Mercurial > repos > scottx611x > qualimap2_bamqc

annotate qualimap_bamqc.py @ 23:cefa83db3ebf draft

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planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
author scottx611x
date Thu, 26 Jul 2018 15:58:53 -0400
parents 4e5e0a116434
children 1f206c5af024
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716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
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1 #!/usr/bin/env python
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
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2 from __future__ import print_function
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
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3 import argparse
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
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4 from subprocess import check_call, CalledProcessError
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cefa83db3ebf planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
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5 import shutil
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6 import sys
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
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9 def qualimap_bamqc(bam_filename, genomecov_file, jv_mem_size):
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10 qualimap_command = [
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11 "qualimap", "bamqc",
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12 "-bam " + bam_filename,
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13 "-oc " + genomecov_file,
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14 "-outdir .",
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716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
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15 "--java-mem-size=" + jv_mem_size
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
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16 ]
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
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18 try:
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19 check_call(qualimap_command)
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20 except CalledProcessError:
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21 print("Error running the qualimap bamqc", file=sys.stderr)
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24 def main():
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25 parser = argparse.ArgumentParser(
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26 description="Generate Bam Quality Statistics"
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27 )
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28 parser.add_argument('--input_file')
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29 parser.add_argument('--out_genome_file')
cefa83db3ebf planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
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30 parser.add_argument('--java_mem_size')
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32 args = parser.parse_args()
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34 qualimap_bamqc(
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
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35 args.input_file,
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
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36 args.out_genome_file,
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
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37 args.java_mem_size
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38 )
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40 shutil.make_archive(
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41 'raw_data_qualimapReport.zip',
cefa83db3ebf planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
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42 'zip',
cefa83db3ebf planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
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43 'qualimap_results/raw_data_qualimapReport/'
cefa83db3ebf planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
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44 )
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48 if __name__ == "__main__":
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49 main()