def testPedSnpBoundary2TPed(self):
pc = PhenoCovar()
ped_parser = TransposedPedigreeParser(self.tfam_filename,
self.tped_filename)
DataParser.boundary = SnpBoundaryCheck(snps=["rs0005-rs0006"])
BoundaryCheck.chrom = 2
ped_parser.load_tfam(pc)
ped_parser.load_genotypes()
pedigree = [x.split() for x in open(self.tped_filename).readlines()]
index = 4
loci = ped_parser.get_loci()
for snp in loci:
self.assertEqual(int(pedigree[index][0]), snp.chr)
self.assertEqual(int(pedigree[index][3]), snp.pos)
self.assertAlmostEqual(self.hetero_freq_tped[index],
snp.hetero_freq,
places=4)
index += 1
self.assertEqual(2, ped_parser.locus_count)
index = 4
for snp in ped_parser:
self.assertEqual(int(pedigree[index][0]), snp.chr)
self.assertEqual(int(pedigree[index][3]), snp.pos)
self.assertEqual(pedigree[index][1], snp.rsid)
self.assertEqual(self.genotypes[index], list(snp.genotype_data))
index += 1
self.assertEqual(6, index)
def testPedRegionBoundaryWithExclusionsTPed(self):
pc = PhenoCovar()
ped_parser = TransposedPedigreeParser(self.tfam_filename,
self.tped_filename)
DataParser.boundary = SnpBoundaryCheck(snps=["rs0005-rs0007"])
DataParser.boundary.LoadExclusions(snps=["rs0007"])
BoundaryCheck.chrom = 2
ped_parser.load_tfam(pc)
ped_parser.load_genotypes()
pedigree = [x.split() for x in open(self.tped_filename).readlines()]
index = 4
loci = ped_parser.get_loci()
for snp in loci:
self.assertEqual(int(pedigree[index][0]), snp.chr)
self.assertEqual(int(pedigree[index][3]), snp.pos)
index += 1
index = 4
for snp in ped_parser:
self.assertEqual(int(pedigree[index][0]), snp.chr)
self.assertEqual(int(pedigree[index][3]), snp.pos)
self.assertEqual(pedigree[index][1], snp.rsid)
self.assertEqual(self.genotypes[index], list(snp.genotype_data))
index += 1
self.assertEqual(6, index)
def testPedSnpBoundary2TPed(self):
pc = PhenoCovar()
ped_parser = TransposedPedigreeParser(self.tfam_filename, self.tped_filename)
DataParser.boundary = SnpBoundaryCheck(snps=["rs0005-rs0006"])
BoundaryCheck.chrom = 2
ped_parser.load_tfam(pc)
ped_parser.load_genotypes()
pedigree = [x.split() for x in open(self.tped_filename).readlines()]
index = 4
loci = ped_parser.get_loci()
for snp in loci:
self.assertEqual(int(pedigree[index][0]), snp.chr)
self.assertEqual(int(pedigree[index][3]), snp.pos)
self.assertAlmostEqual(self.hetero_freq_tped[index], snp.hetero_freq, places=4)
index += 1
self.assertEqual(2, ped_parser.locus_count)
index = 4
for snp in ped_parser:
self.assertEqual(int(pedigree[index][0]), snp.chr)
self.assertEqual(int(pedigree[index][3]), snp.pos)
self.assertEqual(pedigree[index][1], snp.rsid)
self.assertEqual(self.genotypes[index], list(snp.genotype_data))
index += 1
self.assertEqual(6, index)
def testPedRegionBoundaryWithExclusionsTPed(self):
pc = PhenoCovar()
ped_parser = TransposedPedigreeParser(self.tfam_filename, self.tped_filename)
DataParser.boundary = SnpBoundaryCheck(snps=["rs0005-rs0007"])
DataParser.boundary.LoadExclusions(snps=["rs0007"])
BoundaryCheck.chrom = 2
ped_parser.load_tfam(pc)
ped_parser.load_genotypes()
pedigree = [x.split() for x in open(self.tped_filename).readlines()]
index = 4
loci = ped_parser.get_loci()
for snp in loci:
self.assertEqual(int(pedigree[index][0]), snp.chr)
self.assertEqual(int(pedigree[index][3]), snp.pos)
index += 1
index = 4
for snp in ped_parser:
self.assertEqual(int(pedigree[index][0]), snp.chr)
self.assertEqual(int(pedigree[index][3]), snp.pos)
self.assertEqual(pedigree[index][1], snp.rsid)
self.assertEqual(self.genotypes[index], list(snp.genotype_data))
index += 1
self.assertEqual(6, index)
def testPedWithMissingMxIndComplete(self):
pc = PhenoCovar()
DataParser.ind_miss_tol = 0.5 # We should only lose 1
ped_parser = TransposedPedigreeParser(self.tfam_filename, self.miss_tped_filename)
ped_parser.load_tfam(pc)
ped_parser.load_genotypes()
mapdata = [x.strip().split() for x in open(self.miss_tped_filename).readlines()]
genotypes_w_missing = [
[0, -1, -1, -1, -1, -1, -1, -1, -1, -1, 1],
[1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1],
[0, 1, 1, 0, 0, 0, 2, 1, 1, 0, 0],
[0, 2, 1, 1, 0, 0, 1, 2, 1, 1, 0],
[1, 0, 1, 0, 0, 1, 2, 0, 1, 0, 0],
[1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0],
[0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0]
]
self.assertEqual(7, ped_parser.locus_count)
index = 0
loci = ped_parser.get_loci()
for snp in loci:
self.assertEqual(int(mapdata[index][0]), snp.chr)
self.assertEqual(int(mapdata[index][3]), snp.pos)
index += 1
index = 0
for snp in ped_parser:
self.assertEqual(int(mapdata[index][0]), snp.chr)
self.assertEqual(int(mapdata[index][3]), snp.pos)
self.assertEqual(mapdata[index][1], snp.rsid)
self.assertEqual(genotypes_w_missing[index], list(snp.genotype_data))
index += 1
self.assertEqual(7, index)
def testPedSnpBoundaryTPed(self):
pc = PhenoCovar()
ped_parser = TransposedPedigreeParser(self.tfam_filename,
self.tped_filename)
DataParser.boundary = SnpBoundaryCheck(snps=["rs0001-rs0003"])
BoundaryCheck.chrom = 1
ped_parser.load_tfam(pc)
ped_parser.load_genotypes()
pedigree = libgwas.get_lines(self.tped_filename, split=True)
index = 0
loci = ped_parser.get_loci()
for snp in loci:
self.assertEqual(int(pedigree[index][0]), snp.chr)
self.assertEqual(int(pedigree[index][3]), snp.pos)
self.assertAlmostEqual(self.hetero_freq_tped[index],
snp.hetero_freq,
places=4)
index += 1
self.assertEqual(3, ped_parser.locus_count)
index = 0
for snp in ped_parser:
self.assertEqual(int(pedigree[index][0]), snp.chr)
self.assertEqual(int(pedigree[index][3]), snp.pos)
self.assertEqual(pedigree[index][1], snp.rsid)
self.assertEqual(self.genotypes[index], list(snp.genotype_data))
index += 1
self.assertEqual(3, index)
def testPedRegionBoundaryWithExclusionsTPed(self):
pc = PhenoCovar()
ped_parser = TransposedPedigreeParser(self.tfam_filename,
self.tped_filename)
DataParser.boundary = SnpBoundaryCheck(snps=["rs0005-rs0007"])
DataParser.boundary.LoadExclusions(snps=["rs0007"])
BoundaryCheck.chrom = 2
ped_parser.load_tfam(pc)
ped_parser.load_genotypes()
pedigree = get_lines(self.tped_filename, split=True)
index = 4
loci = ped_parser.get_loci()
for snp in loci:
self.assertEqual(int(pedigree[index][0]), snp.chr)
self.assertEqual(int(pedigree[index][3]), snp.pos)
index += 1
index = 4
for snp in ped_parser:
snp_filter = numpy.ones(snp.missing_genotypes.shape[0]) == 1
try:
genodata = snp.get_genotype_data(snp_filter)
self.assertEqual(int(pedigree[index][0]), snp.chr)
self.assertEqual(int(pedigree[index][3]), snp.pos)
self.assertEqual(pedigree[index][1], snp.rsid)
self.assertEqual(self.genotypes[index],
list(genodata.genotypes))
except TooMuchMissing as e:
pass
except InvalidFrequency as e:
pass
index += 1
self.assertEqual(6, index)
def testPedWithMissingMxSnpComplete(self):
pc = PhenoCovar()
DataParser.snp_miss_tol = 0.5 # We should only lose 1
ped_parser = TransposedPedigreeParser(self.tfam_filename,
self.miss_tped_filename)
ped_parser.load_tfam(pc)
ped_parser.load_genotypes()
mapdata = libgwas.get_lines(self.miss_tped_filename, split=True)
genotypes_w_missing = [[0, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 0],
[1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1],
[0, -1, 1, 1, 0, 0, 0, 2, 1, 1, 0, 0],
[0, -1, 2, 1, 1, 0, 0, 1, 2, 1, 1, 0],
[1, -1, 0, 1, 0, 0, 1, 2, 0, 1, 0, 0],
[1, -1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0],
[0, -1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0]]
hetero_freq_tped = [
0.3636, 0.5, 0.3636, 0.4545, 0.3636, 0.2727, 0.2727
]
self.assertEqual(7, ped_parser.locus_count)
index = 0
loci = ped_parser.get_loci()
for snp in loci:
self.assertEqual(int(mapdata[index][0]), snp.chr)
self.assertEqual(int(mapdata[index][3]), snp.pos)
index += 1
self.assertEqual(7, index)
index = 0
missing = 0
valid = 0
for snp in ped_parser:
for y in pc:
(pheno, covars,
nonmissing) = y.get_variables(snp.missing_genotypes)
try:
genodata = snp.get_genotype_data(nonmissing)
self.assertEqual(int(mapdata[index][0]), snp.chr)
self.assertEqual(int(mapdata[index][3]), snp.pos)
self.assertEqual(mapdata[index][1], snp.rsid)
self.assertEqual(genotypes_w_missing[index],
list(snp.genotype_data))
self.assertAlmostEqual(hetero_freq_tped[index],
genodata.hetero_freq,
places=4)
valid += 1
except TooMuchMissing as e:
missing += 1
except InvalidFrequency as e:
pass
index += 1
self.assertEqual(1, missing)
self.assertEqual(6, valid)
self.assertEqual(7, index)
def testAllelesInLoci(self):
pc = PhenoCovar()
ped_parser = TransposedPedigreeParser(self.tfam_filename,
self.tped_filename)
ped_parser.load_tfam(pc)
ped_parser.load_genotypes()
index = 0
for snp in ped_parser.get_loci():
self.assertEqual(self.tped1_alleles[index][1], snp.minor_allele)
self.assertEqual(self.tped1_alleles[index][0], snp.major_allele)
index += 1
self.assertEqual(7, index)
def testPedWithMissingMxSnpComplete(self):
pc = PhenoCovar()
DataParser.snp_miss_tol = 0.5 # We should only lose 1
ped_parser = TransposedPedigreeParser(self.tfam_filename,
self.miss_tped_filename)
ped_parser.load_tfam(pc)
ped_parser.load_genotypes()
mapdata = get_lines(self.miss_tped_filename, split=True)
genotypes_w_missing = [[0, 0], [1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1],
[0, 1, 1, 0, 0, 0, 2, 1, 1, 0, 0],
[0, 2, 1, 1, 0, 0, 1, 2, 1, 1, 0],
[1, 0, 1, 0, 0, 1, 2, 0, 1, 0, 0],
[1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0],
[0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0]]
hetero_freq_tped = [
0.3636, 0.5, 0.3636, 0.4545, 0.3636, 0.2727, 0.2727
]
self.assertEqual(7, ped_parser.locus_count)
index = 0
loci = ped_parser.get_loci()
for snp in loci:
self.assertEqual(int(mapdata[index][0]), snp.chr)
self.assertEqual(int(mapdata[index][3]), snp.pos)
index += 1
index = 0
for snp in ped_parser:
snp_filter = numpy.ones(snp.missing_genotypes.shape[0]) == 1
try:
genodata = snp.get_genotype_data(snp_filter)
self.assertEqual(int(mapdata[index][0]), snp.chr)
self.assertEqual(int(mapdata[index][3]), snp.pos)
self.assertEqual(mapdata[index][1], snp.rsid)
self.assertAlmostEqual(hetero_freq_tped[index],
genodata.hetero_freq,
places=4)
self.assertEqual(genotypes_w_missing[index],
list(genodata.genotypes))
except TooMuchMissing as e:
pass
except InvalidFrequency as e:
pass
index += 1
self.assertEqual(7, index)
def testPedWithMissingMxSnpComplete(self):
pc = PhenoCovar()
DataParser.snp_miss_tol = 0.5 # We should only lose 1
ped_parser = TransposedPedigreeParser(self.tfam_filename,
self.miss_tped_filename)
ped_parser.load_tfam(pc)
ped_parser.load_genotypes()
mapdata = [
x.strip().split()
for x in open(self.miss_tped_filename).readlines()
]
genotypes_w_missing = [[0, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 0],
[1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1],
[0, -1, 1, 1, 0, 0, 0, 2, 1, 1, 0, 0],
[0, -1, 2, 1, 1, 0, 0, 1, 2, 1, 1, 0],
[1, -1, 0, 1, 0, 0, 1, 2, 0, 1, 0, 0],
[1, -1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0],
[0, -1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0]]
hetero_freq_tped = [
0.3636, 0.5, 0.3636, 0.4545, 0.3636, 0.2727, 0.2727
]
self.assertEqual(6, ped_parser.locus_count)
index = 1
loci = ped_parser.get_loci()
for snp in loci:
self.assertEqual(int(mapdata[index][0]), snp.chr)
self.assertEqual(int(mapdata[index][3]), snp.pos)
self.assertAlmostEqual(hetero_freq_tped[index],
snp.hetero_freq,
places=4)
index += 1
index = 1
for snp in ped_parser:
self.assertEqual(int(mapdata[index][0]), snp.chr)
self.assertEqual(int(mapdata[index][3]), snp.pos)
self.assertEqual(mapdata[index][1], snp.rsid)
self.assertEqual(genotypes_w_missing[index],
list(snp.genotype_data))
index += 1
self.assertEqual(7, index)
def testPedWithMissingMxSnpComplete(self):
pc = PhenoCovar()
DataParser.snp_miss_tol = 0.5 # We should only lose 1
ped_parser = TransposedPedigreeParser(self.tfam_filename, self.miss_tped_filename)
ped_parser.load_tfam(pc)
ped_parser.load_genotypes()
mapdata = [x.strip().split() for x in open(self.miss_tped_filename).readlines()]
genotypes_w_missing = [
[0, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 0],
[1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1],
[0, -1, 1, 1, 0, 0, 0, 2, 1, 1, 0, 0],
[0, -1, 2, 1, 1, 0, 0, 1, 2, 1, 1, 0],
[1, -1, 0, 1, 0, 0, 1, 2, 0, 1, 0, 0],
[1, -1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0],
[0, -1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0]
]
hetero_freq_tped = [0.3636, 0.5, 0.3636, 0.4545, 0.3636, 0.2727, 0.2727]
self.assertEqual(6, ped_parser.locus_count)
index = 1
loci = ped_parser.get_loci()
for snp in loci:
self.assertEqual(int(mapdata[index][0]), snp.chr)
self.assertEqual(int(mapdata[index][3]), snp.pos)
self.assertAlmostEqual(hetero_freq_tped[index], snp.hetero_freq, places=4)
index += 1
index = 1
for snp in ped_parser:
self.assertEqual(int(mapdata[index][0]), snp.chr)
self.assertEqual(int(mapdata[index][3]), snp.pos)
self.assertEqual(mapdata[index][1], snp.rsid)
self.assertEqual(genotypes_w_missing[index], list(snp.genotype_data))
index += 1
self.assertEqual(7, index)
def testPedBoundaryTPed(self):
pc = PhenoCovar()
ped_parser = TransposedPedigreeParser(self.tfam_filename,
self.tped_filename)
DataParser.boundary = BoundaryCheck()
BoundaryCheck.chrom = 2
ped_parser.load_tfam(pc)
ped_parser.load_genotypes()
pedigree = get_lines(self.tped_filename, split=True)
index = 4
loci = ped_parser.get_loci()
for snp in loci:
self.assertEqual(int(pedigree[index][0]), snp.chr)
self.assertEqual(int(pedigree[index][3]), snp.pos)
index += 1
self.assertEqual(3, ped_parser.locus_count)
index = 4
for snp in ped_parser:
snp_filter = numpy.ones(snp.missing_genotypes.shape[0]) == 1
try:
genodata = snp.get_genotype_data(snp_filter)
self.assertEqual(int(pedigree[index][0]), snp.chr)
self.assertEqual(int(pedigree[index][3]), snp.pos)
self.assertEqual(pedigree[index][1], snp.rsid)
self.assertAlmostEqual(self.hetero_freq_tped[index],
genodata.hetero_freq,
places=4)
self.assertEqual(self.genotypes[index],
list(genodata.genotypes))
except TooMuchMissing as e:
pass
except InvalidFrequency as e:
pass
index += 1
self.assertEqual(7, index)
def testPedWithMissingMxIndComplete(self):
pc = PhenoCovar()
DataParser.ind_miss_tol = 0.5 # We should only lose 1
ped_parser = TransposedPedigreeParser(self.tfam_filename,
self.miss_tped_filename)
ped_parser.load_tfam(pc)
ped_parser.load_genotypes()
mapdata = [
x.strip().split()
for x in open(self.miss_tped_filename).readlines()
]
genotypes_w_missing = [[0, -1, -1, -1, -1, -1, -1, -1, -1, -1, 1],
[1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1],
[0, 1, 1, 0, 0, 0, 2, 1, 1, 0, 0],
[0, 2, 1, 1, 0, 0, 1, 2, 1, 1, 0],
[1, 0, 1, 0, 0, 1, 2, 0, 1, 0, 0],
[1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0],
[0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0]]
self.assertEqual(7, ped_parser.locus_count)
index = 0
loci = ped_parser.get_loci()
for snp in loci:
self.assertEqual(int(mapdata[index][0]), snp.chr)
self.assertEqual(int(mapdata[index][3]), snp.pos)
index += 1
index = 0
for snp in ped_parser:
self.assertEqual(int(mapdata[index][0]), snp.chr)
self.assertEqual(int(mapdata[index][3]), snp.pos)
self.assertEqual(mapdata[index][1], snp.rsid)
self.assertEqual(genotypes_w_missing[index],
list(snp.genotype_data))
index += 1
self.assertEqual(7, index)
