def test_locations_distance_different_chrom(self):
loc1 = Location(chrom='chr4', pos=1337)
loc2 = Location(chrom='chr7', pos=1001)
distance = loc1 - loc2
inverse_distance = loc2 - loc1
self.assertEqual(distance, None)
self.assertEqual(inverse_distance, None)
def test_locations_distance_same_chrom(self):
loc1 = Location(chrom='chr7', pos=1337)
loc2 = Location(chrom='chr7', pos=1001)
distance = loc1 - loc2
inverse_distance = loc2 - loc1
self.assertEqual(distance, 1337 - 1001)
self.assertEqual(inverse_distance, 1001 - 1337)
def test_location_shift(self):
loc = Location(chrom='chr1', pos=42)
shift = -2
shifted_loc1 = loc + shift
shifted_loc2 = loc.shift(shift)
self.assertIsInstance(shifted_loc1, Location)
self.assertEqual(shifted_loc1.pos, loc.pos + shift)
self.assertEqual(shifted_loc1, shifted_loc2)
def test_parse_vcf_line(self):
line = '\t'.join([
'chr1', '16688', '.', 'G', 'A', '.',
'map_qual;normal_artifact;strand_bias',
'AS_FilterStatus=map_qual,strand_bias;AS_SB_TABLE=327,30|0,13;DP=380;ECNT=3;GERMQ=93;MBQ=37,34;MFRL=260,332;MMQ=22,22;MPOS=21;NALOD=-1.391e+00;NLOD=43.74;POPAF=6.00;ROQ=80;TLOD=7.68',
'GT:AD:AF:DP:F1R2:F2R1:SB',
'0/0:180,4:0.026:184:99,1:80,3:165,15,0,4',
'0/1:177,9:0.052:186:98,4:77,5:162,15,0,9'
])
vcfrow = _parse_vcf_line(line)
self.assertEqual(vcfrow.loc, Location(chrom='chr1', pos=16688))
self.assertEqual(vcfrow.id, '.')
self.assertEqual(vcfrow.ref, 'G')
self.assertEqual(vcfrow.alt, 'A')
self.assertEqual(vcfrow.qual, '.')
self.assertEqual(vcfrow.filter, 'map_qual;normal_artifact;strand_bias')
self.assertEqual(
vcfrow.info,
Info(
'AS_FilterStatus=map_qual,strand_bias;AS_SB_TABLE=327,30|0,13;DP=380;ECNT=3;GERMQ=93;MBQ=37,34;MFRL=260,332;MMQ=22,22;MPOS=21;NALOD=-1.391e+00;NLOD=43.74;POPAF=6.00;ROQ=80;TLOD=7.68'
))
self.assertEqual(vcfrow.format, 'GT:AD:AF:DP:F1R2:F2R1:SB')
self.assertEqual(vcfrow.samples, [
'0/0:180,4:0.026:184:99,1:80,3:165,15,0,4',
'0/1:177,9:0.052:186:98,4:77,5:162,15,0,9'
])
def setUp(self):
self.loc = Location(chrom='chr1', pos=42)
self.vcfrow = VCFrow(loc=self.loc,
id='1234',
ref='A',
alt='G',
qual='.',
filter='PASS',
info='info',
format='format',
samples=['sample1', 'sample2'])
def _parse_vcf_line(line: str) -> VCFrow:
elements = line.split('\t')
loc = Location(chrom=elements[0], pos=int(elements[1]))
return VCFrow(loc=loc,
id=elements[2],
ref=elements[3],
alt=elements[4],
qual=elements[5],
filter=elements[6],
info=Info(elements[7]),
format=elements[8],
samples=elements[9:])
def setUp(self):
loc1 = Location(chrom='chr2', pos=21)
loc2 = Location(chrom='chr16', pos=50)
self.vcfrow1 = VCFrow(loc=loc1,
id='id1',
ref='G',
alt='A',
qual='.',
filter='PASS',
info='info',
format='format',
samples=['sample1', 'sample2'])
self.vcfrow2 = VCFrow(loc=loc2,
id='id2',
ref='T',
alt='ATTGC',
qual='.',
filter='PASS',
info='info',
format='format',
samples=['sample1', 'sample2'])
self.vcf = VCF(rows=[self.vcfrow1, self.vcfrow2])
def test_location(self):
loc = Location(chrom='chr1', pos=42)
self.assertEqual(loc.chrom, 'chr1')
self.assertEqual(loc.pos, 42)
def test_location_greater_than_sex_chrom(self):
loc1 = Location(chrom='Y', pos=42)
loc2 = Location(chrom='4', pos=1001)
self.assertEqual(loc2 > loc1, False)
def test_location_less_than_sex_chrom(self):
loc1 = Location(chrom='7', pos=42)
loc2 = Location(chrom='X', pos=1001)
self.assertEqual(loc1 < loc2, True)
def test_location_less_than_different_chrom(self):
loc1 = Location(chrom='chr7', pos=42)
loc2 = Location(chrom='chr20', pos=1001)
self.assertEqual(loc1 < loc2, True)
def test_location_less_than_same_chrom(self):
loc1 = Location(chrom='chr7', pos=1337)
loc2 = Location(chrom='chr7', pos=1001)
self.assertEqual(loc2 < loc1, True)
self.assertEqual(loc1 > loc2, True)
def test_location_shift_error(self):
loc = Location(chrom='chr1', pos=42)
shift = 'not_valid'
with self.assertRaises(LocationShiftError):
loc + shift