def test_iterate_genbank_with_dict_return():
"""iterate_genbank with default options"""
# first, from text
for entry in iterate_genbank(TEN_DLOOPS_TEXT):
assert isinstance(entry, dict)
# next, from file
for entry in iterate_genbank(TEN_DLOOPS_FILEPATH):
assert isinstance(entry, dict)
def test_iterate_genbank_with_raw_return():
"""iterate_genbank with raw option"""
# first, from text
for entry in iterate_genbank(TEN_DLOOPS_TEXT, raw=True):
assert isinstance(entry, str)
# next, from file
for entry in iterate_genbank(TEN_DLOOPS_FILEPATH, raw=True):
assert isinstance(entry, str)
OUTPUT: list of 2 ints (changed)
"""
five_prime = 50
three_prime = 92
new_positions = [pos_list[0]-five_prime, \
pos_list[1]+three_prime]
return new_positions
if __name__ == '__main__':
hn_sequences = []
all_accessions = []
hn_accessions = []
hn_translations = []
for entry in iterate_genbank(INPUTFILE):
hn = False
accession = entry['accession']
all_accessions.append(accession)
features = entry['features']
if features:
source = features[0]
for element in features:
if element[0] == 'CDS':
cds = element
cds_content = cds[1]
position = make_integers(cds_content.pop(0).split('..'))
product = dict(cds_content).get('product')
translation = Seq(
dict(cds_content).get('translation').strip('"'))
for words in KEYWORDS: