Mercurial > repos > sanbi-uwc > novo_align

annotate novo_align.py @ 6:3938f90c9d91 draft

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planemo upload for repository https://github.com/zipho/novo_align commit 4a89d4d866533a93706ceb29077d2e9bda69aa9f
author sanbi-uwc
date Fri, 11 Mar 2016 02:32:25 -0500
parents d51c5af7a8fe
children 9a6f14e2c8fd
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
diff changeset
1 #!/usr/bin/env python
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
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2 from __future__ import print_function
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
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3 import argparse
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
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4 import shlex
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
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5 import os
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
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6 import logging
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
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7 log = logging.getLogger( __name__ )
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
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8
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
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9 def novo_align(output_filename, index_filename, fwd_file, rev_file ):
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
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10 param = r'@RG\tID:RG\tSM:$i\tPL:ILLUMINA'
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
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11 cmdline_str = "novoalign -c 8 -k -d {} -f {} {} -i PE 250, 100 -o SAM '{}' | samtools view -bS - > {}".format(
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
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12 index_filename,
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
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13 fwd_file,
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
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14 rev_file,
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
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15 param,
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
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16 output_filename)
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3938f90c9d91 planemo upload for repository https://github.com/zipho/novo_align commit 4a89d4d866533a93706ceb29077d2e9bda69aa9f
sanbi-uwc
parents: 5
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17 try:
3938f90c9d91 planemo upload for repository https://github.com/zipho/novo_align commit 4a89d4d866533a93706ceb29077d2e9bda69aa9f
sanbi-uwc
parents: 5
diff changeset
18 os.system(cmdline_str)
3938f90c9d91 planemo upload for repository https://github.com/zipho/novo_align commit 4a89d4d866533a93706ceb29077d2e9bda69aa9f
sanbi-uwc
parents: 5
diff changeset
19 except:
3938f90c9d91 planemo upload for repository https://github.com/zipho/novo_align commit 4a89d4d866533a93706ceb29077d2e9bda69aa9f
sanbi-uwc
parents: 5
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20 print("Error running the nova-align", file=sys.stderr)
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d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
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d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
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22 def newSplit(value):
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
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23 lex = shlex.shlex(value)
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
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24 lex.quotes = '"'
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
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25 lex.whitespace_split = True
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
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26 lex.commenters = ''
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
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27 return list(lex)
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
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d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
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29 def main():
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
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30 parser = argparse.ArgumentParser(description="Generate a BAM file from the Novo Align tool")
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
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31 parser.add_argument('output_filename')
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
diff changeset
32 parser.add_argument('--index_filename')
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
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33 parser.add_argument('--forward_filename')
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
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34 parser.add_argument('--reverse_filename')
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
diff changeset
35 args = parser.parse_args()
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
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d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
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37 #a dirty way of referencing the file
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
diff changeset
38 index_file_path = args.index_filename + "/" + args.index_filename.split("/")[-1]
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
diff changeset
39 novo_align(args.output_filename, index_file_path, args.forward_filename, args.reverse_filename)
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
parents:
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d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
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41 if __name__ == "__main__": main()