Mercurial > repos > scottx611x > qualimap2_bamqc

annotate qualimap_bamqc.py @ 43:2395818cb1f1 draft

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planemo upload for repository https://github.com/scottx611x/qualimap2 commit 9fafbbc012490e70d06fcef4704a1e4a45b382c5-dirty
author scottx611x
date Sun, 29 Jul 2018 14:12:32 -0400
parents c53375e61b33
children 4cfe71d40d44
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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
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4 import os
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5 from subprocess import check_call, CalledProcessError
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6 import shutil
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7 import sys
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9 QUALIMAP_OUPUT_DIR = "qualimap_results"
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12 def qualimap_bamqc(bam_filename, jv_mem_size):
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13 qualimap_command = [
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14 "qualimap", "bamqc",
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15 "-bam " + bam_filename,
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16 "-outdir " + QUALIMAP_OUPUT_DIR,
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17 "--java-mem-size=" + jv_mem_size
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18 ]
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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_dir')
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32 parser.add_argument('--out_results')
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33 parser.add_argument('--out_zip')
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34 parser.add_argument('--java_mem_size')
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36 args = parser.parse_args()
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38 qualimap_bamqc(
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39 args.input_file,
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40 QUALIMAP_OUPUT_DIR,
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41 args.java_mem_size
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42 )
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43
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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 os.path.join(QUALIMAP_OUPUT_DIR, 'raw_data_qualimapReport')
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48 )
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50 shutil.move("raw_data_qualimapReport.zip", args.out_zip)
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51 shutil.move(
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52 os.path.join(QUALIMAP_OUPUT_DIR, "genome_results.txt"),
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53 args.out_results
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54 )
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56 if __name__ == "__main__":
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57 main()