Mercurial > repos > iuc > transtermhp

comparison transtermhp.py @ 3:1a1ec22a7e28 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 581d451609b919893ba53d104a5bcf2e9e565d1d
author iuc
date Wed, 07 Jun 2017 07:53:53 -0400
parents c28817831a24
children 9a90656a1af9
comparison
equal deleted inserted replaced
2:1d8ad7599f02 3:1a1ec22a7e28
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 import sys
3 import re 2 import re
4 import subprocess 3 import subprocess
4 import sys
5
6 from BCBio import GFF
5 from Bio import SeqIO 7 from Bio import SeqIO
6 from BCBio import GFF 8 from Bio.SeqFeature import (
7 from Bio.SeqFeature import SeqFeature, FeatureLocation 9 FeatureLocation,
10 SeqFeature
11 )
8 12
9 13
10 def main(expterm, fasta, gff3): 14 def main(expterm, fasta, gff3):
11 with open(fasta, 'r') as handle: 15 with open(fasta, 'r') as handle:
12 seq_dict = SeqIO.to_dict(SeqIO.parse(handle, "fasta")) 16 seq_dict = SeqIO.to_dict(SeqIO.parse(handle, "fasta"))
63 } 67 }
64 ) 68 )
65 rec.features.append(feature) 69 rec.features.append(feature)
66 yield rec 70 yield rec
67 71
72
68 if __name__ == '__main__': 73 if __name__ == '__main__':
69 for record in main(*sys.argv[1:4]): 74 for record in main(*sys.argv[1:4]):
70 GFF.write([record], sys.stdout) 75 GFF.write([record], sys.stdout)