Mercurial > repos > sanbi-uwc > qualimap2

annotate qualimap_multi_bamqc.py @ 6:8dff744880cd draft

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planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
author sanbi-uwc
date Tue, 05 Apr 2016 04:45:41 -0400
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8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
sanbi-uwc
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1 #!/usr/bin/env python
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
sanbi-uwc
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2 from __future__ import print_function
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
sanbi-uwc
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3 import argparse
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
sanbi-uwc
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4 from subprocess import check_call, CalledProcessError
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
sanbi-uwc
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5 import shlex
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
sanbi-uwc
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6 import sys
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
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7 import logging
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
sanbi-uwc
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8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
sanbi-uwc
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9 log = logging.getLogger(__name__)
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
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8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
sanbi-uwc
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8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
sanbi-uwc
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12 def qualimap_multi_bamqc(input_file, out_dir, jv_mem_size):
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
sanbi-uwc
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13 #multi-bamqc -r -d ./bamlistinput.txt -outdir ./Kaust_kxdr/variants/qualimap -outformat PDF --java-mem-size=16G
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
sanbi-uwc
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14 cmdline_str = "qualimap multi-bamqc -r -d {} -outdir {} -outformat PDF --java-mem-size={}".format(input_file,
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
sanbi-uwc
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15 out_dir,
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
sanbi-uwc
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16 jv_mem_size)
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
sanbi-uwc
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17 cmdline = new_split(cmdline_str)
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
sanbi-uwc
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18 try:
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
sanbi-uwc
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19 check_call(cmdline)
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
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20 except CalledProcessError:
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
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21 print("Error running the qualimap multi bamqc", file=sys.stderr)
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
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8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
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8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
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24 def new_split(value):
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
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25 lex = shlex.shlex(value)
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
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26 lex.quotes = '"'
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
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27 lex.whitespace_split = True
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
sanbi-uwc
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28 lex.commenters = ''
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
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29 return list(lex)
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
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8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
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8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
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32 def main():
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
sanbi-uwc
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33 parser = argparse.ArgumentParser(description="Generate Bam Quality Statistics")
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
sanbi-uwc
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34 parser.add_argument('--input_file')
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
sanbi-uwc
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35 parser.add_argument('--out_dir', default="/tmp/bamstats")
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
sanbi-uwc
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36 parser.add_argument('--java_mem_size', default="8G")
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
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8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
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38 args = parser.parse_args()
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
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8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
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40 qualimap_multi_bamqc(args.input_file, args.out_dir, args.java_mem_size)
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
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8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
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8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
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43 if __name__ == "__main__": main()