Mercurial > repos > peterjc > get_orfs_or_cdss
comparison tools/get_orfs_or_cdss/get_orfs_or_cdss.py @ 9:a06ad07431ba draft
v0.2.1 Adds table 24; Depends on Biopython 1.67 via Tool Shed package or bioconda.
author | peterjc |
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date | Wed, 10 May 2017 13:24:46 -0400 |
parents | 09a8be9247ca |
children | d51db443aaa4 |
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8:09a8be9247ca | 9:a06ad07431ba |
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15 This script is copyright 2011-2013 by Peter Cock, The James Hutton Institute | 15 This script is copyright 2011-2013 by Peter Cock, The James Hutton Institute |
16 (formerly SCRI), Dundee, UK. All rights reserved. | 16 (formerly SCRI), Dundee, UK. All rights reserved. |
17 | 17 |
18 See accompanying text file for licence details (MIT licence). | 18 See accompanying text file for licence details (MIT licence). |
19 """ | 19 """ |
20 | |
21 import re | |
20 import sys | 22 import sys |
21 import re | 23 |
22 from optparse import OptionParser | 24 from optparse import OptionParser |
23 | 25 |
24 usage = """Use as follows: | 26 usage = """Use as follows: |
25 | 27 |
26 $ python get_orfs_or_cdss.py -i genome.fa -f fasta --table 11 -t CDS -e open -m all -s both --on cds.nuc.fa --op cds.protein.fa --ob cds.bed --og cds.gff3 | 28 $ python get_orfs_or_cdss.py -i genome.fa -f fasta --table 11 -t CDS -e open -m all -s both --on cds.nuc.fa --op cds.protein.fa --ob cds.bed --og cds.gff3 |
208 values = list(get_top_peptides(nuc_seq)) | 210 values = list(get_top_peptides(nuc_seq)) |
209 if not values: | 211 if not values: |
210 raise StopIteration | 212 raise StopIteration |
211 yield values[0] | 213 yield values[0] |
212 | 214 |
215 | |
213 if options.mode == "all": | 216 if options.mode == "all": |
214 get_peptides = get_all_peptides | 217 get_peptides = get_all_peptides |
215 elif options.mode == "top": | 218 elif options.mode == "top": |
216 get_peptides = get_top_peptides | 219 get_peptides = get_top_peptides |
217 elif options.mode == "one": | 220 elif options.mode == "one": |