Mercurial > repos > bgruening > glimmer_hmm
comparison glimmerHMM/glimmerhmm_to_sequence.py @ 0:c9699375fcf6 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
author | bgruening |
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date | Wed, 13 Jul 2016 10:55:48 -0400 |
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-1:000000000000 | 0:c9699375fcf6 |
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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:]) |