def load_custom_reference(reference, format='fasta', region=None):
'''Load a custom reference'''
if region is not None:
format = 'gb'
record = SeqIO.read(get_custom_reference_filename(reference, format=format), format)
# BUG: feature id is lost during write, fake it with the 'note' qualifier
if format in ['gb' , 'genbank']:
correct_genbank_features_load(record)
if region is not None:
for feature in record.features:
if feature.id == region:
return feature.extract(record)
return record
def get_reference(self, region, format='fasta'):
'''Get the reference for a genomic region'''
from Bio import SeqIO
fragments = ['F' + str(i) for i in xrange(1, 7)] + ['genomewide']
if region in fragments:
fragment = region
else:
(fragment, start, end) = self.get_fragmented_roi(
(region, 0, '+oo'), include_genomewide=True)
refseq = SeqIO.read(
self.get_reference_filename(fragment, format=format), format)
if format in ('gb', 'genbank'):
from hivwholeseq.utils.sequence import correct_genbank_features_load
correct_genbank_features_load(refseq)
if region not in fragments:
refseq = refseq[start:end]
return refseq
def get_reference(self, region, format='fasta'):
'''Get the reference for a genomic region'''
from Bio import SeqIO
fragments = ['F'+str(i) for i in xrange(1, 7)] + ['genomewide']
if region in fragments:
fragment = region
else:
(fragment, start, end) = self.get_fragmented_roi((region, 0, '+oo'),
include_genomewide=True)
refseq = SeqIO.read(self.get_reference_filename(fragment, format=format),
format)
if format in ('gb', 'genbank'):
from hivwholeseq.utils.sequence import correct_genbank_features_load
correct_genbank_features_load(refseq)
if region not in fragments:
refseq = refseq[start: end]
return refseq
