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annotate sam_to_fastq.py @ 0:4c60ceadc414 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
author drosofff
date Mon, 21 Mar 2016 14:40:06 -0400
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children c1ab6747fb66
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4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
drosofff
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1 #!/usr/bin/python
4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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2 #
4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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3 import sys
4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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4 import argparse
4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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5
4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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6 def Parser():
4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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7 the_parser = argparse.ArgumentParser()
4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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8 the_parser.add_argument(
4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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9 '--input', action="store", type=str, help="input SAM file")
4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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10 the_parser.add_argument(
4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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11 '--output', action="store", type=str, help="output FASTQ file")
4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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12 args = the_parser.parse_args()
4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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13 return args
4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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16 def print_fastq_sequence(samline, file):
4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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17 samfields = samline[:-1].split("\t")
4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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18 print >> file, '@%s\n%s\n+\n%s' % (samfields[0], samfields[9], samfields[10])
4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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20 def main(input, output):
4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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21 infile = open (input, "r")
4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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22 outfile = open (output, "w")
4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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23 for line in infile:
4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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24 if line[0] == "@":
4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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25 continue
4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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26 if line.split("\t")[1] != "4":
4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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27 print_fastq_sequence (line, outfile)
4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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28 infile.close()
4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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29 outfile.close()
4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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31 if __name__ == "__main__":
4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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32 args = Parser()
4c60ceadc414 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 8a467239b4e3aa42c448f5a088c399e53d50c3fd-dirty
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33 main (args.input, args.output)