def save_custom_reference(record, reference, format='fasta', molecule='DNA'):
'''Save a custom reference'''
if format in ['gb' , 'genbank']:
correct_genbank_features_save(record, molecule='DNA')
return SeqIO.write(record,
get_custom_reference_filename(reference, format=format),
format)
print feature.id,
from hivwholeseq.utils.genome_info import genes
if feature.type in ('gene', 'protein'):
print feature.extract(refseq).seq.translate()
else:
print feature.extract(refseq).seq
print ''
try:
refseq_old = patient.get_reference('genomewide', format='gb')
except IOError:
if VERBOSE >= 1:
print "Old annotated reference not found (that's ok)"
refseq_old = None
if refseq_old is not None:
try:
compare_annotations(refseq, refseq_old, VERBOSE=VERBOSE)
except ValueError:
if use_force:
print 'Annotations differ from old sequence'
else:
raise
if use_save:
fn_out = patient.get_reference_filename('genomewide', format='gb')
correct_genbank_features_save(refseq)
SeqIO.write(refseq, fn_out, 'gb')
continue
print feature.id,
from hivwholeseq.utils.genome_info import genes
if feature.type in ('gene', 'protein'):
print feature.extract(refseq).seq.translate()
else:
print feature.extract(refseq).seq
print ''
try:
refseq_old = patient.get_reference('genomewide', format='gb')
except IOError:
if VERBOSE >= 1:
print "Old annotated reference not found (that's ok)"
refseq_old = None
if refseq_old is not None:
try:
compare_annotations(refseq, refseq_old, VERBOSE=VERBOSE)
except ValueError:
if use_force:
print 'Annotations differ from old sequence'
else:
raise
if use_save:
fn_out = patient.get_reference_filename('genomewide', format='gb')
correct_genbank_features_save(refseq)
SeqIO.write(refseq, fn_out, 'gb')
