Mercurial > repos > sanbi-uwc > qualimap2

annotate qualimap_bamqc.py @ 4:a19abfa30ca7 draft

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planemo upload for repository https://github.com/zipho/qualimap2 commit a84c585723c4499569d24c6cdaa7192113013159
author sanbi-uwc
date Tue, 05 Apr 2016 03:34:34 -0400
parents d87d6c0c27f5
children 465131fb4ce9
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d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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1 #!/usr/bin/env python
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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2 from __future__ import print_function
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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3 import argparse
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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4 from subprocess import check_call, CalledProcessError
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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5 import shlex
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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6 import sys
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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7 import logging
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a19abfa30ca7 planemo upload for repository https://github.com/zipho/qualimap2 commit a84c585723c4499569d24c6cdaa7192113013159
sanbi-uwc
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a19abfa30ca7 planemo upload for repository https://github.com/zipho/qualimap2 commit a84c585723c4499569d24c6cdaa7192113013159
sanbi-uwc
parents: 0
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9 log = logging.getLogger(__name__)
a19abfa30ca7 planemo upload for repository https://github.com/zipho/qualimap2 commit a84c585723c4499569d24c6cdaa7192113013159
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d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
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a19abfa30ca7 planemo upload for repository https://github.com/zipho/qualimap2 commit a84c585723c4499569d24c6cdaa7192113013159
sanbi-uwc
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12 def qualimap_bamqc(bam_filename, genomecov_file, out_dir, jv_mem_size):
a19abfa30ca7 planemo upload for repository https://github.com/zipho/qualimap2 commit a84c585723c4499569d24c6cdaa7192113013159
sanbi-uwc
parents: 0
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13 cmdline_str = "qualimap bamqc -bam {} -oc {} -outdir {} --outfile {} --java-mem-size={}".format(bam_filename,
a19abfa30ca7 planemo upload for repository https://github.com/zipho/qualimap2 commit a84c585723c4499569d24c6cdaa7192113013159
sanbi-uwc
parents: 0
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14 genomecov_file,
a19abfa30ca7 planemo upload for repository https://github.com/zipho/qualimap2 commit a84c585723c4499569d24c6cdaa7192113013159
sanbi-uwc
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15 out_dir,
a19abfa30ca7 planemo upload for repository https://github.com/zipho/qualimap2 commit a84c585723c4499569d24c6cdaa7192113013159
sanbi-uwc
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16 jv_mem_size)
a19abfa30ca7 planemo upload for repository https://github.com/zipho/qualimap2 commit a84c585723c4499569d24c6cdaa7192113013159
sanbi-uwc
parents: 0
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17 cmdline = new_split(cmdline_str)
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d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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18 try:
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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19 check_call(cmdline)
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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20 except CalledProcessError:
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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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
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a19abfa30ca7 planemo upload for repository https://github.com/zipho/qualimap2 commit a84c585723c4499569d24c6cdaa7192113013159
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a19abfa30ca7 planemo upload for repository https://github.com/zipho/qualimap2 commit a84c585723c4499569d24c6cdaa7192113013159
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24 def new_split(value):
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d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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25 lex = shlex.shlex(value)
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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26 lex.quotes = '"'
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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27 lex.whitespace_split = True
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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28 lex.commenters = ''
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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29 return list(lex)
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
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a19abfa30ca7 planemo upload for repository https://github.com/zipho/qualimap2 commit a84c585723c4499569d24c6cdaa7192113013159
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d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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32 def main():
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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33 parser = argparse.ArgumentParser(description="Generate Bam Quality Statistics")
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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34 parser.add_argument('--input_file')
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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35 parser.add_argument('--out_genome_file', default="bam_stats.genomecov")
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a19abfa30ca7 planemo upload for repository https://github.com/zipho/qualimap2 commit a84c585723c4499569d24c6cdaa7192113013159
sanbi-uwc
parents: 0
diff changeset
36 parser.add_argument('--out_dir', default="/tmp/bamstats")
a19abfa30ca7 planemo upload for repository https://github.com/zipho/qualimap2 commit a84c585723c4499569d24c6cdaa7192113013159
sanbi-uwc
parents: 0
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37 parser.add_argument('--java_mem_size', default="8G")
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d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
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39 args = parser.parse_args()
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a19abfa30ca7 planemo upload for repository https://github.com/zipho/qualimap2 commit a84c585723c4499569d24c6cdaa7192113013159
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a19abfa30ca7 planemo upload for repository https://github.com/zipho/qualimap2 commit a84c585723c4499569d24c6cdaa7192113013159
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41 qualimap_bamqc(args.input_file, args.out_genome_file, args.out_dir, args.java_mem_size)
a19abfa30ca7 planemo upload for repository https://github.com/zipho/qualimap2 commit a84c585723c4499569d24c6cdaa7192113013159
sanbi-uwc
parents: 0
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d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
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d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
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44 if __name__ == "__main__": main()