def test_load_ped_file_multiple_sibs(self):
""" check that we correctly parse a ped file with multiple siblings
"""
# add an extra sibling
self.tempfile.write("fam_ID sib dad mom F 2 /path/to/sib_vcf.gz\n")
self.tempfile.flush()
# load all the components from the file
mothers, fathers, children, affected, sex, vcfs = load_ped_file(self.path)
# check that they all match
self.assertEqual(mothers, {"mom": "0", "proband": "mom", "dad": "0", "sib": "mom"})
self.assertEqual(fathers, {"mom": "0", "proband": "dad", "dad": "0", "sib": "dad"})
self.assertEqual(children, {"proband": "fam_ID", "sib": "fam_ID"})
self.assertEqual(affected, {"mom": "1", "proband": "2", "dad": "1", "sib": "2"})
self.assertEqual(sex, {"mom": "F", "proband": "F", "dad": "M", "sib": "F"})
self.assertEqual(
vcfs,
{
"mom": "/path/to/mom_vcf.gz",
"proband": "/path/to/proband_vcf.gz",
"dad": "/path/to/dad_vcf.gz",
"sib": "/path/to/sib_vcf.gz",
},
)
def test_load_ped_file_multiple_families(self):
""" check that we correctly parse a ped file with multiple families
"""
# add an extra family, with multiple sibs
self.tempfile.write("fam_ID2 proband2 dad2 mom2 F 2 /path/to/proband2_vcf.gz\n")
self.tempfile.write("fam_ID2 dad2 0 0 M 1 /path/to/dad2_vcf.gz\n")
self.tempfile.write("fam_ID2 mom2 0 0 F 1 /path/to/mom2_vcf.gz\n")
self.tempfile.write("fam_ID2 sib dad2 mom2 F 2 /path/to/sib_vcf.gz\n")
self.tempfile.flush()
# load all the components from the file
mothers, fathers, children, affected, sex, vcfs = load_ped_file(self.path)
# check that they all match
self.assertEqual(mothers, {'mom': '0', 'proband': 'mom', 'dad': '0',
'mom2': '0', 'proband2': 'mom2', 'dad2': '0', 'sib': 'mom2'})
self.assertEqual(fathers, {'mom': '0', 'proband': 'dad', 'dad': '0',
'mom2': '0', 'proband2': 'dad2', 'dad2': '0', 'sib': 'dad2'})
self.assertEqual(children, {'proband': 'fam_ID',
"proband2": "fam_ID2", "sib": "fam_ID2"})
self.assertEqual(affected, {'mom': '1', 'proband': '2', 'dad': '1',
'mom2': '1', 'proband2': '2', 'dad2': '1', 'sib': '2'})
self.assertEqual(sex, {'mom': 'F', 'proband': 'F', 'dad': 'M',
'mom2': 'F', 'proband2': 'F', 'dad2': 'M', 'sib': 'F'})
self.assertEqual(vcfs, {'mom': '/path/to/mom_vcf.gz',
'proband': '/path/to/proband_vcf.gz',
'dad': '/path/to/dad_vcf.gz',
'proband2': '/path/to/proband2_vcf.gz',
'dad2': '/path/to/dad2_vcf.gz',
'mom2': '/path/to/mom2_vcf.gz',
'sib': '/path/to/sib_vcf.gz'})
def test_load_ped_file_single_family(self):
""" check that we correctly parse a ped file with a single trio
"""
# load all the components from the file
mothers, fathers, children, affected, sex, vcfs = load_ped_file(self.path)
# check that they all match
self.assertEqual(mothers, {"mom": "0", "proband": "mom", "dad": "0"})
self.assertEqual(fathers, {"mom": "0", "proband": "dad", "dad": "0"})
self.assertEqual(children, {"proband": "fam_ID"})
self.assertEqual(affected, {"mom": "1", "proband": "2", "dad": "1"})
self.assertEqual(sex, {"mom": "F", "proband": "F", "dad": "M"})
self.assertEqual(
vcfs, {"mom": "/path/to/mom_vcf.gz", "proband": "/path/to/proband_vcf.gz", "dad": "/path/to/dad_vcf.gz"}
)
def test_load_ped_file_single_family(self):
""" check that we correctly parse a ped file with a single trio
"""
# load all the components from the file
mothers, fathers, children, affected, sex, vcfs = load_ped_file(self.path)
# check that they all match
self.assertEqual(mothers, {'mom': '0', 'proband': 'mom', 'dad': '0'})
self.assertEqual(fathers, {'mom': '0', 'proband': 'dad', 'dad': '0'})
self.assertEqual(children, {'proband': 'fam_ID'})
self.assertEqual(affected, {'mom': '1', 'proband': '2', 'dad': '1'})
self.assertEqual(sex, {'mom': 'F', 'proband': 'F', 'dad': 'M'})
self.assertEqual(vcfs, {'mom': '/path/to/mom_vcf.gz', \
'proband': '/path/to/proband_vcf.gz', \
'dad': '/path/to/dad_vcf.gz'})
