def feat_collect(infile, feat_mode):
"""Collect a subset of features from a genbank file."""
from analysis.seqfile_ops import load_genbank
gb_record = load_genbank(infile)
feat_list = gb_record.features
collected = []
# establish collection parameters
types_list = feat_mode['types'] # default entry is ('CDS')
tags_dict = feat_mode['tags'] # default is an empty dictionary
# start collecting features
for feature in feat_list:
if feature.type in types_list:
if len(tags_dict.keys()) is 0:
collected.append(feature)
else:
for tag_key in tags_dict.keys():
if tag_key in feature.qualifiers:
feat_value = feature.qualifiers.get(tag_key)
if feat_value[0] in tags_dict[tag_key]:
collected.append(feature)
else: pass
else: pass
else: pass
## consider adding some info to the log
return collected
def test_write_and_load_single_genbank(self):
count = seqfile_ops.write_genbank(self.gbk_filename,
self.record)
self.assertIs(count, 1)
gbk_record = seqfile_ops.load_genbank(self.gbk_filename)
self.assertEqual(gbk_record.id, self.record.id)
# check features
for index in range (0,1):
self.assertEqual(gbk_record.features[index].type,
self.record.features[index].type)
