Mercurial > repos > bjoern-gruening > glimmer_hmm

comparison glimmerHMM/glimmerhmm_to_sequence.py @ 0:0a15677c6668 default tip

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author bjoern-gruening
date Wed, 11 Jan 2012 09:58:35 -0500
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1 #!/usr/bin/env python
2 """Convert GlimmerHMM gene predictions into protein sequences.
3
4 This works with both the GFF and the costumn Tabular Output.
5 And is only a wrapper to call the appropiate scripts.
6
7 Usage:
8 glimmerhmm_to_sequence.py <glimmer output> <ref fasta> <output file> <format> <protein>
9
10 """
11 import sys
12 import os
13 import glimmerhmm_tabular_to_sequence
14 import glimmerhmm_gff_to_sequence
15
16 def main(glimmer_file, ref_file, out_file, to_protein = False):
17 if to_protein == 'True':
18 to_protein = True
19 else:
20 to_protein = False
21
22 glimmerhmm_gff_to_sequence.main(glimmer_file, ref_file, out_file, to_protein)
23
24
25 if __name__ == "__main__":
26 if len(sys.argv) != 5:
27 print __doc__
28 sys.exit()
29 main(*sys.argv[1:])