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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/kleborate">Debian Med / kleborate</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kleborate/commit/e4516b8636abe8ea2fd32d8468f06e83ec8a66c4">e4516b86</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-24T14:39:32Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Recommends: python3-biopython to run additional scripts
</pre>
</li>
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<strong><a href="https://salsa.debian.org/med-team/kleborate/commit/845b8cf7d51825c6c8568444993444dc78342cb0">845b8cf7</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-24T14:44:04Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Enhance patch for Python3 compatibility
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<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#e246f69e945a7c2e9a8e25cfacfcac7714c92b69">
debian/patches/python3.patch
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<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/kleborate/compare/44ecf104d5ce95dd8e9b9633dd13eb9ce3a7d3e3...845b8cf7d51825c6c8568444993444dc78342cb0#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" 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="18" 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">@@ -18,8 +18,9 @@ Package: kleborate</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Depends: ${python3:Depends},</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> ncbi-blast+ <!nocheck>,</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> mash <!nocheck></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> ncbi-blast+,</span>
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(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="LC22" class="line" lang="plaintext"> mash</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Recommends: python3-biopython</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Description: tool to screen Klebsiella genome assemblies</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> Kleborate is a tool to screen Klebsiella genome assemblies for:</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> .</span>
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<li id="e246f69e945a7c2e9a8e25cfacfcac7714c92b69">
<a href="https://salsa.debian.org/med-team/kleborate/compare/44ecf104d5ce95dd8e9b9633dd13eb9ce3a7d3e3...845b8cf7d51825c6c8568444993444dc78342cb0#e246f69e945a7c2e9a8e25cfacfcac7714c92b69"><strong>debian/patches/python3.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Tue, 24 Sep 2019 12:36:03 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Origin: https://github.com/katholt/Kleborate/issues/17</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Description: When using Python3 the executable is named python3</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff">--- a/kleborate-runner.py</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="18" 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">@@ -17,7 +18,7 @@ Description: When using Python3 the executable is named python3</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> # If resistance genes are on, run the resBLAST.py script to get its headers.</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> if args.resistance:</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- res_out = subprocess.check_output('python ' + resblast +</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ res_out = subprocess.check_output(<span class="idiff left right">'python3 '</span> + resblast +</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ res_out = subprocess.check_output(<span class="idiff left right">sys.executable + ' ' </span> + resblast +</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> ' -s ' + data_folder + '/ARGannot_r2.fasta' +</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"> ' -t ' + data_folder + '/ARGannot_clustered80_r2.csv',</span>
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23
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> shell=True)</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">@@ -26,7 +27,7 @@ Description: When using Python3 the executable is named python3</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> kaptive_table = kaptive_prefix + '_table.txt'</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"> </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;">- p = subprocess.Popen('python ' + kaptive_py +</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ p = subprocess.Popen(<span class="idiff left right">'python3 '</span> + kaptive_py +</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;">+ p = subprocess.Popen(<span class="idiff left right">sys.executable + ' ' </span> + kaptive_py +</span></span>
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"> ' -a ' + contigs +</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"> ' -k ' + kaptive_db +</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"> ' -o ' + kaptive_prefix +</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">@@ -35,7 +36,7 @@ Description: When using Python3 the executable is named python3</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"> def get_chromosome_mlst_results(mlstblast, data_folder, contigs):</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- f = os.popen('python ' + mlstblast +</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ f = os.popen(<span class="idiff left right">'python3 '</span> + mlstblast +</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ f = os.popen(<span class="idiff left right">sys.executable + ' ' </span> + mlstblast +</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="diff"> ' -s ' + data_folder + '/Klebsiella_pneumoniae.fasta' +</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="diff"> ' -d ' + data_folder + '/kpneumoniae.txt' +</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="diff"> ' -i no' +</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">@@ -44,7 +45,7 @@ Description: When using Python3 the executable is named python3</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="diff"> vir_name, vir_st_name, unknown_group_name, min_gene_count,</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="diff"> header_function):</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;">- f = os.popen('python ' + mlstblast +</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ f = os.popen(<span class="idiff left right">'python3 '</span> + mlstblast +</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ f = os.popen(<span class="idiff left right">sys.executable + ' ' </span> + mlstblast +</span></span>
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48
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="diff"> ' -s ' + data_folder + '/' + alleles_fasta +</span>
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49
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"> ' -d ' + data_folder + '/' + profiles_txt +</span>
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50
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff"> ' -i yes' +</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">@@ -53,7 +54,7 @@ Description: When using Python3 the executable is named python3</td>
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53
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="diff"> def get_hypermucoidy_results(rmpablast, data_folder, contigs):</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="diff"> hypermucoidy = '-'</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;">- f = os.popen('python ' + rmpablast +</span></span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ f = os.popen(<span class="idiff left right">'python3 '</span> + rmpablast +</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ f = os.popen(<span class="idiff left right">sys.executable + ' ' </span> + rmpablast +</span></span>
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57
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"> ' -s ' + data_folder + '/hypermucoidy.fasta' +</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="diff"> ' -d ' + data_folder + '/hypermucoidy_rmpA.txt' +</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="diff"> ' ' + contigs)</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">@@ -62,7 +63,7 @@ Description: When using Python3 the executable is named python3</td>
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62
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="diff"> def get_wzi_and_k_locus_results(mlstblast, data_folder, contigs):</span>
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63
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="diff"> wzi_st, k_type = '-', '-'</span>
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64
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- f = os.popen('python ' + mlstblast +</span></span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ f = os.popen(<span class="idiff left right">'python3 '</span> + mlstblast +</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ f = os.popen(<span class="idiff left right">sys.executable + ' ' </span> + mlstblast +</span></span>
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66
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="diff"> ' -s ' + data_folder + '/wzi.fasta' +</span>
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67
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="diff"> ' -d ' + data_folder + '/wzi.txt' +</span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="diff"> ' -i yes' +</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">@@ -71,7 +72,7 @@ Description: When using Python3 the executable is named python3</td>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="diff"> res_hits = []</span>
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72
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="diff"> if args.resistance:</span>
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73
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- f = os.popen('python ' + resblast +</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ f = os.popen(<span class="idiff left right">'python3 '</span> + resblast +</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ f = os.popen(<span class="idiff left right">sys.executable + ' ' </span> + resblast +</span></span>
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75
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="diff"> ' -s ' + data_folder + '/ARGannot_r2.fasta' +</span>
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<td class="diff-line-num old_line" data-linenumber="76" 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">
76
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="diff"> ' -t ' + data_folder + '/ARGannot_clustered80_r2.csv' +</span>
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77
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="diff"> ' -q ' + data_folder + '/QRDR_120.aa' +</span></pre>
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