Mercurial > repos > sanbi-uwc > novo_align

annotate novo_align.py @ 35:93eac6448bbd draft default tip

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planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/novo_align commit bb41321bf6e040faabb024b029df45169cdbca7f
author sanbi-uwc
date Thu, 31 May 2018 05:37:02 -0400
parents fc134b9ac951
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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482aef16b6f5 planemo upload for repository https://github.com/zipho/novo_align commit 3aa343058f631ac4117c9bc86989dc449f84135f
sanbi-uwc
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1 #!/usr/bin/env python
482aef16b6f5 planemo upload for repository https://github.com/zipho/novo_align commit 3aa343058f631ac4117c9bc86989dc449f84135f
sanbi-uwc
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2 from __future__ import print_function
482aef16b6f5 planemo upload for repository https://github.com/zipho/novo_align commit 3aa343058f631ac4117c9bc86989dc449f84135f
sanbi-uwc
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3 import argparse
482aef16b6f5 planemo upload for repository https://github.com/zipho/novo_align commit 3aa343058f631ac4117c9bc86989dc449f84135f
sanbi-uwc
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4 import shlex
482aef16b6f5 planemo upload for repository https://github.com/zipho/novo_align commit 3aa343058f631ac4117c9bc86989dc449f84135f
sanbi-uwc
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5 import os
482aef16b6f5 planemo upload for repository https://github.com/zipho/novo_align commit 3aa343058f631ac4117c9bc86989dc449f84135f
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6 import sys
482aef16b6f5 planemo upload for repository https://github.com/zipho/novo_align commit 3aa343058f631ac4117c9bc86989dc449f84135f
sanbi-uwc
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7 import logging
482aef16b6f5 planemo upload for repository https://github.com/zipho/novo_align commit 3aa343058f631ac4117c9bc86989dc449f84135f
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8 log = logging.getLogger( __name__ )
482aef16b6f5 planemo upload for repository https://github.com/zipho/novo_align commit 3aa343058f631ac4117c9bc86989dc449f84135f
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c6e99afd59a8 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/novo_align commit 928e9337a1e33476053e38f1c07247b2306d3209
sanbi-uwc
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11 def novo_align(out_file, out_stats, index_filename, fwd_file, rev_file ):
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12 param = r'@RG\tID:RG\tSM:$i\tPL:ILLUMINA'
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c6e99afd59a8 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/novo_align commit 928e9337a1e33476053e38f1c07247b2306d3209
sanbi-uwc
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13 cmdline_str = "novoalign -c 8 -k -d {} -f {} {} -i PE 250, 100 -o SAM '{}' 2> {} > {}".format(
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482aef16b6f5 planemo upload for repository https://github.com/zipho/novo_align commit 3aa343058f631ac4117c9bc86989dc449f84135f
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14 index_filename,
482aef16b6f5 planemo upload for repository https://github.com/zipho/novo_align commit 3aa343058f631ac4117c9bc86989dc449f84135f
sanbi-uwc
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15 fwd_file,
482aef16b6f5 planemo upload for repository https://github.com/zipho/novo_align commit 3aa343058f631ac4117c9bc86989dc449f84135f
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16 rev_file,
482aef16b6f5 planemo upload for repository https://github.com/zipho/novo_align commit 3aa343058f631ac4117c9bc86989dc449f84135f
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17 param,
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18 out_stats,
c6e99afd59a8 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/novo_align commit 928e9337a1e33476053e38f1c07247b2306d3209
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19 out_file)
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20 try:
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21 os.system(cmdline_str)
482aef16b6f5 planemo upload for repository https://github.com/zipho/novo_align commit 3aa343058f631ac4117c9bc86989dc449f84135f
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22 except:
482aef16b6f5 planemo upload for repository https://github.com/zipho/novo_align commit 3aa343058f631ac4117c9bc86989dc449f84135f
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23 print("Error running the nova-align", file=sys.stderr)
482aef16b6f5 planemo upload for repository https://github.com/zipho/novo_align commit 3aa343058f631ac4117c9bc86989dc449f84135f
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26 def newSplit(value):
482aef16b6f5 planemo upload for repository https://github.com/zipho/novo_align commit 3aa343058f631ac4117c9bc86989dc449f84135f
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27 lex = shlex.shlex(value)
482aef16b6f5 planemo upload for repository https://github.com/zipho/novo_align commit 3aa343058f631ac4117c9bc86989dc449f84135f
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28 lex.quotes = '"'
482aef16b6f5 planemo upload for repository https://github.com/zipho/novo_align commit 3aa343058f631ac4117c9bc86989dc449f84135f
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29 lex.whitespace_split = True
482aef16b6f5 planemo upload for repository https://github.com/zipho/novo_align commit 3aa343058f631ac4117c9bc86989dc449f84135f
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30 lex.commenters = ''
482aef16b6f5 planemo upload for repository https://github.com/zipho/novo_align commit 3aa343058f631ac4117c9bc86989dc449f84135f
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31 return list(lex)
482aef16b6f5 planemo upload for repository https://github.com/zipho/novo_align commit 3aa343058f631ac4117c9bc86989dc449f84135f
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34 def main():
482aef16b6f5 planemo upload for repository https://github.com/zipho/novo_align commit 3aa343058f631ac4117c9bc86989dc449f84135f
sanbi-uwc
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35 parser = argparse.ArgumentParser(description="Generate a BAM file from the Novo Align tool")
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c6e99afd59a8 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/novo_align commit 928e9337a1e33476053e38f1c07247b2306d3209
sanbi-uwc
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36 parser.add_argument('out_file')
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fc134b9ac951 planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/novo_align commit a5e4ca4a66eb4e315ca564238e27e03936eea6fa
sanbi-uwc
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37 parser.add_argument('--out_stats')
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38 parser.add_argument('--index_filename')
482aef16b6f5 planemo upload for repository https://github.com/zipho/novo_align commit 3aa343058f631ac4117c9bc86989dc449f84135f
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39 parser.add_argument('--forward_filename')
482aef16b6f5 planemo upload for repository https://github.com/zipho/novo_align commit 3aa343058f631ac4117c9bc86989dc449f84135f
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40 parser.add_argument('--reverse_filename')
482aef16b6f5 planemo upload for repository https://github.com/zipho/novo_align commit 3aa343058f631ac4117c9bc86989dc449f84135f
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41 args = parser.parse_args()
482aef16b6f5 planemo upload for repository https://github.com/zipho/novo_align commit 3aa343058f631ac4117c9bc86989dc449f84135f
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42
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parents: 31
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43 novo_align(args.out_file, args.out_stats, args.index_filename, args.forward_filename, args.reverse_filename)
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46 if __name__ == "__main__":
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47 main()