len(seq_weights) != len(col):</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;">- seq_weights = [1.] * len(col)</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;">+ seq_weights = [1.] * len(col)</span></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"> aa_num = 0</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> freq_counts = len(amino_acids)*[pc_amount] # in order defined by amino_acids</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"> for aa in amino_acids:</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;">- for j in range(len(col)):</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;">- if col[j] == aa:</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;">- freq_counts[aa_num] += 1 * seq_weights[j]</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;">+ for j in range(len(col)):</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if col[j] == aa:</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;">+ freq_counts[aa_num] += 1 * seq_weights[j]</span></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;">- aa_num += 1</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ aa_num += 1</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> freqsum = (sum(seq_weights) + len(amino_acids) * pc_amount)</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> for j in range(len(freq_counts)):</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;">- freq_counts[j] = freq_counts[j] / freqsum</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;">+ freq_counts[j] = freq_counts[j] / freqsum</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> return freq_counts</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="p">@@ -152,12 +152,12 @@</span> def weighted_gap_penalty(col, seq_weight</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> # if the weights do not match, use equal weight</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> if len(seq_weights) != len(col):</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;">- seq_weights = [1.] * len(col)</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ seq_weights = [1.] * len(col)</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> gap_sum = 0.</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> for i in range(len(col)):</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;">- if col[i] == '-':</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;">- gap_sum += seq_weights[i]</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if col[i] == '-':</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ gap_sum += seq_weights[i]</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> </span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> return 1 - (gap_sum / sum(seq_weights))</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> </span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="p">@@ -167,7 +167,7 @@</span> def gap_percentage(col):</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> num_gaps = 0.</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> </span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> for aa in col:</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;">- if aa == '-': num_gaps += 1</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;">+ if aa == '-': num_gaps += 1</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> </span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> return num_gaps / len(col)</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> </span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="p">@@ -187,8 +187,8 @@</span> def shannon_entropy(col, sim_matrix, bg_</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> </span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> h = 0. </span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> for i in range(len(fc)):</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;">- if fc[i] != 0:</span></span>
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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;">- h += fc[i] * math.log(fc[i])</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if fc[i] != 0:</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ h += fc[i] * math.log(fc[i])</span></span>
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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"> # h /= math.log(len(fc))</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> h /= math.log(min(len(fc), len(col)))</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="p">@@ -196,9 +196,9 @@</span> def shannon_entropy(col, sim_matrix, bg_</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> inf_score = 1 - (-1 * h)</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> </span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> if gap_penalty == 1: </span>
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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;">- return inf_score * weighted_gap_penalty(col, seq_weights)</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return inf_score * weighted_gap_penalty(col, seq_weights)</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> else: </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;">- return inf_score</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return inf_score</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> </span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> </span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> ################################################################################</span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="p">@@ -221,22 +221,22 @@</span> def property_entropy(col, sim_matrix, bg</span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> # sum the aa frequencies to get the property frequencies</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> prop_fc = [0.] * len(property_partition)</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> for p in range(len(property_partition)):</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;">- for aa in property_partition[p]:</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;">- prop_fc[p] += fc[aa_to_index[aa]]</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for aa in property_partition[p]:</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ prop_fc[p] += fc[aa_to_index[aa]]</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> </span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> h = 0. </span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> for i in range(len(prop_fc)):</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;">- if prop_fc[i] != 0:</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;">- h += prop_fc[i] * math.log(prop_fc[i])</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if prop_fc[i] != 0:</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ h += prop_fc[i] * math.log(prop_fc[i])</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> </span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> h /= math.log(min(len(property_partition), len(col)))</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> </span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> inf_score = 1 - (-1 * h)</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> </span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> if gap_penalty == 1: </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;">- return inf_score * weighted_gap_penalty(col, seq_weights)</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return inf_score * weighted_gap_penalty(col, seq_weights)</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> else: </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;">- return inf_score</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return inf_score</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> </span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"> </span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> ################################################################################</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="p">@@ -257,9 +257,9 @@</span> def property_relative_entropy(col, sim_m</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> </span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> prop_bg_freq = []</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> if len(bg_distr) == len(property_partition):</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;">- prop_bg_freq = bg_distr</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ prop_bg_freq = bg_distr</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> else:</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;">- prop_bg_freq = [0.248, 0.092, 0.114, 0.075, 0.132, 0.111, 0.161, 0.043, 0.024, 0.000] # from BL62</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ prop_bg_freq = [0.248, 0.092, 0.114, 0.075, 0.132, 0.111, 0.161, 0.043, 0.024, 0.000] # from BL62</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> </span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> #fc = weighted_freq_count_ignore_gaps(col, seq_weights)</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> fc = weighted_freq_count_pseudocount(col, seq_weights, PSEUDOCOUNT)</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="p">@@ -267,19 +267,19 @@</span> def property_relative_entropy(col, sim_m</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> # sum the aa frequencies to get the property frequencies</span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> prop_fc = [0.] * len(property_partition)</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> for p in range(len(property_partition)):</span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for aa in property_partition[p]:</span></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- prop_fc[p] += fc[aa_to_index[aa]]</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for aa in property_partition[p]:</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ prop_fc[p] += fc[aa_to_index[aa]]</span></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> d = 0. </span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> for i in range(len(prop_fc)):</span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if prop_fc[i] != 0 and prop_bg_freq[i] != 0:</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- d += prop_fc[i] * math.log(prop_fc[i] / prop_bg_freq[i], 2)</span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if prop_fc[i] != 0 and prop_bg_freq[i] != 0:</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ d += prop_fc[i] * math.log(prop_fc[i] / prop_bg_freq[i], 2)</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"> </span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> </span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> if gap_penalty == 1: </span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return d * weighted_gap_penalty(col, seq_weights)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return d * weighted_gap_penalty(col, seq_weights)</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> else: </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;">- return d</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return d</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"> </span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"> </span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> ################################################################################</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="p">@@ -293,14 +293,14 @@</span> def vn_entropy(col, sim_matrix, bg_distr</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> </span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> aa_counts = [0.] * 20</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"> for aa in col:</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;">- if aa != '-': aa_counts[aa_to_index[aa]] += 1</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if aa != '-': aa_counts[aa_to_index[aa]] += 1</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"> </span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"> dm_size = 0</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"> dm_aas = []</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"> for i in range(len(aa_counts)):</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;">- if aa_counts[i] != 0:</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;">- dm_aas.append(i)</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- dm_size += 1</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if aa_counts[i] != 0:</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ dm_aas.append(i)</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ dm_size += 1</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"> </span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"> if dm_size == 0: return 0.0</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"> </span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"><span class="p">@@ -308,31 +308,31 @@</span> def vn_entropy(col, sim_matrix, bg_distr</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"> col_i = 0</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> dm = zeros((dm_size, dm_size), Float32)</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> for i in range(dm_size):</span>
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<td class="diff-line-num new new_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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;">- row_i = dm_aas[i]</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 j in range(dm_size):</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;">- col_i = dm_aas[j]</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;">- dm[i][j] = aa_counts[row_i] * sim_matrix[row_i][col_i]</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ row_i = dm_aas[i]</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for j in range(dm_size):</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ col_i = dm_aas[j]</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ dm[i][j] = aa_counts[row_i] * sim_matrix[row_i][col_i]</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"> </span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"> ev = la.eigenvalues(dm).real</span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"> </span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"> temp = 0.</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"> for e in ev:</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;">- temp += e</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ temp += e</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"> </span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"> if temp != 0:</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;">- for i in range(len(ev)):</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;">- ev[i] = ev[i] / temp</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(len(ev)):</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ev[i] = ev[i] / temp</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"> </span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"> vne = 0.0</span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"> for e in ev:</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;">- if e > (10**-10):</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;">- vne -= e * math.log(e) / math.log(20)</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if e > (10**-10):</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ vne -= e * math.log(e) / math.log(20)</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"> </span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"> if gap_penalty == 1: </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;">- #return (1-vne) * weighted_gap_penalty(col, seq_weights)</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return (1-vne) * weighted_gap_penalty(col, [1.] * len(col))</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #return (1-vne) * weighted_gap_penalty(col, seq_weights)</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return (1-vne) * weighted_gap_penalty(col, [1.] * len(col))</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"> else: </span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return 1 - vne</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return 1 - vne</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"> </span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"> </span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"> ################################################################################</span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"><span class="p">@@ -350,25 +350,25 @@</span> def relative_entropy(col, sim_matix, bg_</span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"> # remove gap count</span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"> if len(distr) == 20: </span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- new_fc = fc[:-1]</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- s = sum(new_fc)</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in range(len(new_fc)):</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- new_fc[i] = new_fc[i] / s</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fc = new_fc</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ new_fc = fc[:-1]</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ s = sum(new_fc)</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(len(new_fc)):</span></span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ new_fc[i] = new_fc[i] / s</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fc = new_fc</span></span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"> </span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"> if len(fc) != len(distr): return -1</span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"> </span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"> d = 0.</span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"> for i in range(len(fc)):</span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if distr[i] != 0.0:</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- d += fc[i] * math.log(fc[i]/distr[i])</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if distr[i] != 0.0:</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ d += fc[i] * math.log(fc[i]/distr[i])</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"> </span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"> d /= math.log(len(fc))</span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"> </span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"> if gap_penalty == 1: </span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return d * weighted_gap_penalty(col, seq_weights)</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return d * weighted_gap_penalty(col, seq_weights)</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"> else: </span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return d</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return d</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"> </span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"> </span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"> </span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"><span class="p">@@ -386,36 +386,36 @@</span> def js_divergence(col, sim_matrix, bg_di</span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"> </span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"> # if background distrubtion lacks a gap count, remove fc gap count</span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"> if len(distr) == 20: </span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- new_fc = fc[:-1]</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- s = sum(new_fc)</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in range(len(new_fc)):</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- new_fc[i] = new_fc[i] / s</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fc = new_fc</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ new_fc = fc[:-1]</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ s = sum(new_fc)</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(len(new_fc)):</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ new_fc[i] = new_fc[i] / s</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fc = new_fc</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"> </span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"> if len(fc) != len(distr): return -1</span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"> </span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"> # make r distriubtion</span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"> r = []</span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"> for i in range(len(fc)):</span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- r.append(.5 * fc[i] + .5 * distr[i])</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ r.append(.5 * fc[i] + .5 * distr[i])</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"> </span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"> d = 0.</span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"> for i in range(len(fc)):</span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if r[i] != 0.0:</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if fc[i] == 0.0:</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- d += distr[i] * math.log(distr[i]/r[i], 2)</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- elif distr[i] == 0.0:</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- d += fc[i] * math.log(fc[i]/r[i], 2) </span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else:</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- d += fc[i] * math.log(fc[i]/r[i], 2) + distr[i] * math.log(distr[i]/r[i], 2)</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if r[i] != 0.0:</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if fc[i] == 0.0:</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ d += distr[i] * math.log(distr[i]/r[i], 2)</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ elif distr[i] == 0.0:</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ d += fc[i] * math.log(fc[i]/r[i], 2) </span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else:</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ d += fc[i] * math.log(fc[i]/r[i], 2) + distr[i] * math.log(distr[i]/r[i], 2)</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"> </span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"> # d /= 2 * math.log(len(fc))</span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"> d /= 2</span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"> </span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"> if gap_penalty == 1: </span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return d * weighted_gap_penalty(col, seq_weights)</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return d * weighted_gap_penalty(col, seq_weights)</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"> else: </span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return d</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return d</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"> </span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"> </span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"> ################################################################################</span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"><span class="p">@@ -430,20 +430,20 @@</span> def sum_of_pairs(col, sim_matrix, bg_dis</span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"> max_sum = 0.</span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"> </span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"> for i in range(len(col)):</span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for j in range(i):</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if col[i] != '-' and col[j] != '-':</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- max_sum += seq_weights[i] * seq_weights[j]</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sum += seq_weights[i] * seq_weights[j] * sim_matrix[aa_to_index[col[i]]][aa_to_index[col[j]]]</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for j in range(i):</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if col[i] != '-' and col[j] != '-':</span></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ max_sum += seq_weights[i] * seq_weights[j]</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sum += seq_weights[i] * seq_weights[j] * sim_matrix[aa_to_index[col[i]]][aa_to_index[col[j]]]</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"> </span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"> if max_sum != 0: </span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sum /= max_sum</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sum /= max_sum</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sum = 0.</span></span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sum = 0.</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"> if gap_penalty == 1: </span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return sum * weighted_gap_penalty(col, seq_weights)</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return sum * weighted_gap_penalty(col, seq_weights)</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return sum</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return sum</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"><span class="p">@@ -461,18 +461,18 @@</span> def window_score(scores, window_len, lam</span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"> w_scores = scores[:]</span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"> for i in range(window_len, len(scores) - window_len):</span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if scores[i] < 0: </span></span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- continue</span></span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if scores[i] < 0: </span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ continue</span></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"> </span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sum = 0.</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- num_terms = 0.</span></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for j in range(i - window_len, i + window_len + 1):</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if i != j and scores[j] >= 0:</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- num_terms += 1</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sum += scores[j]</span></span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sum = 0.</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ num_terms = 0.</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for j in range(i - window_len, i + window_len + 1):</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if i != j and scores[j] >= 0:</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ num_terms += 1</span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sum += scores[j]</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"> </span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if num_terms > 0:</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- w_scores[i] = (1 - lam) * (sum / num_terms) + lam * scores[i]</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if num_terms > 0:</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ w_scores[i] = (1 - lam) * (sum / num_terms) + lam * scores[i]</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"> </span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"> return w_scores</span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"> </span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"><span class="p">@@ -487,22 +487,22 @@</span> def calc_z_scores(scores, score_cutoff):</span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"> num_scores = 0</span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"> </span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"> for s in scores:</span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if s > score_cutoff:</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- average += s</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- num_scores += 1</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if s > score_cutoff:</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ average += s</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ num_scores += 1</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"> if num_scores != 0:</span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- average /= num_scores</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ average /= num_scores</span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="diff"> </span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"> for s in scores:</span>
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<td class="diff-line-num new new_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if s > score_cutoff:</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- std_dev += ((s - average)**2) / num_scores</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if s > score_cutoff:</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ std_dev += ((s - average)**2) / num_scores</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"> std_dev = math.sqrt(std_dev)</span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff"> </span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="diff"> for s in scores:</span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if s > score_cutoff and std_dev != 0:</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- z_scores.append((s-average)/std_dev)</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else:</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- z_scores.append(-1000.0)</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if s > score_cutoff and std_dev != 0:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ z_scores.append((s-average)/std_dev)</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else:</span></span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ z_scores.append(-1000.0)</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="diff"> </span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="diff"> return z_scores</span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"> </span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="diff"><span class="p">@@ -525,37 +525,37 @@</span> def read_scoring_matrix(sm_file):</span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="diff"> list_sm = [] # hold the matrix in list form</span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="diff"> </span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="diff"> try:</span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- matrix_file = open(sm_file, 'r')</span></span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ matrix_file = open(sm_file, 'r')</span></span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff"> </span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for line in matrix_file:</span></span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for line in matrix_file:</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff"> </span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if line[0] != '#' and first_line:</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- first_line = 0</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if len(amino_acids) == 0:</span></span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for c in line.split():</span></span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- aa_to_index[string.lower(c)] = aa_index</span></span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- amino_acids.append(string.lower(c))</span></span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- aa_index += 1</span></span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- elif line[0] != '#' and first_line == 0:</span></span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if len(line) > 1:</span></span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- row = line.split()</span></span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- list_sm.append(row)</span></span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except IOError, e:</span></span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print( "Could not load similarity matrix: %s. Using identity matrix..." % sm_file, file=sys.stderr )</span></span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- from numpy import identity</span></span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return identity(20)</span></span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if line[0] != '#' and first_line:</span></span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ first_line = 0</span></span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if len(amino_acids) == 0:</span></span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for c in line.split():</span></span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ aa_to_index[string.lower(c)] = aa_index</span></span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ amino_acids.append(string.lower(c))</span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ aa_index += 1</span></span>
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442
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<pre style="margin: 0;">+<span id="LC442" 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="LC443" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ elif line[0] != '#' and first_line == 0:</span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if len(line) > 1:</span></span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ row = line.split()</span></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ list_sm.append(row)</span></span>
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<pre style="margin: 0;">+<span id="LC447" 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="LC448" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except IOError as e:</span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print( "Could not load similarity matrix: %s. Using identity matrix..." % sm_file, file=sys.stderr )</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from numpy import identity</span></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return identity(20)</span></span>
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452
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<pre style="margin: 0;">+<span id="LC452" 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="LC453" class="line" lang="diff"> # if matrix is stored in lower tri form, copy to upper</span>
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454
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="diff"> if len(list_sm[0]) < 20:</span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in range(0,19):</span></span>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for j in range(i+1, 20):</span></span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- list_sm[i].append(list_sm[j][i])</span></span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(0,19):</span></span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for j in range(i+1, 20):</span></span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ list_sm[i].append(list_sm[j][i])</span></span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="diff"> </span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="diff"> for i in range(len(list_sm)):</span>
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for j in range(len(list_sm[i])):</span></span>
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464
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- list_sm[i][j] = float(list_sm[i][j])</span></span>
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465
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for j in range(len(list_sm[i])):</span></span>
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466
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ list_sm[i][j] = float(list_sm[i][j])</span></span>
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467
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="diff"> </span>
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468
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="diff"> return list_sm</span>
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="diff"> #sim_matrix = array(list_sm, type=Float32)</span>
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470
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="diff"><span class="p">@@ -595,16 +595,16 @@</span> def load_sequence_weights(fname):</span>
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471
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="diff"> seq_weights = []</span>
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472
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="diff"> </span>
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473
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="diff"> try:</span>
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474
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- f = open(fname)</span></span>
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475
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ f = open(fname)</span></span>
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476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="diff"> </span>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for line in f:</span></span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- l = line.split()</span></span>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if line[0] != '#' and len(l) == 2:</span></span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- seq_weights.append(float(l[1]))</span></span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except IOError, e:</span></span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- pass</span></span>
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<td class="diff-line-num new new_line" data-linenumber="484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #print "No sequence weights. Can't find: ", fname</span></span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for line in f:</span></span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ l = line.split()</span></span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if line[0] != '#' and len(l) == 2:</span></span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ seq_weights.append(float(l[1]))</span></span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except IOError as e:</span></span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pass</span></span>
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<td class="diff-line-num new new_line" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #print "No sequence weights. Can't find: ", fname</span></span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="diff"> </span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="diff"> return seq_weights</span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="diff"> </span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="diff"><span class="p">@@ -612,7 +612,7 @@</span> def get_column(col_num, alignment):</span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="diff"> """Return the col_num column of alignment as a list."""</span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="diff"> col = []</span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="diff"> for seq in alignment:</span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if col_num < len(seq): col.append(seq[col_num])</span></span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if col_num < len(seq): col.append(seq[col_num])</span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="diff"> </span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="diff"> return col</span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="diff"> </span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="diff"><span class="p">@@ -623,23 +623,23 @@</span> def get_distribution_from_file(fname):</span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="diff"> distribution = []</span>
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<td class="diff-line-num new new_line" data-linenumber="508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="diff"> try:</span>
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<td class="diff-line-num new new_line" data-linenumber="509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- f = open(fname)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for line in f:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if line[0] == '#': continue</span></span>
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<td class="diff-line-num new new_line" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- line = line[:-1]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- distribution = line.split()</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- distribution = map(float, distribution)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<td class="diff-line-num new new_line" data-linenumber="516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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<td class="diff-line-num new new_line" data-linenumber="517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
517
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC517" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except IOError, e:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print( e, "Using default (BLOSUM62) background.", file=sys.stderr )</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return []</span></span>
</pre>
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520
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC520" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ f = open(fname)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
521
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC521" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for line in f:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
522
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC522" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if line[0] == '#': continue</span></span>
</pre>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ line = line[:-1]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
524
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC524" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ distribution = line.split()</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ distribution = list(map(float, distribution))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ </span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except IOError as e:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
529
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC529" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print( e, "Using default (BLOSUM62) background.", file=sys.stderr )</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return []</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="diff"> </span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="diff"> # use a range to be flexible about round off</span>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="diff"> if .997 > sum(distribution) or sum(distribution) > 1.003:</span>
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534
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print( "Distribution does not sum to 1. Using default (BLOSUM62) background.", file=sys.stderr )</span></span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print( sum(distribution), file=sys.stderr )</span></span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return []</span></span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print( "Distribution does not sum to 1. Using default (BLOSUM62) background.", file=sys.stderr )</span></span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print( sum(distribution), file=sys.stderr )</span></span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return []</span></span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="diff"> </span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="diff"> return distribution</span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="diff"> </span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="diff"><span class="p">@@ -655,22 +655,22 @@</span> def read_fasta_alignment(filename):</span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="diff"> cur_seq = ''</span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="diff"> </span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="diff"> for line in f:</span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- line = line[:-1]</span></span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if len(line) == 0: continue</span></span>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ line = line[:-1]</span></span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if len(line) == 0: continue</span></span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="diff"> </span>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if line[0] == ';': continue</span></span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if line[0] == '>':</span></span>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- names.append(line[1:].replace('\r', ''))</span></span>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if line[0] == ';': continue</span></span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if line[0] == '>':</span></span>
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<td class="diff-line-num new new_line" data-linenumber="557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ names.append(line[1:].replace('\r', ''))</span></span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="diff"> </span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if cur_seq != '':</span></span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if cur_seq != '':</span></span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="diff"> cur_seq = cur_seq.upper()</span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="diff"> for i, aa in enumerate(cur_seq):</span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="diff"> if aa not in iupac_alphabet:</span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="diff"> cur_seq = cur_seq.replace(aa, '-')</span>
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<td class="diff-line-num new new_line" data-linenumber="565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- alignment.append(cur_seq.replace('B', 'D').replace('Z', 'Q').replace('X', '-'))</span></span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cur_seq = ''</span></span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- elif line[0] in iupac_alphabet:</span></span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cur_seq += line.replace('\r', '')</span></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ alignment.append(cur_seq.replace('B', 'D').replace('Z', 'Q').replace('X', '-'))</span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cur_seq = ''</span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ elif line[0] in iupac_alphabet:</span></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cur_seq += line.replace('\r', '')</span></span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="diff"> </span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="diff"> # add the last sequence</span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="diff"> cur_seq = cur_seq.upper()</span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="diff"><span class="p">@@ -680,7 +680,7 @@</span> def read_fasta_alignment(filename):</span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="diff"> alignment.append(cur_seq.replace('B', 'D').replace('Z', 'Q').replace('X', '-'))</span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="diff"> </span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="diff"> return names, alignment</span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ </span></span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="diff"> def read_clustal_alignment(filename):</span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="diff"> """ Read in the alignment stored in the CLUSTAL or Stockholm file, filename. Return</span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="diff"> two lists: the names and sequences. """</span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="diff"><span class="p">@@ -693,26 +693,26 @@</span> def read_clustal_alignment(filename):</span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="diff"> f = open(filename)</span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="diff"> </span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="diff"> for line in f:</span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- line = line[:-1]</span></span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if len(line) == 0: continue</span></span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if '*' in line: continue</span></span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if line[0:7] == 'CLUSTAL': continue</span></span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if line[0:11] == '# STOCKHOLM': continue</span></span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if line[0:2] == '//': continue</span></span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if re_stock_markup.match(line): continue</span></span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- t = line.split()</span></span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if len(t) == 2 and t[1][0] in iupac_alphabet:</span></span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ali = t[1].upper().replace('B', 'D').replace('Z', 'Q').replace('X', '-').replace('\r', '').replace('.', '-')</span></span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if t[0] not in names:</span></span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- names.append(t[0])</span></span>
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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- alignment.append(ali)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- alignment[names.index(t[0])] += ali</span></span>
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<td class="diff-line-num new new_line" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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<td class="diff-line-num new new_line" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ line = line[:-1]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
610
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC610" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if len(line) == 0: continue</span></span>
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<td class="diff-line-num new new_line" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
611
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC611" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if '*' in line: continue</span></span>
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<td class="diff-line-num new new_line" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
613
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC613" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if line[0:7] == 'CLUSTAL': continue</span></span>
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<td class="diff-line-num new new_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
614
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC614" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if line[0:11] == '# STOCKHOLM': continue</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
615
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC615" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if line[0:2] == '//': continue</span></span>
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<td class="diff-line-num new new_line" data-linenumber="616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if re_stock_markup.match(line): continue</span></span>
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<td class="diff-line-num new new_line" data-linenumber="618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ t = line.split()</span></span>
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620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if len(t) == 2 and t[1][0] in iupac_alphabet:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ali = t[1].upper().replace('B', 'D').replace('Z', 'Q').replace('X', '-').replace('\r', '').replace('.', '-')</span></span>
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<td class="diff-line-num new new_line" data-linenumber="623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if t[0] not in names:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ names.append(t[0])</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ alignment.append(ali)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ alignment[names.index(t[0])] += ali</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ </span></span>
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<td class="diff-line-num new new_line" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="diff"> return names, alignment</span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="diff"> </span>
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631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="diff"> </span>
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632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="diff"><span class="p">@@ -756,57 +756,57 @@</span> if len(args) < 1:</span>
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633
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="diff"> </span>
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634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="diff"> for opt, arg in opts:</span>
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635
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="diff"> if opt == "-h":</span>
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636
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- usage()</span></span>
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637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sys.exit()</span></span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ usage()</span></span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sys.exit()</span></span>
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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="diff"> if opt == "-o":</span>
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641
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- outfile_name = arg</span></span>
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642
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ outfile_name = arg</span></span>
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643
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="diff"> elif opt == "-l":</span>
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644
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if 'false' in arg.lower():</span></span>
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645
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- use_seq_weights = False</span></span>
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646
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if 'false' in arg.lower():</span></span>
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647
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ use_seq_weights = False</span></span>
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648
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="diff"> elif opt == "-p":</span>
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649
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if 'false' in arg.lower():</span></span>
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650
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- use_gap_penalty = 0</span></span>
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651
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if 'false' in arg.lower():</span></span>
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652
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ use_gap_penalty = 0</span></span>
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653
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="diff"> elif opt == "-m":</span>
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654
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- s_matrix_file = arg</span></span>
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<td class="diff-line-num new new_line" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
655
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ s_matrix_file = arg</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
656
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="diff"> elif opt == "-d":</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
657
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- d = get_distribution_from_file(arg)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if d != []: </span></span>
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<td class="diff-line-num new new_line" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bg_distribution = d</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
660
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- background_name = arg</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
661
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC661" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ d = get_distribution_from_file(arg)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
662
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC662" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if d != []: </span></span>
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<td class="diff-line-num new new_line" data-linenumber="663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
663
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC663" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ bg_distribution = d</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
664
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ background_name = arg</span></span>
</pre>
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665
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="diff"> elif opt == "-w":</span>
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666
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- try:</span></span>
</pre>
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667
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- window_size = int(arg)</span></span>
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668
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except ValueError:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print( "ERROR: Window size must be an integer. Using window_size 3...", file=sys.stderr )</span></span>
</pre>
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670
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- window_size = 3</span></span>
</pre>
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671
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ try:</span></span>
</pre>
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672
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ window_size = int(arg)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
673
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except ValueError:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
674
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print( "ERROR: Window size must be an integer. Using window_size 3...", file=sys.stderr )</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ window_size = 3</span></span>
</pre>
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676
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="diff"> elif opt == "-b":</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
677
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC677" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- try:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
678
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- win_lam = float(arg)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not (0. <= win_lam <= 1.): raise ValueError</span></span>
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<td class="diff-line-num new new_line" data-linenumber="680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except ValueError:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print( "ERROR: Window lambda must be a real in [0,1]. Using lambda = .5...", file=sys.stderr )</span></span>
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<td class="diff-line-num new new_line" data-linenumber="682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
682
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- win_lam = .5</span></span>
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<td class="diff-line-num new new_line" data-linenumber="683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ try:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ win_lam = float(arg)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
685
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC685" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if not (0. <= win_lam <= 1.): raise ValueError</span></span>
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<td class="diff-line-num new new_line" data-linenumber="686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except ValueError:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
687
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC687" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print( "ERROR: Window lambda must be a real in [0,1]. Using lambda = .5...", file=sys.stderr )</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ win_lam = .5</span></span>
</pre>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="diff"> elif opt == "-g":</span>
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<td class="diff-line-num new new_line" data-linenumber="690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
690
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- try:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- gap_cutoff = float(arg)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not (0. <= gap_cutoff < 1.): raise ValueError</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except ValueError:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print( "ERROR: Gap cutoff must be a real in [0,1). Using a gap cutoff of .3...", file=sys.stderr )</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- gap_cutoff = .3</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ try:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
697
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC697" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ gap_cutoff = float(arg)</span></span>
</pre>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if not (0. <= gap_cutoff < 1.): raise ValueError</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except ValueError:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print( "ERROR: Gap cutoff must be a real in [0,1). Using a gap cutoff of .3...", file=sys.stderr )</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ gap_cutoff = .3</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="diff"> elif opt == '-a':</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- seq_specific_output = arg</span></span>
</pre>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ seq_specific_output = arg</span></span>
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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="diff"> elif opt == '-n':</span>
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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- normalize_scores = True</span></span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ normalize_scores = True</span></span>
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708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="diff"> elif opt == '-s':</span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if arg == 'shannon_entropy': scoring_function = shannon_entropy</span></span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- elif arg == 'property_entropy': scoring_function = property_entropy</span></span>
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711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- elif arg == 'property_relative_entropy': scoring_function = property_relative_entropy</span></span>
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712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- elif arg == 'vn_entropy': scoring_function = vn_entropy; from numpy.numarray import *; import numpy.numarray.linear_algebra as la</span></span>
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713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- elif arg == 'relative_entropy': scoring_function = relative_entropy</span></span>
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715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- elif arg == 'js_divergence': scoring_function = js_divergence</span></span>
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716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- elif arg == 'sum_of_pairs': scoring_function = sum_of_pairs</span></span>
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else: print( "%s is not a valid scoring method. Using %s.\n" % (arg, scoring_function.__name__), file=sys.stderr )</span></span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if arg == 'shannon_entropy': scoring_function = shannon_entropy</span></span>
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719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ elif arg == 'property_entropy': scoring_function = property_entropy</span></span>
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720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ elif arg == 'property_relative_entropy': scoring_function = property_relative_entropy</span></span>
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721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ elif arg == 'vn_entropy': scoring_function = vn_entropy; from numpy.numarray import *; import numpy.numarray.linear_algebra as la</span></span>
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722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ elif arg == 'relative_entropy': scoring_function = relative_entropy</span></span>
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724
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ elif arg == 'js_divergence': scoring_function = js_divergence</span></span>
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725
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ elif arg == 'sum_of_pairs': scoring_function = sum_of_pairs</span></span>
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else: print( "%s is not a valid scoring method. Using %s.\n" % (arg, scoring_function.__name__), file=sys.stderr )</span></span>
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="diff"> </span>
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728
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="diff"> </span>
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729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="diff"> align_file = args[0]</span>
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730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="diff"><span class="p">@@ -821,27 +821,27 @@</span> seq_weights = []</span>
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731
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="diff"> try:</span>
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<td class="diff-line-num new new_line" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="diff"> names, alignment = read_clustal_alignment(align_file)</span>
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<td class="diff-line-num new new_line" data-linenumber="733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
733
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="diff"> if names == []:</span>
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<td class="diff-line-num new new_line" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
734
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- names, alignment = read_fasta_alignment(align_file)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-except IOError, e:</span></span>
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736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ names, alignment = read_fasta_alignment(align_file)</span></span>
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737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+except IOError as e:</span></span>
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738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="diff"> print( e, "Could not find %s. Exiting..." % align_file, file=sys.stderr )</span>
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739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="diff"> sys.exit(1)</span>
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740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="diff"> </span>
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741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="diff"> </span>
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742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="diff"> if len(alignment) != len(names) or alignment == []:</span>
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743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="diff"> print( "Unable to parse alignment.\n", file=sys.stderr )</span>
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744
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sys.exit(1)</span></span>
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745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sys.exit(1)</span></span>
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746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="diff"> </span>
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747
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="diff"> seq_len = len(alignment[0])</span>
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748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="diff"> for i, seq in enumerate(alignment):</span>
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749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="diff"> if len(seq) != seq_len:</span>
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750
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print( "ERROR: Sequences of different lengths: %s (%d) != %s (%d).\n" % (names[0], seq_len, names[i], len(seq)), file=sys.stderr )</span></span>
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751
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sys.exit(1)</span></span>
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752
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print( "ERROR: Sequences of different lengths: %s (%d) != %s (%d).\n" % (names[0], seq_len, names[i], len(seq)), file=sys.stderr )</span></span>
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753
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sys.exit(1)</span></span>
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754
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="diff"> </span>
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755
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="diff"> </span>
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756
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="diff"> if use_seq_weights:</span>
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="diff"> seq_weights = load_sequence_weights(align_file.replace('.%s' % align_suffix, '.weights'))</span>
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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="diff"> if seq_weights == []:</span>
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759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- seq_weights = calculate_sequence_weights(alignment)</span></span>
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760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ seq_weights = calculate_sequence_weights(alignment)</span></span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="diff"> </span>
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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="diff"> if len(seq_weights) != len(alignment): seq_weights = [1.] * len(alignment)</span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="diff"> </span>
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764
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="diff"><span class="p">@@ -859,10 +859,10 @@</span> for i in range(len(alignment[0])):</span>
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765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="diff"> col = get_column(i, alignment)</span>
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766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="diff"> </span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="diff"> if len(col) == len(alignment):</span>
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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if gap_percentage(col) <= gap_cutoff:</span></span>
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769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- scores.append(scoring_function(col, s_matrix, bg_distribution, seq_weights, use_gap_penalty))</span></span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else:</span></span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- scores.append(-1000.)</span></span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if gap_percentage(col) <= gap_cutoff:</span></span>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ scores.append(scoring_function(col, s_matrix, bg_distribution, seq_weights, use_gap_penalty))</span></span>
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774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else:</span></span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ scores.append(-1000.)</span></span>
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776
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="diff"> </span>
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777
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="diff"> if window_size > 0:</span>
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778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="diff"> scores = window_score(scores, window_size, win_lam)</span>
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<td class="diff-line-num new new_line" data-linenumber="779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
779
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="diff"><span class="p">@@ -874,36 +874,36 @@</span> if normalize_scores:</span>
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780
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="diff"> # print to file/stdout</span>
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781
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="diff"> try:</span>
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782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="diff"> if outfile_name != "": </span>
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<td class="diff-line-num new new_line" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- outfile = open(outfile_name, 'w')</span></span>
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<td class="diff-line-num new new_line" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
784
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- outfile.write("# %s -- %s - window_size: %d - window lambda: %.2f - background: %s - seq. weighting: %s - gap penalty: %d - normalized: %s\n" % (align_file, scoring_function.__name__, window_size, win_lam, background_name, use_seq_weights, use_gap_penalty, normalize_scores))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if seq_specific_output: </span></span>
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<td class="diff-line-num new new_line" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
786
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- outfile.write("# reference sequence: %s\n" % seq_specific_output)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- outfile.write("# align_column_number\tamino acid\tscore\n")</span></span>
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<td class="diff-line-num new new_line" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
789
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- outfile.write("# align_column_number\tscore\tcolumn\n")</span></span>
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790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ outfile = open(outfile_name, 'w')</span></span>
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<td class="diff-line-num new new_line" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
791
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ outfile.write("# %s -- %s - window_size: %d - window lambda: %.2f - background: %s - seq. weighting: %s - gap penalty: %d - normalized: %s\n" % (align_file, scoring_function.__name__, window_size, win_lam, background_name, use_seq_weights, use_gap_penalty, normalize_scores))</span></span>
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if seq_specific_output: </span></span>
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793
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ outfile.write("# reference sequence: %s\n" % seq_specific_output)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
794
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ outfile.write("# align_column_number\tamino acid\tscore\n")</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
796
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ outfile.write("# align_column_number\tscore\tcolumn\n")</span></span>
</pre>
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797
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="diff"> else:</span>
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<td class="diff-line-num new new_line" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print( "# %s -- %s - window_size: %d - background: %s - seq. weighting: %s - gap penalty: %d - normalized: %s" % (align_file, scoring_function.__name__, window_size, background_name, use_seq_weights, use_gap_penalty, normalize_scores) )</span></span>
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799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if seq_specific_output: </span></span>
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<td class="diff-line-num new new_line" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
800
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print( "# reference sequence: %s" % seq_specific_output )</span></span>
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<td class="diff-line-num new new_line" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
801
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC801" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print( "# align_column_number\tamino acid\tscore\n" )</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
802
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC802" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
803
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print( "# align_column_number\tscore\tcolumn\n" )</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print( "# %s -- %s - window_size: %d - background: %s - seq. weighting: %s - gap penalty: %d - normalized: %s" % (align_file, scoring_function.__name__, window_size, background_name, use_seq_weights, use_gap_penalty, normalize_scores) )</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
805
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if seq_specific_output: </span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
806
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC806" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print( "# reference sequence: %s" % seq_specific_output )</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
807
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC807" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print( "# align_column_number\tamino acid\tscore\n" )</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
808
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC808" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
809
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC809" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print( "# align_column_number\tscore\tcolumn\n" )</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
810
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
811
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-except IOError, e:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
812
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+except IOError as e:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
813
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="diff"> print( "Could not open %s for output. Printing results to standard out..." % outfile_name, file=sys.stderr )</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
814
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="diff"> outfile_name = ""</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
815
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
816
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="diff"> for i, score in enumerate(scores):</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
817
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="diff"> if seq_specific_output:</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
818
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cur_aa = get_column(i, alignment)[ref_seq_num]</span></span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
819
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if cur_aa == '-': continue</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
820
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC820" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if outfile_name == "":</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
821
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC821" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print( "%d\t%s\t%.5f" % (i, cur_aa, score) )</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
822
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC822" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else:</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
823
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC823" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- outfile.write("%d\t%s\t%5f\n" % (i, cur_aa, score))</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
824
</td>
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cur_aa = get_column(i, alignment)[ref_seq_num]</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
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<td class="diff-line-num new new_line" data-linenumber="825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
825
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if cur_aa == '-': continue</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
826
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC826" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if outfile_name == "":</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
827
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print( "%d\t%s\t%.5f" % (i, cur_aa, score) )</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
828
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else:</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
829
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ outfile.write("%d\t%s\t%5f\n" % (i, cur_aa, score))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
830
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="diff"> else:</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
831
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC831" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if outfile_name == "":</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
832
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC832" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print( "%d\t%.5f\t%s" % (i, score, "".join(get_column(i, alignment))) )</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
833
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else:</span></span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
834
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC834" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- outfile.write("%d\t%5f\t%s\n" % (i, score, "".join(get_column(i, alignment))))</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
835
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC835" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if outfile_name == "":</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
836
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC836" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print( "%d\t%.5f\t%s" % (i, score, "".join(get_column(i, alignment))) )</span></span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
837
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC837" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else:</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
838
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<pre style="margin: 0;">+<span id="LC838" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ outfile.write("%d\t%5f\t%s\n" % (i, score, "".join(get_column(i, alignment))))</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
839
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="diff"> </span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/conservation-code/compare/b7176bea5f3d9c048e9f041adb86b26f376afa56...f83e1fd4e55bf279d5ee76bf46a9451ca5522861#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7" 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="7" 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">@@ -7,3 +7,4 @@ stockholm_format</td>
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<td class="diff-line-num old_line" data-linenumber="7" 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">
7
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<td class="diff-line-num new_line" data-linenumber="7" 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">
7
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Python3-prints</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="8" 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">
8
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<td class="diff-line-num new_line" data-linenumber="8" 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">
8
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">usage</span>
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<td class="diff-line-num old_line" data-linenumber="9" 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">
9
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<td class="diff-line-num new_line" data-linenumber="9" 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">
9
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">fix_load_identity_matrix</span>
</pre>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">2to3.patch</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/conservation-code/compare/b7176bea5f3d9c048e9f041adb86b26f376afa56...f83e1fd4e55bf279d5ee76bf46a9451ca5522861#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 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">@@ -15,7 +15,7 @@ pkgdatadir:=${datarootdir}/$(DEB_SOURCE)</td>
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15
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="16" 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">
16
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<td class="diff-line-num new_line" data-linenumber="16" 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">
16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
17
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> dh $@ --with python<span class="idiff left right">2</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> dh $@ --with python<span class="idiff left right">3</span></span>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">override_dh_auto_build: $(MANS)</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></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">@@ -37,19 +37,3 @@ override_dh_auto_clean:</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> rm -f $(MANS) ChangeLog</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"># Policy §4.9 says that the get-orig-source target 'may be invoked in any directory'. So we do not use variables set from dpkg-parsechangelog.</span></pre>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">get-orig-source:</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext"> set -e; \</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"> if ! ( which xz >/dev/null ); then \</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"> echo "Could not find 'xz' tool for compression. Please install the package 'xz-utils'." >&2; \</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext"> exit 1; \</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext"> fi ; \</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext"> t=$$(mktemp -d) || exit 1; \</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext"> trap "rm -rf -- '$$t'" EXIT; \</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"> ( cd "$$t"; \</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext"> wget -O conservation-code_20110309.0.orig.tar.gz http://compbio.cs.princeton.edu/conservation/conservation_code.tar.gz; \</span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext"> gunzip *.tar.gz; \</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"> tar --owner=root --group=root --mode=a+rX --delete -f *.tar --wildcards '*/._*'; \</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext"> xz --best *.tar; \</span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext"> ); \</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext"> mv $$t/*.tar.?z ./</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/conservation-code/compare/b7176bea5f3d9c048e9f041adb86b26f376afa56...f83e1fd4e55bf279d5ee76bf46a9451ca5522861#17d8869115f55e024a85a6d17443302815985358"><strong>debian/tests/installation-test</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">@@ -6,12 +6,12 @@ set -e</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>conservation-code</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$A<span class="idiff left right">DT</span>TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">A<span class="idiff left right">DT</span>TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: #008080;">$A<span class="idiff left right">DT</span>TMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$A<span class="idiff left right">UTOPKGTEST_</span>TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">A<span class="idiff left right">UTOPKGTEST_</span>TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: #008080;">$A<span class="idiff left right">UTOPKGTEST_</span>TMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$A<span class="idiff left right">DT</span>TMP</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$A<span class="idiff left right">UTOPKGTEST_</span>TMP</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">.</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"></span>
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<li id="cdcfe09f6e63c35ce29bc1d25e7958efb82eef69">
<a href="https://salsa.debian.org/med-team/conservation-code/compare/b7176bea5f3d9c048e9f041adb86b26f376afa56...f83e1fd4e55bf279d5ee76bf46a9451ca5522861#cdcfe09f6e63c35ce29bc1d25e7958efb82eef69"><strong>debian/tests/non-default-params-test</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,12 +6,12 @@ set -e</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>conservation-code</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$A<span class="idiff left right">DT</span>TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">A<span class="idiff left right">DT</span>TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: #008080;">$A<span class="idiff left right">DT</span>TMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$A<span class="idiff left right">UTOPKGTEST_</span>TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">A<span class="idiff left right">UTOPKGTEST_</span>TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: #008080;">$A<span class="idiff left right">UTOPKGTEST_</span>TMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$A<span class="idiff left right">DT</span>TMP</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$A<span class="idiff left right">UTOPKGTEST_</span>TMP</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">.</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"></span>
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<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<a href="https://salsa.debian.org/med-team/conservation-code/compare/b7176bea5f3d9c048e9f041adb86b26f376afa56...f83e1fd4e55bf279d5ee76bf46a9451ca5522861#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Name: conservation-code</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Contact: Tony Capra <http://compbio.cs.princeton.edu/conservation/></span>
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3
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Reference:</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"><span class="idiff left right"> </span>- Author: John A. Capra and Mona Singh</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> <span class="idiff left right"> </span>Title: Predicting functionally important residues from sequence conservation</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> <span class="idiff left right"> </span>Journal: Bioinformatics</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> <span class="idiff left right"> </span>Volume: 23</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> <span class="idiff left right"> </span>Number: 15</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> <span class="idiff left right"> </span>Pages: 1875-82</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> <span class="idiff left right"> </span>Year: 2007</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> <span class="idiff left right"> </span>URL: http://bioinformatics.oxfordjournals.org/content/23/15/1875.full</span>
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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> <span class="idiff left right"> </span>DOI: 10.1093/bioinformatics/btm270</span>
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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> <span class="idiff left right"> </span>PMID: 17519246</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">- Author: John A. Capra and Mona Singh</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Title: Predicting functionally important residues from sequence conservation</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Journal: Bioinformatics</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Volume: 23</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> Number: 15</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> Pages: 1875-82</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> Year: 2007</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> URL: http://bioinformatics.oxfordjournals.org/content/23/15/1875.full</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> DOI: 10.1093/bioinformatics/btm270</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> PMID: 17519246</span>
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14
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12
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Registry:</span>
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<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"><span class="idiff left right"> </span>- Name: OMICtools</span>
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<td class="diff-line-num old old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> <span class="idiff left right"> </span>Entry: OMICS_06943</span>
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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
17
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<td class="diff-line-num new_line old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"><span class="idiff left right"> </span>- Name: SciCrunch</span>
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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> <span class="idiff left right"> </span>Entry: NA</span>
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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
19
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<td class="diff-line-num new_line old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"><span class="idiff left right"> </span>- Name: bio.tools</span>
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<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> <span class="idiff left right"> </span>Entry: NA</span></pre>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">- Name: OMICtools</span>
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<td class="diff-line-num new old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> Entry: OMICS_06943</span>
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<td class="diff-line-num new old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">- Name: SciCrunch</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> Entry: NA</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">- Name: bio.tools</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> Entry: NA</span></pre>
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