Mercurial > repos > scottx611x > qualimap2_bamqc

annotate qualimap_bamqc.py @ 30:418ee04dd1b2 draft

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planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
author scottx611x
date Thu, 26 Jul 2018 16:40:19 -0400
parents 71af3fbe85be
children a77bae54b1c7
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1 #!/usr/bin/env python
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2 from __future__ import print_function
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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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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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8 OUTPUT_DIR = "qualimap_results"
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11 def qualimap_bamqc(bam_filename, genomecov_file, jv_mem_size):
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12 qualimap_command = [
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13 "qualimap", "bamqc",
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14 "-bam " + bam_filename,
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15 "-oc " + genomecov_file,
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16 "-outdir " + OUTPUT_DIR,
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17 "--java-mem-size=" + jv_mem_size
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18 ]
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
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20 try:
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21 check_call(qualimap_command)
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22 except CalledProcessError:
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23 print("Error running the qualimap bamqc", file=sys.stderr)
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26 def main():
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27 parser = argparse.ArgumentParser(
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28 description="Generate Bam Quality Statistics"
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29 )
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30 parser.add_argument('--input_file')
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31 parser.add_argument('--out_genome_file')
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32 parser.add_argument('--java_mem_size')
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34 args = parser.parse_args()
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36 qualimap_bamqc(
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37 args.input_file,
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38 args.out_genome_file,
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39 args.java_mem_size
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40 )
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42 shutil.move(OUTPUT_DIR + "/genome_results.txt", "genome_results.txt")
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43 shutil.move(OUTPUT_DIR + "/qualimapReport.html", "qualimapReport.html")
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44 shutil.make_archive(
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45 'raw_data_qualimapReport',
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46 'zip',
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47 OUTPUT_DIR + '/raw_data_qualimapReport'
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48 )
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51 if __name__ == "__main__":
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52 main()