def test_compare1():
with TemporaryDirectory() as tempdir:
outtsv = tempdir + '/output.tsv'
run_compare(vcf=['tests/data/phased1.vcf', 'tests/data/phased2.vcf'],
names='p1,p2',
tsv_pairwise=outtsv,
sample='sample1')
lines = [l.split('\t') for l in open(outtsv)]
assert len(lines) == 3
Fields = namedtuple('Fields', [f.strip('#\n') for f in lines[0]])
entry_chrA, entry_chrB = [Fields(*l) for l in lines[1:]]
assert entry_chrA.chromosome == 'chrA'
assert entry_chrA.all_assessed_pairs == '4'
assert entry_chrA.all_switches == '1'
assert entry_chrA.all_switchflips == '1/0'
assert entry_chrA.blockwise_hamming == '1'
assert entry_chrA.largestblock_assessed_pairs == '2'
assert entry_chrA.largestblock_switches == '1'
assert entry_chrA.largestblock_hamming == '1'
assert entry_chrB.chromosome == 'chrB'
assert entry_chrB.all_assessed_pairs == '1'
assert entry_chrB.all_switches == '0'
assert entry_chrB.all_switchflips == '0/0'
assert entry_chrB.blockwise_hamming == '0'
assert entry_chrB.largestblock_assessed_pairs == '1'
assert entry_chrB.largestblock_switches == '0'
assert entry_chrB.largestblock_hamming == '0'
def test_compare_unphased():
with TemporaryDirectory() as tempdir:
run_compare(vcf=[
'tests/data/unphased.vcf', 'tests/data/unphased.vcf',
'tests/data/unphased.vcf'
],
sample='sample1')