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
