Mercurial > repos > drosofff > sam_to_fastq

comparison sam_to_fastq.py @ 1:c1ab6747fb66 draft

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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 17:32:37 -0400
parents 4c60ceadc414
children de6fd19d1576
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0:4c60ceadc414 1:c1ab6747fb66
13 return args 13 return args
14 14
15 15
16 def print_fastq_sequence(samline, file): 16 def print_fastq_sequence(samline, file):
17 samfields = samline[:-1].split("\t") 17 samfields = samline[:-1].split("\t")
18 print >> file, '@%s\n%s\n+\n%s' % (samfields[0], samfields[9], samfields[10]) 18 file.write ( '@%s\n%s\n+\n%s' % (samfields[0], samfields[9], samfields[10]) )
19 19
20 def main(input, output): 20 def main(input, output):
21 infile = open (input, "r") 21 infile = open (input, "r")
22 outfile = open (output, "w") 22 outfile = open (output, "w")
23 for line in infile: 23 with open (input, "r") as infile:
24 if line[0] == "@": 24 with open (output, "w") as outfile:
25 continue 25 for line in infile:
26 if line.split("\t")[1] != "4": 26 if line[0] == "@":
27 print_fastq_sequence (line, outfile) 27 continue
28 infile.close() 28 if line.split("\t")[1] != "4":
29 outfile.close() 29 print_fastq_sequence (line, outfile)
30 30
31 if __name__ == "__main__": 31 if __name__ == "__main__":
32 args = Parser() 32 args = Parser()
33 main (args.input, args.output) 33 main (args.input, args.output)