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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/macsyfinder">Debian Med / macsyfinder</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/macsyfinder/commit/a26a252e0b4163f24aec5489d382f776bf03e085">a26a252e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-06T08:44:35Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use 2to3 to port to Python3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/macsyfinder/commit/994f55a1c15bca7567d6e6cde968499c54efbf82">994f55a1</a></strong>
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<span>by Andreas Tille</span>
<i>at 2019-09-06T08:55:01Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Attempt to use 2to3 to port to Python3 failed
</pre>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
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+
debian/patches/2to3.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/macsyfinder/compare/15a3838e173bbbdf8a2de52119d50165ea66d0db...994f55a1c15bca7567d6e6cde968499c54efbf82#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">macsyfinder (1.0.5-4) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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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"> * Attempt to use 2to3 to port to Python3 failed</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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> not yet closed: #936977</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> See also https://github.com/gem-pasteur/macsyfinder/issues/21</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></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"> -- Andreas Tille <tille@debian.org> Fri, 06 Sep 2019 10:40:05 +0200</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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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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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">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">macsyfinder (1.0.5-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Team upload.</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/macsyfinder/compare/15a3838e173bbbdf8a2de52119d50165ea66d0db...994f55a1c15bca7567d6e6cde968499c54efbf82#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5" 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="5" 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">@@ -5,7 +5,7 @@ Section: science</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>
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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">
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> python,</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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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> python<span class="idiff left right">3</span>,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python3-sphinx,</span>
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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> texlive-latex-recommended,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> texlive-plain-generic,</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">@@ -21,7 +21,7 @@ Homepage: https://github.com/gem-pasteur/macsyfinder</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Package: macsyfinder</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">Depends: ${python:Depends},</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Depends: ${python<span class="idiff left right">3</span>:Depends},</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> hmmer,</span>
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> ncbi-blast+,</span>
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<li id="555c85016bd79aa8bbb523506af81b69d9c69534">
<a href="https://salsa.debian.org/med-team/macsyfinder/compare/15a3838e173bbbdf8a2de52119d50165ea66d0db...994f55a1c15bca7567d6e6cde968499c54efbf82#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 to Python3</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> Unfortunately it is more complex than just 2to3</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/936977</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Last-Update: Fri, 06 Sep 2019 10:40:05 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">diff --git a/README.md b/README.md</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gh" style="color: #999;">index 6387b97..d21701e 100644</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;">--- a/README.md</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/README.md</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">@@ -41,22 +41,22 @@</span> cd macsyfinder-x.x</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> 3. Build </span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> ```bash</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python setup.py build</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 setup.py build</span></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>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> 4. Test </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> ```bash</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-python setup.py test -vv</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+python3 setup.py test -vv</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> ```</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> 5. Install</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> ```bash</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-sudo python setup.py install</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+sudo python3 setup.py install</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> ```</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- To see all installation options "python setup.py --help"</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ To see all installation options "python3 setup.py --help"</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> See the INSTALL file for more details.</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/bin/macsyfinder b/bin/macsyfinder</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gh" style="color: #999;">index a676991..8cce1e7 100755</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bin/macsyfinder</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bin/macsyfinder</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> ################################################################################</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/doc/conf.py b/doc/conf.py</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gh" style="color: #999;">index 172fba7..b2146d9 100644</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/doc/conf.py</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/doc/conf.py</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="p">@@ -48,9 +48,9 @@</span> source_suffix = '.rst'</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> master_doc = 'index'</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> # General information about the project.</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-project = u'MacSyFinder'</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+project = 'MacSyFinder'</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> #copyright = u'2014, Sophie Abby, Bertrand Néron'</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-copyright = u'2014, Sophie Abby, Bertrand Néron'</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+copyright = '2014, Sophie Abby, Bertrand Néron'</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> # The version info for the project you're documenting, acts as replacement for</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> # |version| and |release|, also used in various other places throughout the</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="p">@@ -192,8 +192,8 @@</span> latex_elements = {</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> # Grouping the document tree into LaTeX files. List of tuples</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> # (source start file, target name, title, author, documentclass [howto/manual]).</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> latex_documents = [</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ('index', 'Macsyfinder.tex', u'MacSyFinder Documentation',</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- u'Sophie Abby, Bertrand Néron', 'manual'),</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ('index', 'Macsyfinder.tex', 'MacSyFinder Documentation',</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 'Sophie Abby, Bertrand Néron', 'manual'),</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> ]</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> # The name of an image file (relative to this directory) to place at the top of</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="p">@@ -222,8 +222,8 @@</span> latex_use_parts = True</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> # One entry per manual page. List of tuples</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> # (source start file, name, description, authors, manual section).</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> man_pages = [</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ('index', 'macsyfinder', u'MacsSyFinder Documentation',</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [u'Sophie Abby, Bertrand Néron'], 1)</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ('index', 'macsyfinder', 'MacsSyFinder Documentation',</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;">+ ['Sophie Abby, Bertrand Néron'], 1)</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> ]</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"> # If true, show URL addresses after external links.</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="p">@@ -236,8 +236,8 @@</span> man_pages = [</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> # (source start file, target name, title, author,</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> # dir menu entry, description, category)</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> texinfo_documents = [</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ('index', 'MacSyFinder', u'MacSyFinder Documentation',</span></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;">- u'Sophie Abby, Bertrand Néron', 'MacSyFinder', 'A tool for macromolecular systems\' modelling and detection.',</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;">+ ('index', 'MacSyFinder', 'MacSyFinder Documentation',</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 'Sophie Abby, Bertrand Néron', 'MacSyFinder', 'A tool for macromolecular systems\' modelling and detection.',</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> 'Miscellaneous'),</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> ]</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 class="gh" style="color: #999;">diff --git a/macsypy/config.py b/macsypy/config.py</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gh" style="color: #999;">index 013606e..6286a56 100644</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/macsypy/config.py</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/macsypy/config.py</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="p">@@ -16,7 +16,7 @@</span> import os</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> import sys</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> import inspect</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> from time import strftime</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from ConfigParser import SafeConfigParser, NoSectionError, NoOptionError</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;">+from configparser import SafeConfigParser, NoSectionError, NoOptionError</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"> _prefix_path = '$PREFIX'</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> _prefix_conf = '$PREFIXCONF'</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="p">@@ -361,7 +361,7 @@</span> class Config(object):</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> it = iter(inter_gene_max_space)</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> try:</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> for system in it:</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- interval = it.next()</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ interval = next(it)</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> try:</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> interval = int(interval)</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> options['inter_gene_max_space'][system] = interval</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="p">@@ -390,7 +390,7 @@</span> class Config(object):</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> it = iter(min_mandatory_genes_required)</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> try:</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> for system in it:</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;">- quorum_mandatory_genes = it.next()</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;">+ quorum_mandatory_genes = next(it)</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> try:</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"> quorum_mandatory_genes = int(quorum_mandatory_genes)</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> options['min_mandatory_genes_required'][system] = quorum_mandatory_genes</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="p">@@ -421,7 +421,7 @@</span> class Config(object):</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> it = iter(min_genes_required)</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> try:</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> for system in it:</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;">- quorum_genes = it.next()</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;">+ quorum_genes = next(it)</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> try:</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> quorum_genes = int(quorum_genes)</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> options['min_genes_required'][system] = quorum_genes</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="p">@@ -450,7 +450,7 @@</span> class Config(object):</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> it = iter(max_nb_genes)</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> try:</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> for system in it:</span>
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<td class="diff-line-num new new_line" data-linenumber="141" 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">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- max_genes = it.next()</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ max_genes = next(it)</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> try:</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> max_genes = int(max_genes)</span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> options['max_nb_genes'][system] = max_genes</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="p">@@ -634,7 +634,7 @@</span> class Config(object):</span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"> if self.options[directive] is not None:</span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> if directive in ('inter_gene_max_space', 'min_mandatory_genes_required', 'min_genes_required', 'max_nb_genes'):</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> s = ''</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for system, space in self.options[directive].items():</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for system, space in list(self.options[directive].items()):</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> s += " {0} {1}".format(system, space)</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> parser.set(section, directive, s)</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> elif directive != 'log_file' or self.options[directive] != os.path.join(self.options['working_dir'], 'macsyfinder.log'):</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/macsypy/database.py b/macsypy/database.py</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="gh" style="color: #999;">index a547a19..391de5f 100644</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/macsypy/database.py</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/macsypy/database.py</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="p">@@ -42,7 +42,7 @@</span> def fasta_iter(fasta_file):</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> header = header.split()</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> _id = header[0]</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> comment = ' '.join(header[1:])</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- seq = ''.join(s.strip() for s in faiter.next())</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ seq = ''.join(s.strip() for s in next(faiter))</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> length = len(seq)</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> yield _id, comment, length</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"><span class="p">@@ -339,7 +339,7 @@</span> class RepliconDB(object):</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"> replicons = (x[1] for x in groupby(idx_f, grp_replicon))</span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"> for replicon in replicons:</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"> genes = []</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- entry = replicon.next()</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ entry = next(replicon)</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"> replicon_name, seq_name, seq_length, _min = parse_entry(entry)</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"> genes.append((seq_name, seq_length))</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> for entry in replicon:</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"><span class="p">@@ -392,21 +392,21 @@</span> class RepliconDB(object):</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> """</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"> :return: a copy of the RepliconDB as a list of (replicon_name, RepliconInfo) pairs</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"> """</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return self._DB.items()</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return list(self._DB.items())</span></span>
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"> def iteritems(self):</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"> """</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> :return: an iterator over the RepliconDB as a list (replicon_name, RepliconInfo) pairs</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> """</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return self._DB.iteritems()</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return iter(self._DB.items())</span></span>
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"> def replicon_names(self):</span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"> :return: a copy of the RepliconDB as a list of replicon_names</span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"> """</span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return self._DB.keys()</span></span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return list(self._DB.keys())</span></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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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"> def replicon_infos(self):</span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"><span class="p">@@ -414,4 +414,4 @@</span> class RepliconDB(object):</span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"> :return: a copy of the RepliconDB as list of replicons info</span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"> :rtype: RepliconInfo instance</span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return self._DB.values()</span></span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return list(self._DB.values())</span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/macsypy/gene.py b/macsypy/gene.py</span></span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"><span class="gh" style="color: #999;">index e94d80c..7b4d0da 100644</span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/macsypy/gene.py</span></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/macsypy/gene.py</span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"><span class="p">@@ -53,13 +53,13 @@</span> class GeneBank(object):</span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"> :return: True if the gene is in, False otherwise</span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"> :rtype: boolean</span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return gene in self._genes_bank.values()</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return gene in list(self._genes_bank.values())</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"> def __iter__(self):</span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"> Return an iterator object on the genes contained in the bank</span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return self._genes_bank.itervalues()</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return iter(self._genes_bank.values())</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"> def add_gene(self, gene):</span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/macsypy/report.py b/macsypy/report.py</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"><span class="gh" style="color: #999;">index 3e4af27..6f8b36f 100644</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/macsypy/report.py</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/macsypy/report.py</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"><span class="p">@@ -23,7 +23,7 @@</span> from itertools import groupby</span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"> from .database import Indexes, RepliconDB</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-class HMMReport(object):</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+class HMMReport(object, metaclass=abc.ABCMeta):</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"> Handle the results from the HMM search. Extract a synthetic report from the raw hmmer output,</span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"> after having applied a hit filtering.</span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"><span class="p">@@ -32,8 +32,6 @@</span> class HMMReport(object):</span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"> or not ("unordered" or "unordered_replicon" db_type).</span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- __metaclass__ = abc.ABCMeta</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"> def __init__(self, gene, hmmer_output, cfg):</span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"> :param gene: the gene corresponding to the profile search reported here</span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"><span class="p">@@ -182,7 +180,7 @@</span> class HMMReport(object):</span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"> :rtype: list of :class:`macsypy.report.Hit` objects</span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- first_line = b_grp.next()</span></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ first_line = next(b_grp)</span></span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"> if not first_line.startswith(' # score'):</span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"> return []</span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"><span class="p">@@ -252,7 +250,7 @@</span> class GeneralHMMReport(HMMReport):</span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"> gene_profile_lg = len(self.gene.profile)</span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"> hmm_hits = (x[1] for x in groupby(hmm_out, self._hit_start))</span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"> # drop summary</span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- hmm_hits.next()</span></span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ next(hmm_hits)</span></span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"> for hmm_hit in hmm_hits:</span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"> hit_id = self._parse_hmm_header(hmm_hit)</span>
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"> seq_lg, position_hit = my_db[hit_id]</span>
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"><span class="p">@@ -260,7 +258,7 @@</span> class GeneralHMMReport(HMMReport):</span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"> # replicon_name = self.cfg. # Define a variable in further devt</span>
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"> replicon_name = "Unordered"</span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"> </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;">- body = hmm_hits.next()</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;">+ body = next(hmm_hits)</span></span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"> h = self._parse_hmm_body(hit_id, gene_profile_lg, seq_lg, coverage_threshold,</span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"> replicon_name, position_hit, i_evalue_sel, body)</span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"> self.hits += h</span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"><span class="p">@@ -298,13 +296,13 @@</span> class OrderedHMMReport(HMMReport):</span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"> gene_profile_lg = len(self.gene.profile)</span>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"> hmm_hits = (x[1] for x in groupby(hmm_out, self._hit_start))</span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"> # drop summary</span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- hmm_hits.next()</span></span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ next(hmm_hits)</span></span>
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"> for hmm_hit in hmm_hits:</span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"> hit_id = self._parse_hmm_header(hmm_hit)</span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"> seq_lg, position_hit = my_db[hit_id]</span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"> replicon_name = RepliconDB.ordered_replicon_name</span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- body = hmm_hits.next()</span></span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ body = next(hmm_hits)</span></span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"> h = self._parse_hmm_body(hit_id, gene_profile_lg, seq_lg, coverage_threshold,</span>
</pre>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"> replicon_name, position_hit, i_evalue_sel, body)</span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"> self.hits += h</span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"><span class="p">@@ -341,12 +339,12 @@</span> class GembaseHMMReport(HMMReport):</span>
</pre>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"> gene_profile_lg = len(self.gene.profile)</span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"> hmm_hits = (x[1] for x in groupby(hmm_out, self._hit_start))</span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"> # drop summary</span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- hmm_hits.next()</span></span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ next(hmm_hits)</span></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"> for hmm_hit in hmm_hits:</span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"> hit_id = self._parse_hmm_header(hmm_hit)</span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"> seq_lg, position_hit = my_db[hit_id]</span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"> replicon_name = "_".join(hit_id.split('_')[:-1])</span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- body = hmm_hits.next()</span></span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ body = next(hmm_hits)</span></span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"> h = self._parse_hmm_body(hit_id, gene_profile_lg, seq_lg, coverage_threshold,</span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"> replicon_name, position_hit, i_evalue_sel, body)</span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"> self.hits += h</span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/macsypy/search_systems.py b/macsypy/search_systems.py</span></span>
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"><span class="gh" style="color: #999;">index d523290..b13995c 100644</span></span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/macsypy/search_systems.py</span></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/macsypy/search_systems.py</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"><span class="p">@@ -21,9 +21,9 @@</span> import itertools</span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"> import operator</span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"> import json</span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from macsypy_error import MacsypyError, SystemDetectionError</span></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from database import RepliconDB</span></span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from system import system_bank</span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from .macsypy_error import MacsypyError, SystemDetectionError</span></span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from .database import RepliconDB</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from .system import system_bank</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"> _log = logging.getLogger('macsyfinder.' + __name__)</span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"><span class="p">@@ -303,7 +303,7 @@</span> class Cluster(object):</span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"> # Version with hits "reference" systems</span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"> for h in self.hits:</span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"> syst = h.system.name</span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not systems.has_key(syst):</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if syst not in systems:</span></span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"> systems[syst] = 1</span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"> #systems_object[syst]=h.system</span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"><span class="p">@@ -316,7 +316,7 @@</span> class Cluster(object):</span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"> # Useless ?! Or change? </span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"> max_syst = 0</span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"> tmp_syst_name = ""</span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for x, y in systems.iteritems():</span></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for x, y in systems.items():</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"> if y >= max_syst:</span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"> tmp_syst_name = x</span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"> max_syst = y</span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"><span class="p">@@ -332,7 +332,7 @@</span> class Cluster(object):</span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"> #syst_list=h.gene.get_compatible_systems(self.systems_to_detect, True) # Need the list of systems (obj!) to be detected... in the cfg? # tmp before yep</span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"> for syst in syst_list:</span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"> syst_name = syst.name</span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not systems_compat.has_key(syst_name):</span></span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if syst_name not in systems_compat:</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"> systems_compat[syst_name] = 1</span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"> #systems_object[syst]=h.system</span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"> else:</span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"><span class="p">@@ -342,7 +342,7 @@</span> class Cluster(object):</span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"> #print systems_compat</span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"> # We sort the list of compatible systems per decreasing nb of systems occurrences</span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- systems_compat = OrderedDict(sorted(systems_compat.items(), reverse=True, key=lambda t: t[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="gi" style="color: #000; background-color: #dfd;">+ systems_compat = OrderedDict(sorted(list(systems_compat.items()), reverse=True, key=lambda t: t[1]))</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"> #print systems_compat</span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"> #print self</span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"> </span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"><span class="p">@@ -354,10 +354,10 @@</span> class Cluster(object):</span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"> # Also deal with foreign "exchangeable" genes for the same reasons... NB !!</span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"> # Maybe just not add the system to the list if exchangeable?</span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"> #if len(systems.keys()) == 1:</span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if len(systems_compat.keys()) == 1:</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if len(list(systems_compat.keys())) == 1:</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"> self._state = "clear"</span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"> #syst = systems.keys()[0]</span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- syst = systems_compat.keys()[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;">+ syst = list(systems_compat.keys())[0]</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"> #print syst</span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"> self._putative_system = syst</span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"> #self._compatible_systems.append(system_bank[syst])</span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"><span class="p">@@ -416,7 +416,7 @@</span> class Cluster(object):</span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"> </span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"> # Sort systems to consider by decreasing counts.</span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"> cluster_compatible_systems = []</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;">- for putative_system in systems_compat.keys():</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for putative_system in list(systems_compat.keys()):</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"> # Add that it has to be done first from the most rep systems by decreasing order of systems.values.</span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="diff"> state = try_system(self.hits, putative_system, systems_compat)</span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff"> if state == "clear":</span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"><span class="p">@@ -577,20 +577,20 @@</span> class SystemOccurence(object):</span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"> out = ""</span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff"> if self.mandatory_genes: </span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="diff"> out += "Mandatory genes: \n"</span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for k, g in self.mandatory_genes.iteritems():</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for k, g in self.mandatory_genes.items():</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="diff"> out += "{0}\t{1:d}\n".format(k, g)</span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff"> if self.accessory_genes:</span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"> out += "Accessory genes: \n"</span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for k, g in self.accessory_genes.iteritems():</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for k, g in self.accessory_genes.items():</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff"> out += "{0}\t{1:d}\n".format(k, g)</span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="diff"> if self.forbidden_genes:</span>
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<td class="diff-line-num new new_line" data-linenumber="396" 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">
396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff"> out += "Forbidden genes: \n"</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;">- for k, g in self.forbidden_genes.iteritems():</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for k, g in self.forbidden_genes.items():</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="diff"> out += "{0}\t{1:d}\n".format(k, g)</span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="diff"> # NEW</span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="diff"> if self.multi_syst_genes:</span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="diff"> out += "Multi_syst genes:\n"</span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for k, g in self.multi_syst_genes.iteritems():</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for k, g in self.multi_syst_genes.items():</span></span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="diff"> out += "{0}\t{1:d}\n".format(k, g)</span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"> return out</span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="diff"> </span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="diff"><span class="p">@@ -697,7 +697,7 @@</span> class SystemOccurence(object):</span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="diff"> :rtype: integer</span>
</pre>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="diff"> """</span>
</pre>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="diff"> total = 0</span>
</pre>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for v in gene_dict.values():</span></span>
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<td class="diff-line-num new new_line" data-linenumber="413" 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">
413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for v in list(gene_dict.values()):</span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="diff"> if v > 0:</span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="diff"> total += 1</span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff"> return total</span>
</pre>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff"><span class="p">@@ -711,7 +711,7 @@</span> class SystemOccurence(object):</span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="diff"> :rtype: integer</span>
</pre>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="diff"> """</span>
</pre>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="diff"> total = 0</span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for v in gene_dict.values():</span></span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for v in list(gene_dict.values()):</span></span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="diff"> total += v</span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="diff"> return total</span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff"> </span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="diff"><span class="p">@@ -723,7 +723,7 @@</span> class SystemOccurence(object):</span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"> :rtype: list</span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"> """</span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="diff"> missing = []</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;">- for k, v in gene_dict.iteritems():</span></span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for k, v in gene_dict.items():</span></span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="diff"> if v == 0:</span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="diff"> missing.append(k)</span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="diff"> return missing</span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="diff"><span class="p">@@ -897,16 +897,16 @@</span> class SystemOccurence(object):</span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="diff"> self.forbidden_genes[hit.gene.name] += 1</span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="diff"> included = False</span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if hit.gene.name in self.exmandatory_genes.keys():</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;">+ if hit.gene.name in list(self.exmandatory_genes.keys()):</span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="diff"> self.mandatory_genes[self.exmandatory_genes[hit.gene.name]] += 1</span>
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442
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="diff"> valid_hit = validSystemHit(hit, self.system_name, "mandatory")</span>
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443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="diff"> self.valid_hits.append(valid_hit)</span>
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444
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- elif hit.gene.name in self.exaccessory_genes.keys():</span></span>
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445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ elif hit.gene.name in list(self.exaccessory_genes.keys()):</span></span>
</pre>
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446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="diff"> self.accessory_genes[self.exaccessory_genes[hit.gene.name]] += 1</span>
</pre>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="diff"> valid_hit = validSystemHit(hit, self.system_name, "accessory")</span>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="diff"> self.valid_hits.append(valid_hit)</span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="diff"> # NEW: exforbidden_genes considered</span>
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450
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- elif hit.gene.name in self.exforbidden_genes.keys():</span></span>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ elif hit.gene.name in list(self.exforbidden_genes.keys()):</span></span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="diff"> self.forbidden_genes[self.exforbidden_genes[hit.gene.name]] += 1</span>
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453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="diff"> valid_hit = validSystemHit(hit, self.system_name, "forbidden")</span>
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454
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="diff"> self.valid_hits.append(valid_hit) </span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="diff"><span class="p">@@ -954,16 +954,16 @@</span> class SystemOccurence(object):</span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="diff"> valid_hit = validSystemHit(hit, self.system_name, "forbidden")</span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="diff"> self.valid_hits.append(valid_hit)</span>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if hit.gene.name in self.exmandatory_genes.keys():</span></span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if hit.gene.name in list(self.exmandatory_genes.keys()):</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="diff"> self.mandatory_genes[self.exmandatory_genes[hit.gene.name]] += 1</span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="diff"> valid_hit = validSystemHit(hit, self.system_name, "mandatory")</span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="diff"> self.valid_hits.append(valid_hit)</span>
</pre>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- elif hit.gene.name in self.exaccessory_genes.keys():</span></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ elif hit.gene.name in list(self.exaccessory_genes.keys()):</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="diff"> self.accessory_genes[self.exaccessory_genes[hit.gene.name]] += 1</span>
</pre>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="diff"> valid_hit = validSystemHit(hit, self.system_name, "accessory")</span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="diff"> self.valid_hits.append(valid_hit)</span>
</pre>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="diff"> # NEW: exforbidden_genes considered</span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- elif hit.gene.name in self.exforbidden_genes.keys():</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ elif hit.gene.name in list(self.exforbidden_genes.keys()):</span></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="diff"> self.forbidden_genes[self.exforbidden_genes[hit.gene.name]] += 1</span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="diff"> valid_hit = validSystemHit(hit, self.system_name, "forbidden")</span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="diff"> self.valid_hits.append(valid_hit)</span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="diff"><span class="p">@@ -988,14 +988,14 @@</span> class SystemOccurence(object):</span>
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476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="diff"> #if g in multi_gene_names in [multi_gene.name for multi_gene in [hit.gene for hit in multi_systems_hits]]:</span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="diff"> if g in [multi_gene.name for multi_gene in [hit.gene for hit in multi_systems_hits]]:</span>
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="diff"> # If so, then the SystemOccurrence is filled with this:</span>
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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 g in self.accessory_genes.keys():</span></span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if g in list(self.accessory_genes.keys()):</span></span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="diff"> self.accessory_genes[g] += 1</span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="diff"> # Add a valid_hit with a special status? e.g "accessory_multi_system"?</span>
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="diff"> #self.accessory_genes[hit.gene.name]+=1</span>
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="diff"> #valid_hit=validSystemHit(hit, self.system_name, "accessory")</span>
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="diff"> #self.valid_hits.append(valid_hit)</span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- elif g in self.mandatory_genes.keys():</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;">+ elif g in list(self.mandatory_genes.keys()):</span></span>
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="diff"> self.mandatory_genes[g] += 1</span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="diff"> # Add a valid_hit with a special status? e.g "mandatory_multi_system"?</span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="diff"> #self.mandatory_genes[hit.gene.name]+=1</span>
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="diff"><span class="p">@@ -1018,7 +1018,7 @@</span> class SystemOccurence(object):</span>
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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"> - "\single_locus\" when a complete system in the form of a single cluster was found</span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="diff"> - "\multi_loci\" when a complete system in the form of several clusters was found</span>
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- - "\uncomplete\" when no system was assessed (quorum not reached)</span></span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ - "\\uncomplete\" when no system was assessed (quorum not reached)</span></span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="diff"> - "\empty\" when no gene for this system was found</span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="diff"> - "\exclude\" when no system was assessed (at least one forbidden gene was found)</span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="diff"><span class="p">@@ -1151,9 +1151,7 @@</span> class validSystemHit(object):</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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<pre style="margin: 0;">+<span id="LC503" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-class systemDetectionReport(object):</span></span>
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- __metaclass__ = abc.ABCMeta</span></span>
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+class systemDetectionReport(object, metaclass=abc.ABCMeta):</span></span>
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="diff"> def __init__(self, systems_occurrences_list, cfg):</span>
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="diff"> self._systems_occurrences_list = systems_occurrences_list</span>
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="diff"><span class="p">@@ -1425,10 +1423,10 @@</span> class systemDetectionReportOrdered(systemDetectionReport):</span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="diff"> pos_max = rep_info.max</span>
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="diff"> if pos_min < pos_max:</span>
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- pos_in_bk_2_display = range(pos_min, pos_max + 1)</span></span>
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pos_in_bk_2_display = list(range(pos_min, pos_max + 1))</span></span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="diff"> else:</span>
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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;">- before_orig = range(pos_min, rep_info.max + 1)</span></span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- after_orig = range(rep_info.min, pos_max + 1)</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ before_orig = list(range(pos_min, rep_info.max + 1))</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ after_orig = list(range(rep_info.min, pos_max + 1))</span></span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="diff"> pos_in_bk_2_display = before_orig + after_orig</span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="diff"> pos_in_rep_2_display = [pos - rep_info.min for pos in pos_in_bk_2_display]</span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="diff"> for curr_position in pos_in_rep_2_display:</span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="diff"><span class="p">@@ -1673,7 +1671,7 @@</span> def disambiguate_cluster(cluster):</span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="diff"> #print cur_cluster</span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="diff"> res_clusters.append(cur_cluster)</span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="diff"> for syst in cur_compatible: # Good list of compatible??</span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not counter_genes_compat_systems.has_key(syst.name):</span></span>
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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if syst.name not in counter_genes_compat_systems:</span></span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="diff"> counter_genes_compat_systems[syst.name] = len(cur_cluster.hits)</span>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="diff"> else:</span>
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534
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="diff"> counter_genes_compat_systems[syst.name] += len(cur_cluster.hits)</span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="diff"><span class="p">@@ -1686,7 +1684,7 @@</span> def disambiguate_cluster(cluster):</span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="diff"> #h_compat = h_clust.gene.get_compatible_systems(cluster.systems_to_detect) # tmp before yep</span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="diff"> h_compat = h_clust.gene.get_compatible_systems(cluster.systems_to_detect, False) # tmp before nope</span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="diff"> for syst in h_compat:</span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not counter_genes_compat_systems.has_key(syst.name):</span></span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if syst.name not in counter_genes_compat_systems:</span></span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="diff"> counter_genes_compat_systems[syst.name] = 1</span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="diff"> else:</span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="diff"> counter_genes_compat_systems[syst.name] += 1</span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="diff"><span class="p">@@ -1705,7 +1703,7 @@</span> def disambiguate_cluster(cluster):</span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="diff"> res_clusters.append(cur_cluster) </span>
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="diff"> for syst in cur_compatible: # Good list of compatible??</span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="diff"> #print syst.name</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 not counter_genes_compat_systems.has_key(syst.name):</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;">+ if syst.name not in counter_genes_compat_systems:</span></span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="diff"> counter_genes_compat_systems[syst.name] = len(cur_cluster.hits)</span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="diff"> else:</span>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="diff"> counter_genes_compat_systems[syst.name] += len(cur_cluster.hits)</span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="diff"><span class="p">@@ -1717,7 +1715,7 @@</span> def disambiguate_cluster(cluster):</span>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="diff"> h_compat = h_clust.gene.get_compatible_systems(cluster.systems_to_detect, False) # tmp before nope</span>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="diff"> for syst in h_compat:</span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="diff"> #print syst.name</span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not counter_genes_compat_systems.has_key(syst.name):</span></span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if syst.name not in counter_genes_compat_systems:</span></span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="diff"> counter_genes_compat_systems[syst.name] = 1</span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="diff"> counter_genes_compat_systems[syst.name] += 1</span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="diff"><span class="p">@@ -1804,11 +1802,11 @@</span> def analyze_clusters_replicon(clusters, systems, multi_systems_genes):</span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="diff"> #for putative_system in clust.compatible_systems:</span>
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="diff"> for putative_system in [s.name for s in systems_to_consider]:</span>
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="diff"> _log_out.info("Considering {}: ".format(putative_system))</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;">- if putative_system in syst_dict.keys():</span></span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if putative_system in list(syst_dict.keys()):</span></span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="diff"> so = SystemOccurence(syst_dict[putative_system])</span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="diff"> so.fill_with_cluster(clust)</span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="diff"> # NEW!</span>
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if putative_system in multi_systems_genes.keys():</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;">+ if putative_system in list(multi_systems_genes.keys()):</span></span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="diff"> so.fill_with_multi_systems_genes(multi_systems_genes[putative_system])</span>
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<td class="diff-line-num new new_line" data-linenumber="574" 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">
574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="diff"> msg = so.decision_rule()</span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="diff"> so_state = so.state</span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="diff"><span class="p">@@ -1949,7 +1947,7 @@</span> def build_clusters(hits, systems_to_detect, rep_info):</span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="diff"> positions.append(prev.position)</span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="diff"> # New : Storage of multi_system genes:</span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="diff"> if prev.gene.multi_system:</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;">- if not prev.system.name in multi_system_genes_system_wise.keys():</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;">+ if not prev.system.name in list(multi_system_genes_system_wise.keys()):</span></span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="diff"> multi_system_genes_system_wise[prev.system.name] = []</span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="diff"> multi_system_genes_system_wise[prev.system.name].append(prev)</span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="diff"> </span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="diff"><span class="p">@@ -1959,7 +1957,7 @@</span> def build_clusters(hits, systems_to_detect, rep_info):</span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="diff"> positions.append(cur.position)</span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="diff"> # New : Storage of multi_system genes:</span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="diff"> if cur.gene.multi_system:</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;">- if not cur.system.name in multi_system_genes_system_wise.keys():</span></span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if not cur.system.name in list(multi_system_genes_system_wise.keys()):</span></span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="diff"> multi_system_genes_system_wise[cur.system.name] = []</span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="diff"> multi_system_genes_system_wise[cur.system.name].append(cur)</span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="diff"> </span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="diff"><span class="p">@@ -2000,7 +1998,7 @@</span> def build_clusters(hits, systems_to_detect, rep_info):</span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="diff"> # New : Storage of multi_system genes:</span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="diff"> if prev.gene.multi_system:</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;">- if not prev.system.name in multi_system_genes_system_wise.keys():</span></span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if not prev.system.name in list(multi_system_genes_system_wise.keys()):</span></span>
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="diff"> multi_system_genes_system_wise[prev.system.name] = []</span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="diff"> multi_system_genes_system_wise[prev.system.name].append(prev)</span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="diff"> </span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="diff"><span class="p">@@ -2025,7 +2023,7 @@</span> def build_clusters(hits, systems_to_detect, rep_info):</span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="diff"> clusters.add(cur_cluster)</span>
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="diff"> # New : Storage of multi_system genes:</span>
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="diff"> if prev.gene.multi_system:</span>
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not prev.system.name in multi_system_genes_system_wise.keys():</span></span>
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if not prev.system.name in list(multi_system_genes_system_wise.keys()):</span></span>
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="diff"> multi_system_genes_system_wise[prev.system.name] = []</span>
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="diff"> multi_system_genes_system_wise[prev.system.name].append(prev)</span>
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/macsypy/system.py b/macsypy/system.py</span></span>
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613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="diff"><span class="gh" style="color: #999;">index cd37926..a0f584e 100644</span></span>
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/macsypy/system.py</span></span>
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/macsypy/system.py</span></span>
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="diff"><span class="p">@@ -52,13 +52,13 @@</span> class SystemBank(object):</span>
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="diff"> :return: True if the system is in the System factory, False otherwise</span>
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="diff"> :rtype: boolean</span>
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return system in self._system_bank.values()</span></span>
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return system in list(self._system_bank.values())</span></span>
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="diff"> def __iter__(self):</span>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="diff"> Return an iterator object on the systems contained in the bank</span>
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626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="diff"> """</span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return self._system_bank.itervalues()</span></span>
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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;">+ return iter(self._system_bank.values())</span></span>
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629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="diff"> </span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="diff"> def __len__(self):</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="gh" style="color: #999;">diff --git a/macsypy/system_parser.py b/macsypy/system_parser.py</span></span>
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633
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="diff"><span class="gh" style="color: #999;">index 2b8bd01..ad6bce0 100644</span></span>
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634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/macsypy/system_parser.py</span></span>
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/macsypy/system_parser.py</span></span>
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="diff"><span class="p">@@ -60,7 +60,7 @@</span> class SystemParser(object):</span>
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637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="diff"> diff_sys_2 = list(set(sys_2_parse.keys()) - set(parsed_systems.keys()))</span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="diff"> diff_sys += diff_sys_2</span>
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="diff"> if diff_sys == []:</span>
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return sys_2_parse.keys()</span></span>
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return list(sys_2_parse.keys())</span></span>
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="diff"> else: </span>
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="diff"> for system_name in diff_sys:</span>
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="diff"> parsed_systems[system_name] = None</span>
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/setup.py b/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="diff"><span class="gh" style="color: #999;">index c9ae28b..bea8faa 100644</span></span>
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</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;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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653
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="diff"> ################################################################################</span>
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="diff"><span class="p">@@ -17,7 +17,7 @@</span> import time</span>
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="diff"> import sys</span>
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="diff"> import os</span>
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from ConfigParser import SafeConfigParser, NoSectionError, NoOptionError</span></span>
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from configparser import SafeConfigParser, NoSectionError, NoOptionError</span></span>
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="diff"> try:</span>
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="diff"> import warnings</span>
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="diff"> except ImportError:</span>
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="diff"><span class="p">@@ -51,13 +51,13 @@</span> class check_and_build( build ):</span>
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="diff"> build.run(self)</span>
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="diff"> log.info("""</span>
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="diff"> Unit tests are available. It is _highly_ recommended to run tests now.</span>
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-to run test, run 'python setup.py test -vv'""")</span></span>
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+to run test, run 'python3 setup.py test -vv'""")</span></span>
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="diff"> def check_python(self, req):</span>
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672
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="diff"> chk = VersionPredicate(req)</span>
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673
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="diff"> ver = '.'.join([str(v) for v in sys.version_info[:2]])</span>
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674
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="diff"> if not chk.satisfied_by(ver):</span>
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675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- log.error("Invalid python version, expected {0}".format(req))</span></span>
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676
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ log.error("Invalid python3 version, expected {0}".format(req))</span></span>
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677
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="diff"> return False</span>
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678
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="diff"> return True</span>
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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="diff"> </span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="diff"><span class="p">@@ -147,7 +147,7 @@</span> class test(Command):</span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="diff"> </span>
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682
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="diff"> plat_specifier = ".{0}-{1}".format(self.plat_name, sys.version[0:3])</span>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="diff"> </span>
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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # Make it so Python 2.x and Python 2.x with --with-pydebug don't</span></span>
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685
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # Make it so Python 3.x and Python 3.x with --with-pydebug don't</span></span>
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686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="diff"> # share the same build directories. Doing so confuses the build</span>
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687
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="diff"> # process for C modules</span>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="diff"> if hasattr(sys, 'gettotalrefcount'):</span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="diff"><span class="p">@@ -200,7 +200,7 @@</span> class test(Command):</span>
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690
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="diff"> unit_res = unit_main.run(self.build_lib, [], verbosity=self.verbosity)</span>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="diff"> for test in unit_res.skipped:</span>
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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="diff"> kind_of_skipped[test[1]] = True</span>
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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;">- for skip_reason in kind_of_skipped.keys():</span></span>
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694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for skip_reason in list(kind_of_skipped.keys()):</span></span>
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695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="diff"> if skip_reason == "neither makeblast nor formatdb found in PATH":</span>
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696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="diff"> msg = """</span>
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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="diff"> #####################################################################</span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="diff"><span class="p">@@ -228,7 +228,7 @@</span> hmmsearch in config file or command line to run macsyfinder</span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="diff"> if all(result_all_tests):</span>
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700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="diff"> sys.exit(0)</span>
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701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="diff"> else:</span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sys.exit("some tests fails. Run python setup.py test -vv to have more details")</span></span>
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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sys.exit("some tests fails. Run python3 setup.py test -vv to have more details")</span></span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="diff"> </span>
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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="diff"> </span>
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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="diff"> </span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="diff"><span class="p">@@ -552,7 +552,7 @@</span> class Uninstall(Command):</span>
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708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="diff"> def clean_tree(_dir):</span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="diff"> find_prefix = False</span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="diff"> for prefix in prefixes:</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;">- print "== ", prefix, ".find(", _dir, ") = ", prefix.find(_dir)</span></span>
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712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("== ", prefix, ".find(", _dir, ") = ", prefix.find(_dir))</span></span>
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713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="diff"> if prefix.find(_dir) != -1:</span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="diff"> find_prefix = True</span>
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715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="diff"> return prefix</span>
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716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="diff"><span class="p">@@ -612,7 +612,7 @@</span> class sdist_macsy(sdist):</span>
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717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="diff"> def run(self):</span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="diff"> inst = self.distribution.command_options.get('sdist')</span>
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719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="diff"> self.macsyview_link_name = 'macsyview'</span>
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720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not inst.has_key('macsyview_dir'):</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;">+ if 'macsyview_dir' not in inst:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="722" 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">
722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="diff"> self.must_clean = False</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="723" 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">
723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="diff"> if not os.path.exists(self.macsyview_link_name):</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="724" 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">
724
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="diff"> sys.exit('Missing mandatory macsyview-dir to specify the location of macsyview project')</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="725" 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">
725
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="diff"><span class="p">@@ -710,11 +710,11 @@</span> def subst_vars(src, dst, vars):</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="726" 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">
726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="diff"> try:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="727" 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">
727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="diff"> src_file = open(src, "r")</span>
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<td class="diff-line-num new new_line" data-linenumber="728" 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">
728
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="diff"> except os.error as err:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="729" 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">
729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- raise DistutilsFileError, "could not open '{0}': {1)".format(src, err)</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="730" 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">
730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ raise DistutilsFileError("could not open '{0}': {1)".format(src, err))</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="731" 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">
731
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="diff"> try:</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="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"> dest_file = open(dst, "w")</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="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"> except os.error as err:</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="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;">- raise DistutilsFileError, "could not create '{0}': {1}".format(dst, err)</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="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="gi" style="color: #000; background-color: #dfd;">+ raise DistutilsFileError("could not create '{0}': {1}".format(dst, err))</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="736" 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">
736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="diff"> with src_file:</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="737" 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">
737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="diff"> with dest_file:</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="738" 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">
738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="diff"> for line in src_file:</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="739" 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">
739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="diff"><span class="p">@@ -722,7 +722,7 @@</span> def subst_vars(src, dst, vars):</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="740" 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">
740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="diff"> dest_file.write(new_line)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="741" 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">
741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="742" 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">
742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="diff"> </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="743" 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">
743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-require_python = ['python (>=2.7, <3.0)']</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="744" 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">
744
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+require_python = ['python (>=3.0, <4.0)']</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="745" 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">
745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="diff"> require_packages = []</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="746" 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">
746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="diff"> </span>
</pre>
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747
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="diff"> version='1.0.5'</span>
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748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="diff"><span class="p">@@ -737,7 +737,7 @@</span> in protein datasets using systems modelling and similarity search""",</span>
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749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="diff"> author_email="sabby@pasteur.fr, bneron@pasteur.fr",</span>
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750
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="diff"> classifiers=[</span>
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751
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="diff"> 'Operating System :: POSIX',</span>
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752
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 'Programming Language :: Python :: 2.7 :: Only',</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;">+ 'Programming Language :: Python :: 3.7 :: Only',</span></span>
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754
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="diff"> 'Topic :: Bioinformatics',</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"> packages=['macsypy'],</span>
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757
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/tests.py b/tests.py</span></span>
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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="diff"><span class="gh" style="color: #999;">index eb2a93d..c87af19 100644</span></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;">--- a/tests.py</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;">+++ b/tests.py</span></span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="diff"><span class="p">@@ -117,9 +117,9 @@</span> if __name__ == '__main__':</span>
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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="diff"> result_all_tests = []</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"> if args.unit:</span>
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765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\n", "#" * 70</span></span>
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766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Test Runner: Unit tests"</span></span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "#" * 70</span></span>
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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\n", "#" * 70)</span></span>
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769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Test Runner: Unit tests")</span></span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("#" * 70)</span></span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="772" 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">
772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="diff"> old_path = sys.path</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="773" 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">
773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="diff"> if 'MACSY_HOME' in os.environ:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="774" 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">
774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="diff"><span class="p">@@ -131,9 +131,9 @@</span> if __name__ == '__main__':</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="775" 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">
775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="diff"> sys.path = old_path</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="776" 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">
776
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="777" 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">
777
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="diff"> if args.functional:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="778" 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">
778
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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="LC778" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\n", "#" * 70</span></span>
</pre>
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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="gd" style="color: #000; background-color: #fdd;">- print "Test Runner: Functional tests"</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="780" 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">
780
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "#" * 70</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="781" 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">
781
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\n", "#" * 70)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="782" 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">
782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Test Runner: Functional tests")</span></span>
</pre>
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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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC783" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("#" * 70)</span></span>
</pre>
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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>
</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="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"> old_path = sys.path</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="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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC786" class="line" lang="diff"> if 'MACSY_HOME' in os.environ:</span>
</pre>
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<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="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
</td>
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="diff"><span class="p">@@ -154,9 +154,9 @@</span> if __name__ == '__main__':</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="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"> sys.path = old_path</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="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>
</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="790" 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">
790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="diff"> if args.integration:</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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC791" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\n", "#" * 70</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="792" 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">
792
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC792" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Test Runner: Integration tests"</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="793" 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">
793
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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="LC793" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "#" * 70</span></span>
</pre>
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<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="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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC794" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\n", "#" * 70)</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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC795" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Test Runner: Integration tests")</span></span>
</pre>
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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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC796" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("#" * 70)</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="diff"> old_path = sys.path</span>
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798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="diff"> integration_results = run_integration_tests(args.tests, verbosity=args.verbosity)</span>
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799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="diff"> result_all_tests.append(integration_results)</span>
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800
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/tests/functional/main.py b/tests/functional/main.py</span></span>
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801
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="diff"><span class="gh" style="color: #999;">index 4ee53a9..72ff690 100755</span></span>
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802
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/functional/main.py</span></span>
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803
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/functional/main.py</span></span>
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804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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805
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#! /usr/bin/env python</span></span>
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806
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<pre style="margin: 0;">+<span id="LC806" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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807
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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808
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="diff"> </span>
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809
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="diff"> ################################################################################</span>
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810
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/tests/functional/test_first_test.py b/tests/functional/test_first_test.py</span></span>
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="diff"><span class="gh" style="color: #999;">index a851578..501da19 100644</span></span>
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812
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/functional/test_first_test.py</span></span>
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813
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/functional/test_first_test.py</span></span>
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814
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="diff"><span class="p">@@ -84,8 +84,8 @@</span> class Test(MacsyTest):</span>
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815
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="diff"> )</span>
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816
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="diff"> except Exception as err:</span>
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817
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="diff"> msg = "macsyfinder execution failed: command = {0} : {1}".format(command, err)</span>
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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;">- print</span></span>
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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;">- print msg</span></span>
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820
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print()</span></span>
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821
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(msg)</span></span>
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822
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="diff"> raise err</span>
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823
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="diff"> </span>
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824
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="diff"> macsy_process.wait()</span>
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825
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/tests/unit/main.py b/tests/unit/main.py</span></span>
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826
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="diff"><span class="gh" style="color: #999;">index 1b66b0e..a086ff2 100755</span></span>
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827
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/unit/main.py</span></span>
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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;">+++ b/tests/unit/main.py</span></span>
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829
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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830
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#! /usr/bin/env python</span></span>
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831
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#! /usr/bin/python3</span></span>
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832
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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833
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="diff"> </span>
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834
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="diff"> ################################################################################</span>
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835
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/tests/unit/test_Config.py b/tests/unit/test_Config.py</span></span>
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836
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="diff"><span class="gh" style="color: #999;">index 3350bfd..b180482 100644</span></span>
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837
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/unit/test_Config.py</span></span>
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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;">+++ b/tests/unit/test_Config.py</span></span>
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839
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="diff"><span class="p">@@ -544,7 +544,7 @@</span> class Test(MacsyTest):</span>
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840
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="diff"> shutil.rmtree(out_dir)</span>
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841
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="diff"> except:</span>
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842
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="diff"> pass</span>
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843
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- os.makedirs(out_dir, 0775)</span></span>
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844
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ os.makedirs(out_dir, 0o775)</span></span>
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845
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<pre style="margin: 0;">+<span id="LC845" class="line" lang="diff"> f = open(os.path.join(out_dir, 'fake'), 'w')</span>
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846
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="diff"> f.close()</span>
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847
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="diff"> kwargs = {'cfg_file': "nimportnaoik",</span>
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848
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="diff"><span class="p">@@ -559,7 +559,7 @@</span> class Test(MacsyTest):</span>
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849
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="diff"> shutil.rmtree(out_dir)</span>
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850
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<pre style="margin: 0;">+<span id="LC850" class="line" lang="diff"> self.tearDown()</span>
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851
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<pre style="margin: 0;">+<span id="LC851" class="line" lang="diff"> </span>
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852
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<pre style="margin: 0;">+<span id="LC852" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- os.makedirs(out_dir, 0775)</span></span>
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853
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<pre style="margin: 0;">+<span id="LC853" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ os.makedirs(out_dir, 0o775)</span></span>
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<pre style="margin: 0;">+<span id="LC854" class="line" lang="diff"> self.cfg = Config(cfg_file="nimportnaoik",</span>
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855
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<pre style="margin: 0;">+<span id="LC855" class="line" lang="diff"> sequence_db=os.path.join(self._data_dir, "base", "test_base.fa"),</span>
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856
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="diff"> db_type='gembase',</span>
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857
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/tests/unit/test_Indexes.py b/tests/unit/test_Indexes.py</span></span>
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858
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<pre style="margin: 0;">+<span id="LC858" class="line" lang="diff"><span class="gh" style="color: #999;">index 57deb7d..b97734c 100644</span></span>
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859
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/unit/test_Indexes.py</span></span>
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860
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/unit/test_Indexes.py</span></span>
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861
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="diff"><span class="p">@@ -219,5 +219,5 @@</span> class Test(MacsyTest):</span>
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862
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="diff"> idx_dir = os.path.join(os.path.dirname(self.cfg.sequence_db))</span>
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863
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="diff"> os.chmod(idx_dir, 0000)</span>
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864
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="diff"> self.assertRaises(IOError, idx.build)</span>
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865
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- os.chmod(idx_dir, 0777)</span></span>
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866
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ os.chmod(idx_dir, 0o777)</span></span>
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867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="diff"> </span>
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868
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<pre style="margin: 0;">+<span id="LC868" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/tests/unit/test_RepliconDB.py b/tests/unit/test_RepliconDB.py</span></span>
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869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="diff"><span class="gh" style="color: #999;">index d6843be..167cbdc 100644</span></span>
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870
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/unit/test_RepliconDB.py</span></span>
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/unit/test_RepliconDB.py</span></span>
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="diff"><span class="p">@@ -120,7 +120,7 @@</span> class Test(MacsyTest):</span>
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873
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="diff"> 'PSAE001c01' : 'linear'</span>
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874
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="diff"> }</span>
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875
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="diff"> with open(self.cfg.topology_file , 'w') as f:</span>
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for k, v in db_send.items():</span></span>
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877
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for k, v in list(db_send.items()):</span></span>
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="diff"> f.write('{0} : {1}\n'.format(k,v))</span>
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879
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="diff"> RepliconDB.__init__ = self.fake_init</span>
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880
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="diff"> db = RepliconDB(self.cfg)</span>
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="diff"><span class="p">@@ -245,5 +245,5 @@</span> class Test(MacsyTest):</span>
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="diff"> ESCO030p01 = RepliconInfo(self.cfg.replicon_topology, 1, 67, self.ESCO030p01_genes)</span>
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="diff"> PSAE001c01 = RepliconInfo(self.cfg.replicon_topology, 68, 133, self.PSAE001c01_genes)</span>
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="diff"> NCXX = RepliconInfo("circular", 134, 141, self.NCDB_genes)</span>
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885
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<pre style="margin: 0;">+<span id="LC885" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertItemsEqual(db.items(), [('ESCO030p01',ESCO030p01), ('NC_xxxxx_xx',NCXX),</span></span>
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886
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<pre style="margin: 0;">+<span id="LC886" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertItemsEqual(list(db.items()), [('ESCO030p01',ESCO030p01), ('NC_xxxxx_xx',NCXX),</span></span>
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887
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<pre style="margin: 0;">+<span id="LC887" class="line" lang="diff"> ('PSAE001c01',PSAE001c01)])</span>
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888
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span></pre>
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<a href="https://salsa.debian.org/med-team/macsyfinder/compare/15a3838e173bbbdf8a2de52119d50165ea66d0db...994f55a1c15bca7567d6e6cde968499c54efbf82#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">skip_tests.patch</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"># 2to3.patch # deactivate - its more complex than this</span></pre>
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<a href="https://salsa.debian.org/med-team/macsyfinder/compare/15a3838e173bbbdf8a2de52119d50165ea66d0db...994f55a1c15bca7567d6e6cde968499c54efbf82#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,21 +4,21 @@</td>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">#export DH_VERBOSE=1</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> dh $@ --with python<span class="idiff left right">2</span> --buildsystem=pybuild</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> dh $@ --with python<span class="idiff left right">3</span> --buildsystem=pybuild</span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">override_dh_auto_install:</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> cd doc && make html</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> cd doc && make latexpdf</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> ln -sf $(shell pybuild --print build_dir --interpreter python<span class="idiff left right">) build/lib.$(shell dpkg-architecture -qDEB_BUILD_ARCH_OS)-$(shell dpkg-architecture -qDEB_BUILD_GNU_CPU)-$(shell py</span>versions -vs)</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> python setup.py install --prefix=debian/macsyfinder/usr/ --install-conf=debian/macsyfinder/etc/ --no-viewer</span>
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<td class="diff-line-num new old_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="LC12" class="line" lang="plaintext"> ln -sf $(shell pybuild --print build_dir --interpreter python<span class="idiff left right">3) build/lib.$(shell dpkg-architecture -qDEB_BUILD_ARCH_OS)-$(shell dpkg-architecture -qDEB_BUILD_GNU_CPU)-$(shell py3</span>versions -vs)</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> python<span class="idiff left right">3</span> setup.py install --prefix=debian/macsyfinder/usr/ --install-conf=debian/macsyfinder/etc/ --no-viewer</span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> # The better solution would be to use</span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> # dh_auto_install -- --prefix=/usr --install-conf=/etc --no-viewer</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> # and fiy setup.py to use --root as install location (which is ignored unfortunately)</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> # Since I have no idea how to fix setup.py here the broken config files are hacked afterwards</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> for conffile in \</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> etc/macsyfinder/macsyfinder.conf.new \</span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> usr/lib/python<span class="idiff left right">2.7</span>/site-packages/macsypy/config.py \</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> usr/lib/python<span class="idiff left right">2.7</span>/site-packages/macsypy/registries.py \</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> usr/lib/python<span class="idiff left right">3*</span>/site-packages/macsypy/config.py \</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> usr/lib/python<span class="idiff left right">3*</span>/site-packages/macsypy/registries.py \</span>
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> ; do \</span>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> sed -i 's:debian/macsyfinder::g' debian/macsyfinder/$${conffile} ; \</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> done</span>
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