Mercurial > repos > sanbi-uwc > novo_align

annotate novo_align.py @ 16:a2bc4041241c draft

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planemo upload for repository https://github.com/zipho/novo_align commit 5f66b8469dedd0905e0d9fd8d37194575f77ed26-dirty
author sanbi-uwc
date Mon, 09 Jan 2017 08:34:13 -0500
parents 8553432eb6d8
children 94ae1dd64bca
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d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
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1 #!/usr/bin/env python
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
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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
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3 import argparse
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
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4 import shlex
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
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5 import os
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bfe39c503a40 planemo upload for repository https://github.com/zipho/novo_align commit 896a5a73f2a5f71a7b38dc0403f54afba1f27643
sanbi-uwc
parents: 10
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6 import sys
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d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
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7 import logging
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
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8 log = logging.getLogger( __name__ )
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
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d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
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11 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
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12 param = r'@RG\tID:RG\tSM:$i\tPL:ILLUMINA'
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
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13 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
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14 index_filename,
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
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15 fwd_file,
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
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16 rev_file,
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
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17 param,
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
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18 output_filename)
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sanbi-uwc
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19 try:
3938f90c9d91 planemo upload for repository https://github.com/zipho/novo_align commit 4a89d4d866533a93706ceb29077d2e9bda69aa9f
sanbi-uwc
parents: 5
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20 os.system(cmdline_str)
3938f90c9d91 planemo upload for repository https://github.com/zipho/novo_align commit 4a89d4d866533a93706ceb29077d2e9bda69aa9f
sanbi-uwc
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21 except:
3938f90c9d91 planemo upload for repository https://github.com/zipho/novo_align commit 4a89d4d866533a93706ceb29077d2e9bda69aa9f
sanbi-uwc
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22 print("Error running the nova-align", file=sys.stderr)
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25 def newSplit(value):
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
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26 lex = shlex.shlex(value)
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
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27 lex.quotes = '"'
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
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28 lex.whitespace_split = True
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
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29 lex.commenters = ''
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
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30 return list(lex)
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
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bfe39c503a40 planemo upload for repository https://github.com/zipho/novo_align commit 896a5a73f2a5f71a7b38dc0403f54afba1f27643
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33 def main():
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
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34 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
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35 parser.add_argument('output_filename')
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
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36 parser.add_argument('--index_filename')
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
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37 parser.add_argument('--forward_filename')
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
sanbi-uwc
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38 parser.add_argument('--reverse_filename')
d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
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39 args = parser.parse_args()
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bfe39c503a40 planemo upload for repository https://github.com/zipho/novo_align commit 896a5a73f2a5f71a7b38dc0403f54afba1f27643
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41 # a dirty way of referencing the file
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sanbi-uwc
parents: 12
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42 index_file_path = args.index_filename # not sure of the logic here: + "/" + args.index_filename.split("/")[-1]
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d51c5af7a8fe planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21
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43 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
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46 if __name__ == "__main__":
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parents: 10
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47 main()