["Unk"])[0]
if 'Name' in feature.qualifiers:
if feature.qualifiers['Name'][0].startswith('tRNA-'):
tRNA_type = feature.qualifiers['Name'][0]
newfeature = wa.annotations.addFeature(featureData,
trustme=True)
def func0():
wa.annotations.setName(
newfeature['features'][0]['uniquename'],
tRNA_type,
)
retry(func0)
if args.source:
gene_id = newfeature['features'][0]['parent_id']
def setSource():
wa.annotations.addAttributes(
gene_id, {'DatasetSource': [args.source]})
retry(setSource)
sys.stdout.write('\t'.join([
feature.id,
newfeature['features'][0]['uniquename'],
'success',
]))
new_name = data[feature["parent_id"]]
elif feature["uniquename"] in data:
new_name = data[feature["uniquename"]]
else:
sys.stdout.write("%s\tNot Found\n" % feature["uniquename"])
continue
else:
if feature["uniquename"] in data:
new_name = data[feature["uniquename"]]
else:
sys.stdout.write("%s\tNot Found\n" % feature["uniquename"])
continue
if args.set == "name":
def fn0():
wa.annotations.setName(feature["parent_id"], new_name)
def fn1():
wa.annotations.setName(feature["uniquename"], new_name)
retry(fn0)
retry(fn1)
else:
def fn0():
wa.annotations.addAttributes(feature["parent_id"],
{"locus_tag": [new_name]})
retry(fn0)
sys.stdout.write("%s\t%s\n" % (feature["uniquename"], new_name))
# Then get a list of features.
features = wa.annotations.getFeatures()
# For each feature in the features
for feature in sorted(features['features'],
key=lambda x: random.random()):
if args.type:
if args.type == 'tRNA':
if feature['type']['name'] != 'tRNA':
continue
elif args.type == 'terminator':
if feature['type']['name'] != 'terminator':
continue
elif args.type == 'mRNA':
if feature['type']['name'] != 'mRNA':
continue
else:
raise Exception("Unknown type")
# We see that deleteFeatures wants a uniqueName, and so we pass
# is the uniquename field in the feature.
def fn():
wa.annotations.deleteFeatures([feature['uniquename']])
print('Deleted %s [type=%s]' %
(feature['uniquename'], feature['type']['name']))
if not retry(fn, limit=3):
print('Error %s' % feature['uniquename'])