Mercurial > repos > sanbi-uwc > qualimap2

annotate qualimap_bamqc.py @ 0:d87d6c0c27f5 draft

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planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
author sanbi-uwc
date Wed, 30 Mar 2016 03:19:15 -0400
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children a19abfa30ca7
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d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
diff changeset
1 #!/usr/bin/env python
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
diff changeset
2 from __future__ import print_function
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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3 import argparse
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
diff changeset
4 from subprocess import check_call, CalledProcessError
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
diff changeset
5 import shlex
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
diff changeset
6 import sys
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
diff changeset
7 import logging
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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8 log = logging.getLogger( __name__ )
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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9
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
diff changeset
10 def qualimap_bamqc( bam_filename, genomecov_file, out_dir, pdf_file, jv_mem_size):
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
diff changeset
11 #qualimap bamqc -bam R.bam.sorted_dedup.bam_realigned.bam -oc ./test.genomecov -outdir ./Kaust_kxdr/variants/qualimap/bamqc_report --outfile test.pdf --java-mem-size=16G
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
diff changeset
12 cmdline_str = "qualimap bamqc -bam {} -oc {} -outdir {} --outfile {} --java-mem-size={}".format( bam_filename,
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
diff changeset
13 genomecov_file,
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
diff changeset
14 out_dir,
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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15 pdf_file,
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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16 jv_mem_size)
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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17 cmdline = newSplit(cmdline_str)
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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18 try:
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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19 check_call(cmdline)
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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20 except CalledProcessError:
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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21 print("Error running the qualimap bamqc", file=sys.stderr)
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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23 def newSplit(value):
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
diff changeset
24 lex = shlex.shlex(value)
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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25 lex.quotes = '"'
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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26 lex.whitespace_split = True
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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27 lex.commenters = ''
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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28 return list(lex)
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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30 def main():
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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31 parser = argparse.ArgumentParser(description="Generate Bam Quality Statistics")
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
diff changeset
32 parser.add_argument('--input_file')
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
diff changeset
33 parser.add_argument('--out_genome_file', default="bam_stats.genomecov")
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
diff changeset
34 parser.add_argument('--out_dir', default="/tmp/bamstats")
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
diff changeset
35 parser.add_argument('--out_pdf_file', default="bam_stats.pdf")
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
diff changeset
36 parser.add_argument('--java_mem_size', default="8G" )
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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37
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
diff changeset
38 args = parser.parse_args()
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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39
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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40 qualimap_bamqc(args.input_file, args.out_genome_file, args.out_dir, args.out_pdf_file, args.java_mem_size)
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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41
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
diff changeset
42 if __name__ == "__main__": main()