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)
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