def test_mappings():
"""This is a simple inclusion test for genome -> proteme mutation mappings.
Knowing the data, we demand the items from the right side (of test data)
to be in the results of queries specified on the left side.
"""
test_data = (
# (chrom, dna_pos, dna_ref, dna_alt), (name, pos, ref, alt)
(('17', '7572934', 'G', 'A'), ('TP53', 353, 'S', 'L')),
(('17', '19282215', 't', 'a'), ('MAPK7', 1, 'M', 'K')),
(('21', '40547520', 'g', 'a'), ('PSMG1', 283, 'T', 'I')),
(('9', '125616157', 't', 'a'), ('RC3H2', 1064, 'Y', 'F')),
(('11', '120198175', 'g', 'a'), ('TMEM136', 31, 'V', 'M')),
(('10', '81838457', 't', 'a'), ('TMEM254', 1, 'M', 'K')),
(('13', '111267940', 't', 'a'), ('CARKD', 1, 'M', 'K')),
(('6', '30539266', 't', 'a'), ('ABCF1', 1, 'M', 'K')),
(('6', '36765430', 'g', 'a'), ('CPNE5', 140, 'L', 'F')),
(('12', '123464753', 't', 'a'), ('ARL6IP4', 1, 'M', 'K')),
)
for genomic_data, protein_data in test_data:
snv = make_snv_key(*genomic_data)
items = [decode_csv(item) for item in bdb[snv]]
for item in items:
retrieved_data = (Protein.query.get(item['protein_id']).gene.name,
item['pos'], item['ref'], item['alt'])
if retrieved_data == protein_data:
break
else:
raise Exception(retrieved_data, protein_data)
def test_decode_csv():
keys = ('strand', 'ref', 'alt', 'pos', 'cdna_pos', 'exon', 'protein_id', 'is_ptm')
test_data = (
('+RH0cc:exon1:7b', ('+', 'R', 'H', 68, 204, 'exon1', 123, False)),
('-RH1cc:exon1:7b', ('-', 'R', 'H', 68, 204, 'exon1', 123, True)),
)
for encoded_csv, correct_result in test_data:
result = genomic_mappings.decode_csv(encoded_csv)
assert result == dict(zip(keys, correct_result))