def test_extract_region(): test_seqs = [ ('AAAABBBBCCCC', (0, 12), (0, 12), 'AAAABBBBCCCC'), ('AAAABBBBCCCC', (0, 12), (4, 8), 'BBBB'), ('AAAABBBBCCCC', (4, 16), (3, 7), '-AAA'), ('AAAABBBBCCCC', (4, 16), (0, 4), '----'), ('AAAABBBBCCCC', (4, 16), (14, 18), 'CC--'), ] for found_seq, (fs, fe), (rs, re), cor in test_seqs: out = HIVTransTool.extract_region(found_seq, fs, fe, rs, re) eq_(out, cor, '(%i, %i), (%i, %i)' % (fs, fe, rs, re))
def test_known_mappings(): with open('TestData/LocatorRes.tsv') as handle: cor_res = list(csv.DictReader(handle, delimiter='\t')) with open('TestData/testSeqs.fasta') as handle: test_seqs = list(fasta_reader(handle)) for row, crow in zip(HIVTransTool.process_seqs(test_seqs, extract_regions=True), cor_res): for f in crow.keys(): if row[f] is None: row[f] = '' yield eq_, str(row[f]), crow[f], f