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.

8:09a8be9247ca

This script is copyright 2011-2013 by Peter Cock, The James Hutton Institute
(formerly SCRI), Dundee, UK. All rights reserved.

See accompanying text file for licence details (MIT licence).
"""
import sys
import re
from optparse import OptionParser

usage = """Use as follows:

$ 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

    values = list(get_top_peptides(nuc_seq))
    if not values:
        raise StopIteration
    yield values[0]

if options.mode == "all":
    get_peptides = get_all_peptides
elif options.mode == "top":
    get_peptides = get_top_peptides
elif options.mode == "one":

9:a06ad07431ba

This script is copyright 2011-2013 by Peter Cock, The James Hutton Institute
(formerly SCRI), Dundee, UK. All rights reserved.

See accompanying text file for licence details (MIT licence).
"""

import re
import sys

from optparse import OptionParser

usage = """Use as follows:

$ 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

    values = list(get_top_peptides(nuc_seq))
    if not values:
        raise StopIteration
    yield values[0]


if options.mode == "all":
    get_peptides = get_all_peptides
elif options.mode == "top":
    get_peptides = get_top_peptides
elif options.mode == "one":