def process(self):
for feature in self.record.features():
if feature.type != 'CDS':
continue
if len(feature.location.regions) != 1:
continue
region = feature.location.regions[0]
start = region.start - 1
end = region.end
feat_id = self._get_feature_id(feature)
sequence = self.record.sequence[start:end].upper()
if region.complement:
sequence = genbank.reverseComplement(sequence)
if not sequence.startswith('ATG'):
msg = ('Feature %s don\'t start with ATG. It starts '
'with %s') % (str(feat_id), sequence[0:3])
print >> sys.stderr, msg
if type(self.enzyme) is str:
parts = sequence.split(self.enzyme)
else:
parts = self.enzyme.split(sequence)
if len(parts) == 1:
insert_in_dict_with_list(self.tags, '', feat_id)
else:
part = parts[-1]
key = self.originalEnzyme + part[0:self.tag_length]
insert_in_dict_with_list(self.tags, key, feat_id)
self._genes_c += 1
def main(args):
parser = OptionParser(('usage: %prog [options] '
'<qualifier to use as gene name>'))
parser.add_option('-g', '--gi', dest='gi', type='int',
help='gi of the genbank record to analyze.')
parser.add_option('-r', '--record', dest='record', type='string',
help='read genbank record from FILE',
metavar='FILE')
parser.add_option('-o', '--output', dest="output",
help='name of output file.')
parser.add_option('-c', '--clobber', dest="clobber",
help='Clobber the output files.',
action='store_true', default=False)
(options, args) = parser.parse_args(args)
if not options.gi and not options.record:
print >> sys.stderr, 'Usage error: a record file (-r) or ' + \
'a gi (-g) is required'
print >> sys.stderr, parser.format_help()
sys.exit(1)
if options.output:
filenameOut = options.output
else:
if options.record:
filenameOut = '%s' % options.record
else:
filenameOut = '%s' % options.gi
if len(args) < 2:
print >> sys.stderr, 'Qualifier name is required'
print >> sys.stderr, parser.format_help()
sys.exit(1)
if options.record:
record = genbank.Record(file(options.record))
else:
record = giInfo.GiRecord(options.gi, True)
qualifierName = args[1]
fastaFh = safeOFW('%s.fasta' % filenameOut,
clobber=options.clobber)
print >> fastaFh, record.fasta()
fastaFh.close()
genesFh = safeOFW('%s.genes.fasta' % filenameOut,
clobber=options.clobber)
genes = []
for feature in record.features():
if len(feature.location.regions) != 1:
continue
if feature.type != 'gene':
continue
region = feature.location.regions[0]
seq = record.sequence[region.start - 1:region.end]
seq = seq.upper()
if region.complement:
seq = genbank.reverseComplement(seq)
if feature.qualifiers.has_key(qualifierName):
feat_name = feature.qualifiers[qualifierName]
else:
print >> sys.stderr, ("Feature doesn't have qualifier "
"'%s'.\nQualifiers: %s" %
(qualifierName, feature.qualifiers))
continue
print >> genesFh, fasta.Record(title=feat_name, sequence=seq)
print >> genesFh, ''
genesFh.close()
