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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/mcaller">Debian Med / mcaller</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mcaller/-/commit/b524abd39247bdbec9d982c4d19a66787d05fe08">b524abd3</a></strong>
<div>
<span>by Steffen Möller</span>
<i>at 2021-06-20T00:23:29+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adjusted patches.
</pre>
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<h4>6 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#a513ae7946ecc441acbe503d01f239c9b0aae70e">
<span class="deleted-file">
−
debian/patches/pickl3latin.patch
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</a>
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<li class="file-stats">
<a href="#c95b49fcdcf94cb632aec008933196e57cb26c3c">
debian/patches/python2to3.patch
</a>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#21f07864a3929c097dd38d0ed1d1b912b1f34a64">
debian/patches/shebang.patch
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</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/mcaller/-/commit/b524abd39247bdbec9d982c4d19a66787d05fe08#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,14 +4,13 @@ mcaller (1.0.3+git20210331.f7a616a-1) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> -- Steffen Möller <moeller@debian.org> Sat, 19 Jun 2021 23:59:32 +0200</span>
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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">mcaller (1.0-1) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">mcaller (1.0-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * Initial release (Closes: #969558)</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num" 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"> BLOCKER:</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> - installation should be done properly - needs setup.py ?!?</span>
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<td class="old_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> - .py in executables (secondary)</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> - README and test files does seem to be in sync with current code.</span>
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<td class="old_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> * New upstream version</span>
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<td class="old_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> * Standards-Version: 4.5.1 (routine-update)</span>
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<td class="old_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> * Remove trailing whitespace in debian/rules (routine-update)</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/mcaller/-/commit/b524abd39247bdbec9d982c4d19a66787d05fe08#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,6 +7,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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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"> python3-all,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python3-setuptools,</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> python3-seaborn,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> help2man</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Standards-Version: 4.5.1</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/mcaller</span>
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<a href="https://salsa.debian.org/med-team/mcaller/-/commit/b524abd39247bdbec9d982c4d19a66787d05fe08#a513ae7946ecc441acbe503d01f239c9b0aae70e"><strong>debian/patches/pickl3latin.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: mcaller/extract_contexts.py</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mcaller.orig/extract_contexts.py</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mcaller/extract_contexts.py</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">@@ -120,7 +120,7 @@</span> def extract_features(tsv_input,fasta_inp</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> if not train:</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> tsv_output = '.'.join(tsv_input.split('.')[:-1])+'.diffs.'+str(k)+'.tmp'+str(startline)</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> modfi = open(modelfile,'rb')</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;">- model = pickle.load(modfi)</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;">+ model = pickle.load(modfi,encoding="latin1")</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> modfi.close()</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> if type(model) != dict:</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> model = {'general':model} #for compatibility with previously trained model</span></pre>
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<a href="https://salsa.debian.org/med-team/mcaller/-/commit/b524abd39247bdbec9d982c4d19a66787d05fe08#c95b49fcdcf94cb632aec008933196e57cb26c3c"><strong>debian/patches/python2to3.patch</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: mcaller/compare_genomes.py</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mcaller.orig/compare_genomes.py</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mcaller/compare_genomes.py</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">@@ -28,7 +28,7 @@</span> def compare_by_position(bed1,bed2,xmfa):</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> t,pval3 = 'none','missing df'</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> d,pval4 = ks_2samp(pos_dict[0][pos][1],pos_dict[0][pos][1])</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> if pval4 < 0.9:</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print pos, pos_dict[0][pos][0], pos_dict[1][pos][0], pval, pval2, pval3, pval4</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(pos, pos_dict[0][pos][0], pos_dict[1][pos][0], pval, pval2, pval3, pval4)</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="p">@@ -43,7 +43,7 @@</span> def main():</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> args = parser.parse_args()</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> if args.version:</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print 'mCallerNP 0.1'</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('mCallerNP 0.1')</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> sys.exit(0)</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"> assert os.path.isfile(args.bed1), 'file not found at '+args.bed1</span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: mcaller/make_bed.py</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mcaller.orig/make_bed.py</span></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">@@ -33,51 +11,11 @@ Index: mcaller/make_bed.py</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> try:</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> csome,read,pos,context,values,strand,label,prob = tuple(line.split('\t'))</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> except: #for backwards compatibility; does not work with verbose results</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="p">@@ -157,9 +157,9 @@</span> def aggregate_by_pos(meth_fi,aggfi,depth</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"> outfi.write(out_line+'\n')</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"> if not pos_list:</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"> if not control:</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;">- print count, 'methylated loci found with min depth', depth_thresh, 'reads'</span></span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(count, 'methylated loci found with min depth', depth_thresh, 'reads')</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"> else:</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;">- print count, 'unmethylated loci found with min depth', depth_thresh, 'reads'</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;">+ print(count, 'unmethylated loci found with min depth', depth_thresh, 'reads')</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"> def main():</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"> #parse command line options</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"><span class="p">@@ -180,7 +180,7 @@</span> def main():</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"> args = parser.parse_args()</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"> if args.version:</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print 'mCallerNP 0.3'</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('mCallerNP 0.3')</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"> sys.exit(0)</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"> assert os.path.isfile(args.mCaller_file), 'file not found at '+args.mCaller_file</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"><span class="p">@@ -197,7 +197,7 @@</span> def main():</span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"> if not os.path.isdir(args.plotdir):</span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"> os.mkdir(args.plotdir)</span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print args.mCaller_file</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(args.mCaller_file)</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"> aggregate_by_pos(args.mCaller_file,output_file,args.min_read_depth,args.mod_threshold,args.positions,args.control,args.vo,args.gff,args.ref,args.plot,args.plotdir,args.plotsummary)</span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: mcaller/extract_contexts.py</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mcaller.orig/extract_contexts.py</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mcaller/extract_contexts.py</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"><span class="p">@@ -2,8 +2,7 @@</span> from collections import defaultdict</span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"> from Bio import SeqIO</span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"> import scipy.stats as ss</span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"> import numpy as np</span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import cPickle</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#import _pickle as cPickle</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import pickle</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="diff"> import sys</span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="diff"> import re</span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="diff"> import os</span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="diff"><span class="p">@@ -52,7 +51,7 @@</span> def methylate_positions(ref_seq,position</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -52,7 +52,7 @@</span> def methylate_positions(ref_seq,position</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> print('Base {} does not correspond to methylated base - check reference positions are 0-based - quitting thread now'.format(pos))</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> sys.exit(0)</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">@@ -86,7 +24,7 @@ Index: mcaller/extract_contexts.py</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> return meth_seq</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"> #extract signals around methylated positions from tsv</span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="diff"><span class="p">@@ -61,7 +6<span class="idiff left right">0</span>,7 @@</span> def methylate_references(ref_seq,base,mo</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="p">@@ -61,7 +6<span class="idiff left right">1</span>,7 @@</span> def methylate_references(ref_seq,base,mo</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"> if not positions and motif:</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"> meth_fwd = methylate_motifs(ref_seq,motif,base)</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"> meth_rev = methylate_motifs(ref_seq,revcomp(motif),base_comps[base])</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">@@ -95,48 +33,7 @@ Index: mcaller/extract_contexts.py</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"> elif positions:</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="diff"> fwd_pos = [int(pos.split()[1]) for pos in open(positions,'r').read().split('\n') if len(pos.split()) > 1 and pos.split()[2] == '+' and pos.split()[0] == contig]</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"> rev_pos = [int(pos.split()[1]) for pos in open(positions,'r').read().split('\n') if len(pos.split()) > 1 and pos.split()[2] == '-' and pos.split()[0] == contig]</span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="diff"><span class="p">@@ -121,7 +120,7 @@</span> def extract_features(tsv_input,fasta_inp</span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="diff"> if not train:</span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="diff"> tsv_output = '.'.join(tsv_input.split('.')[:-1])+'.diffs.'+str(k)+'.tmp'+str(startline)</span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="diff"> modfi = open(modelfile,'rb')</span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- model = cPickle.load(modfi)</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ model = pickle.load(modfi)</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="diff"> modfi.close()</span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="diff"> if type(model) != dict:</span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="diff"> model = {'general':model} #for compatibility with previously trained model</span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="diff"><span class="p">@@ -168,7 +167,7 @@</span> def extract_features(tsv_input,fasta_inp</span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="diff"> read_pos = int(read_pos)</span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="diff"> reference_kmer = meth_ref[read_pos:read_pos+k]</span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="diff"> #if read_name == last_read and (reference_kmer != revcomp('M'.join(ref_kmer.split('A')),rev) and reference_kmer != revcomp('M'.join(ref_kmer.split('T')),rev)) : #true at pseudomethylated positions (to check) TODO: remove this</span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # print 'issue with reference kmer in line', line, reference_kmer, rev, revcomp('M'.join(ref_kmer.split('A')),rev)</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # print('issue with reference kmer in line', line, reference_kmer, rev, revcomp('M'.join(ref_kmer.split('A')),rev))</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="diff"> # sys.exit(0)</span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="diff"> #if finished context for previous potentially modified position, save and reset</span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="diff"><span class="p">@@ -212,15 +211,15 @@</span> def extract_features(tsv_input,fasta_inp</span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="diff"> towrite.append([chrom,last_read,str(mpos),context,','.join([str(diff) for diff in diffs]),strand(last_rev),label])</span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="diff"> last_info = last_read+'\t'+str(mpos)+'\t'+context+'\t'+','.join([str(diff) for diff in diffs])+'\t'+strand(last_rev)</span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="diff"> except (IndexError,KeyError) as e:</span>
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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print last_read+'\t'+str(mpos)+'\t'+context+'\t'+','.join([str(diff) for diff in diffs])+'\t'+strand(last_rev),'- Index or Key Error'</span></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print model.keys(), base_model.keys(), context[int(len(context)/2):int(len(context)/2)+2]</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print e</span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print model[twobase_model].predict_proba([diffs])</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;">+ print(last_read+'\t'+str(mpos)+'\t'+context+'\t'+','.join([str(diff) for diff in diffs])+'\t'+strand(last_rev),'- Index or Key Error')</span></span>
</pre>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(model.keys(), base_model.keys(), context[int(len(context)/2):int(len(context)/2)+2])</span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(e)</span></span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(model[twobase_model].predict_proba([diffs]))</span></span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="diff"> sys.exit(0)</span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="diff"> else:</span>
</pre>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print last_read+'\t'+str(mpos)+'\t'+context+'\t'+','.join([str(diff) for diff in diffs])+'\t'+strand(last_rev)</span></span>
</pre>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print read_name, rev, last_read, last_rev, last_first</span></span>
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<td class="old_line diff-line-num old" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print read_kmer,reference_kmer, ref_kmer, last_pos_in_kmer, mspacing, pos_in_kmer</span></span>
</pre>
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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;">+ print(last_read+'\t'+str(mpos)+'\t'+context+'\t'+','.join([str(diff) for diff in diffs])+'\t'+strand(last_rev))</span></span>
</pre>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(read_name, rev, last_read, last_rev, last_first)</span></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(read_kmer,reference_kmer, ref_kmer, last_pos_in_kmer, mspacing, pos_in_kmer)</span></span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="diff"> sys.exit(0)</span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="diff"> num_observations += 1</span>
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<td class="old_line diff-line-num old" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="diff"> if num_observations%5000 == 0:</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="diff"><span class="p">@@ -229,7 +228,7 @@</span> def extract_features(tsv_input,fasta_inp</span>
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<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="p">@@ -233,7 +233,7 @@</span> def extract_features(tsv_input,fasta_inp</span>
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140
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"> pos_set.add(mpos)</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="141" 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">
141
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="diff"> read_set.add(last_read)</span>
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<td class="old_line diff-line-num" data-linenumber="142" 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">
142
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="diff"> if len(read_set)%1000 == 0 and len(read_set) > last_read_num:</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">@@ -145,48 +42,11 @@ Index: mcaller/extract_contexts.py</td>
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145
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="diff"> last_read_num = len(read_set)</span>
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146
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="diff"> else:</span>
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147
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44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="diff"> skipped_skips.add((last_read,mpos))</span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="diff"><span class="p">@@ -252,12 +251,12 @@</span> def extract_features(tsv_input,fasta_inp</span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="diff"> diff_col = diffs</span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="diff"> if len(diff_col) != k:</span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="diff"> try:</span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print last_info,'- n diffs off'</span></span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(last_info,'- n diffs off')</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="diff"> except:</span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="diff"> pass</span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="diff"> #GGCGCM 613883 613878 False 2289b392-746e-4fa0-8226-d3ac661c9620_Basecall_2D_template 2289b392-746e-4fa0-8226-d3ac661c9620_Basecall_2D_template [[], [], [], [], [], [], []] 7</span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="diff"> </span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print reference_kmer,last_mpos,mpos,mspacing,read_pos,read_pos-last_mpos,read_name,last_read,diff_col,mspacing, last_diff_col, last_diff_col[:-mspacing]</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(reference_kmer,last_mpos,mpos,mspacing,read_pos,read_pos-last_mpos,read_name,last_read,diff_col,mspacing, last_diff_col, last_diff_col[:-mspacing])</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="diff"> diff_col = [[] for i in range(k)]</span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="diff"> sys.exit(0)</span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="diff"> </span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: mcaller/mCaller.py</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mcaller.orig/mCaller.py</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mcaller/mCaller.py</span></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="diff"><span class="p">@@ -3,8 +3,8 @@</span></span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="diff"> #Alexa McIntyre, 2016-2018</span>
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="diff"> import sys</span>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-assert sys.version_info >= (2,7) and sys.version_info < (3,0), 'please use python 2.7'</span></span>
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import cPickle</span></span>
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#assert sys.version_info >= (2,7) and sys.version_info < (3,0), 'please use python 2.7'</span></span>
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import pickle</span></span>
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="diff"> #import _pickle as cPickle</span>
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="diff"> from collections import defaultdict</span>
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="diff"> import numpy as np</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: mcaller/train_model.py</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mcaller.orig/train_model.py</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mcaller/train_model.py</span></span>
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="diff"><span class="p">@@ -1,5 +1,4 @@</span></span>
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import cPickle</span></span>
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#import _pickle as cPickle</span></span>
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import pickle</span></span>
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="diff"> import numpy as np</span>
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="diff"> from plotlib import *</span>
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="diff"> from sklearn.model_selection import RandomizedSearchCV</span>
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="diff"><span class="p">@@ -34,7 +33,7 @@</span> def report(results, n_top):</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="p">@@ -33,7 +33,7 @@</span> def report(results, n_top):</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"> def train_classifier(signals,groups,modelfile,classifier='NN',plot=False): #TODO: set order of labels</span>
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191
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff"> models = {}</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="diff"> for twobase_model in signals:</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">@@ -195,35 +55,3 @@ Index: mcaller/train_model.py</td>
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195
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55
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="diff"> #sys.exit(0)</span>
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196
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"> #print(twobase_model)</span>
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57
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"> if classifier == 'RF':</span></pre>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="diff"><span class="p">@@ -86,9 +85,9 @@</span> def train_classifier(signals,groups,mode</span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="diff"> sigs = sigs + signals[twobase_model][label][:num_examples]</span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="diff"> grps = grps + groups[twobase_model][label][:num_examples]</span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="diff"> </span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print labs[:10]</span></span>
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print sigs[:10]</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print grps[:10]</span></span>
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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(labs[:10])</span></span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(sigs[:10])</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;">+ print(grps[:10])</span></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="diff"> </span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="diff"> scores = cross_val_score(model,sigs,labs,cv=gfk,groups=grps)</span>
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210
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="diff"> print("%s %s model scores: %s" %(classifier,twobase_model,','.join([str(s) for s in scores])))</span>
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="diff"><span class="p">@@ -109,7 +108,7 @@</span> def train_classifier(signals,groups,mode</span>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="diff"> plot_training_probabilities(prob_scores,twobase_model) </span>
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="diff"> modfi = open(modelfile,'wb')</span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cPickle.dump(models,modfi)</span></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pickle.dump(models,modfi)</span></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="diff"> modfi.close()</span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="diff"> return models</span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: mcaller/plotlib.py</span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mcaller.orig/plotlib.py</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mcaller/plotlib.py</span></span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">-<span id="LC226" 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="LC227" class="line" lang="diff"> import sys</span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="diff"> import os</span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="diff"> import matplotlib.pyplot as plt</span></pre>
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<a href="https://salsa.debian.org/med-team/mcaller/-/commit/b524abd39247bdbec9d982c4d19a66787d05fe08#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">shebang.patch</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">python2to3.patch</span></pre>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">pickl3latin.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/mcaller/-/commit/b524abd39247bdbec9d982c4d19a66787d05fe08#21f07864a3929c097dd38d0ed1d1b912b1f34a64"><strong>debian/patches/shebang.patch</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">@@ -28,3 +28,13 @@ Index: mcaller-0.0/make_bed.py</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"> import sys</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"> import numpy as np</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"> from Bio import SeqIO</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">Index: mcaller/plotlib.py</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mcaller.orig/plotlib.py</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;">+++ mcaller/plotlib.py</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> import sys</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> import os</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> import matplotlib.pyplot as plt</span></pre>
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