Download Sequences from GenBank, Keeping Only Codons

#! /usr/bin/env python
 
###############################################################################
##  get-codons.py
##
##  Copyright 2009 Jeet Sukumaran.
##
##  This program is free software; you can redistribute it and/or modify
##  it under the terms of the GNU General Public License as published by
##  the Free Software Foundation; either version 3 of the License, or
##  (at your option) any later version.
##
##  This program is distributed in the hope that it will be useful,
##  but WITHOUT ANY WARRANTY; without even the implied warranty of
##  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
##  GNU General Public License for more details.
##
##  You should have received a copy of the GNU General Public License along
##  with this program. If not, see <http://www.gnu.org/licenses/>.
##
###############################################################################
 
"""
Downloads nucleotide sequences from GenBank, trimming out non-coding DNA.
"""
 
from optparse import OptionGroup
from optparse import OptionParser
import os
import sys
import textwrap
 
import StringIO
 
from Bio import Entrez
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
 
_prog_usage = '%prog [options] <GENBANK ACCESSION NUMBERS>'
_prog_version = 'GET-CODONS Version 1.0'
_prog_description = 'Downloads nucleotide sequences from GenBank, trimming out non-coding DNA.'
_prog_author = 'Jeet Sukumaran'
_prog_copyright = 'Copyright (C) 2009 Jeet Sukumaran.'
 
class Gene(object):
 
    def __init__(self, seq_record, feature):
        self.gb_num = seq_record.id
        self.type = feature.type
        self.start = feature.location.start.position
        self.end = feature.location.end.position
        self.seq = seq_record.seq[self.start:self.end]
        try:        
            self.name = feature.qualifiers['gene'][0]
        except KeyError:
            self.name = None
        try:            
            self.codon_start = feature.qualifiers['codon_start'][0]
        except KeyError:
            self.codon_start = None
        try:            
            self.translation = feature.qualifiers['translation'][0]
        except KeyError:
            self.translation = None
 
    def __len__(self):
        return len(self.seq)
 
    def chars(self):
        return str(self.seq)
 
def main():
    """
    Main CLI handler.
    """
 
    parser = OptionParser(usage=_prog_usage, 
        add_help_option=True, 
        version=_prog_version, 
        description=_prog_description)    
 
    parser.add_option('-o', '--output',
        action='store_const',
        dest='output',
        metavar='PREFIX',
        help='prefix for output file names')
 
    parser.add_option('-w', '--wrap',
        action='store_true',
        dest='wrap',
        default=False,
        help='wrap sequences (slows things down ...)')          
 
    (opts, args) = parser.parse_args()
 
    if len(args) == 0:
        args = sys.stdin.read()
        args = [a for a in args.split("\n") if a]
 
    if opts.output is None:
        out = sys.stdout
    else:
        out = open(opts.output, "w")
 
    gb_recs = Entrez.efetch(db="nucleotide", rettype="gb", id=",".join(args))
 
    for seq_record in SeqIO.parse(gb_recs, "genbank"):
        dp = seq_record.description.split(' ')
        label = seq_record.id + "_" + dp[0] + "_" + dp[1]      
        sys.stderr.write("[%s: %s]\n" % (seq_record.id, seq_record.description))
        sys.stderr.write("%10s    % 7s    % 7s    % 8s\n" \
                    % ("Gene",
                       "Start",
                       "End",
                       "Length"))
        codons = StringIO.StringIO()
        for f in seq_record.features:
            if f.type == "CDS":
                g = Gene(seq_record, f)
                sys.stderr.write("%10s    % 7d    % 7d    % 8d\n" \
                    % (g.name,
                       g.start,
                       g.end,
                       len(g)))
                codons.write(g.chars())
 
        out.write(">%s\n" % label)
        codons = codons.getvalue()
        if opts.wrap:
            out.write("%s\n\n" % textwrap.fill(codons, width=76))
        else:
            out.write("%s\n\n" % codons)
 
if __name__ == '__main__':
    main()