Mercurial > repos > drosofff > sam_to_fastq
comparison sam_to_fastq.py @ 0:55107d4a728c draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 0651eb8c86d890e4b223fec82ab3980932710030
| author | drosofff |
|---|---|
| date | Mon, 21 Mar 2016 17:33:26 -0400 |
| parents | |
| children | 8acb72264319 |
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| -1:000000000000 | 0:55107d4a728c |
|---|---|
| 1 #!/usr/bin/python | |
| 2 # | |
| 3 import sys | |
| 4 import argparse | |
| 5 | |
| 6 def Parser(): | |
| 7 the_parser = argparse.ArgumentParser() | |
| 8 the_parser.add_argument( | |
| 9 '--input', action="store", type=str, help="input SAM file") | |
| 10 the_parser.add_argument( | |
| 11 '--output', action="store", type=str, help="output FASTQ file") | |
| 12 args = the_parser.parse_args() | |
| 13 return args | |
| 14 | |
| 15 | |
| 16 def print_fastq_sequence(samline, file): | |
| 17 samfields = samline[:-1].split("\t") | |
| 18 file.write ( '@%s\n%s\n+\n%s' % (samfields[0], samfields[9], samfields[10]) ) | |
| 19 | |
| 20 def main(input, output): | |
| 21 infile = open (input, "r") | |
| 22 outfile = open (output, "w") | |
| 23 with open (input, "r") as infile: | |
| 24 with open (output, "w") as outfile: | |
| 25 for line in infile: | |
| 26 if line[0] == "@": | |
| 27 continue | |
| 28 if line.split("\t")[1] != "4": | |
| 29 print_fastq_sequence (line, outfile) | |
| 30 | |
| 31 if __name__ == "__main__": | |
| 32 args = Parser() | |
| 33 main (args.input, args.output) |