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: