def testPedigreeNoFamId(self):
DataParser.has_fid = False
f = open(self.ped_filename, "w")
f.write(
"""1 0 0 1 0.1 A A G T A A G G C T G T T T
2 0 0 1 0.4 A C G T G G C G T T G G C T
3 0 0 2 1.0 A A G G A G C C C C G T C T
4 0 0 2 0.5 A A G G A G C G C T G G T T
5 0 0 1 0.9 A C G G A A C G C C G G T T
6 0 0 1 1.0 A A G T A A G G C C G G T T
7 0 0 1 0.1 A A G T A A G G C T G G T T
8 0 0 1 0.4 A C G T G G C G T T G G C T
9 0 0 2 1.0 A A G G A G C C C C G T C T
10 0 0 2 0.5 A A G G A G C G C T G G T T
11 0 0 1 0.9 A C G G A A C G C C G G T T
12 0 0 1 1.0 A A G T A A G G C C G G T T"""
)
f.close()
pc = PhenoCovar()
ped_parser = PedigreeParser(self.map_filename, self.ped_filename)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
mapdata = [x.strip().split() for x in open(self.map_filename).readlines()]
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(self.genotypes[index], list(snp.genotype_data))
index += 1
self.assertEqual(7, index)
def testPedigreeIndExclusionsMissingIndThresh(self):
pc = PhenoCovar()
DataParser.ind_exclusions = ["11:11", "12:12"]
DataParser.ind_miss_tol = 0.5 # We should only lose 1
ped_parser = PedigreeParser(self.map_filename,
self.ped_filename_missing)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
mapdata = get_lines(self.map_filename, split=True)
genotypes = [[1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
[-1, -1, -1, -1, 1, -1, -1, -1, 0, 0, 1],
[2, 1, 1, 0, 0, 0, 2, 1, 1, 0, 0],
[1, 0, 1, 1, 2, 2, 1, 0, 1, 1, 2],
[2, 0, 1, 0, 0, 1, 2, 0, 1, 0, 0],
[0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0],
[1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0]]
index = 0
map_idx = 0
for snp in ped_parser:
self.assertEqual(int(mapdata[map_idx][0]), snp.chr)
self.assertEqual(int(mapdata[map_idx][3]), snp.pos)
self.assertEqual(mapdata[map_idx][1], snp.rsid)
self.assertEqual(genotypes[index][0:9], list(snp.genotype_data))
index += 1
map_idx += 1
self.assertEqual(7, index)
def testPedigreeIndExclusionsMissingComplete(self):
DataParser.ind_exclusions = ["11:11", "12:12"]
pc = PhenoCovar()
ped_parser = PedigreeParser(self.map_filename, self.ped_filename_missing)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
mapdata = [x.strip().split() for x in open(self.map_filename).readlines()]
genotypes = [
[0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
[-1, -1, -1, -1, -1, 1, -1, -1, -1, 0, 0, 1],
[-1, 2, 1, 1, 0, 0, 0, 2, 1, 1, 0, 0],
[-1, 1, 0, 1, 1, 2, 2, 1, 0, 1, 1, 2],
[-1, 2, 0, 1, 0, 0, 1, 2, 0, 1, 0, 0],
[-1, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0],
[0, 1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0]
]
index = 0
for snp in ped_parser:
self.assertEqual(genotypes[index][0:10], list(snp.genotype_data))
self.assertEqual(int(mapdata[index][0]), snp.chr)
self.assertEqual(int(mapdata[index][3]), snp.pos)
self.assertEqual(mapdata[index][1], snp.rsid)
index += 1
self.assertEqual(7, index)
def testPedigreeNoPheno(self):
DataParser.has_pheno = False
with open(self.ped_filename, "w") as f:
f.write("""1 1 0 0 1 A A G T A A G G C T G T T T
2 2 0 0 1 A C G T G G C G T T G G C T
3 3 0 0 2 A A G G A G C C C C G T C T
4 4 0 0 2 A A G G A G C G C T G G T T
5 5 0 0 1 A C G G A A C G C C G G T T
6 6 0 0 1 A A G T A A G G C C G G T T
7 7 0 0 1 A A G T A A G G C T G G T T
8 8 0 0 1 A C G T G G C G T T G G C T
9 9 0 0 2 A A G G A G C C C C G T C T
10 10 0 0 2 A A G G A G C G C T G G T T
11 11 0 0 1 A C G G A A C G C C G G T T
12 12 0 0 1 A A G T A A G G C C G G T T""")
PhenoCovar.sex_as_covariate = True
pc = PhenoCovar()
ped_parser = PedigreeParser(self.map_filename, self.ped_filename)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
mapdata = get_lines(self.map_filename, split=True)
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(self.genotypes[index], list(snp.genotype_data))
index += 1
self.assertEqual(7, index)
def testPedigreeWithLiability(self):
DataParser.has_liability = True
f = open(self.ped_filename, "w")
f.write("""1 1 0 0 1 0.1 1 A A G T A A G G C T G T T T
2 2 0 0 1 0.4 1 A C G T G G C G T T G G C T
3 3 0 0 2 1.0 1 A A G G A G C C C C G T C T
4 4 0 0 2 0.5 1 A A G G A G C G C T G G T T
5 5 0 0 1 0.9 1 A C G G A A C G C C G G T T
6 6 0 0 1 1.0 1 A A G T A A G G C C G G T T
7 7 0 0 1 0.1 1 A A G T A A G G C T G G T T
8 8 0 0 1 0.4 1 A C G T G G C G T T G G C T
9 9 0 0 2 1.0 1 A A G G A G C C C C G T C T
10 10 0 0 2 0.5 1 A A G G A G C G C T G G T T
11 11 0 0 1 0.9 1 A C G G A A C G C C G G T T
12 12 0 0 1 1.0 1 A A G T A A G G C C G G T T""")
f.close()
pc = PhenoCovar()
ped_parser = PedigreeParser(self.map_filename, self.ped_filename)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
mapdata = [x.strip().split() for x in open(self.map_filename).readlines()]
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(self.genotypes[index], list(snp.genotype_data))
index += 1
self.assertEqual(7, index)
def testPedigreeNoFamId(self):
DataParser.has_fid = False
f = open(self.ped_filename, "w")
f.write("""1 0 0 1 0.1 A A G T A A G G C T G T T T
2 0 0 1 0.4 A C G T G G C G T T G G C T
3 0 0 2 1.0 A A G G A G C C C C G T C T
4 0 0 2 0.5 A A G G A G C G C T G G T T
5 0 0 1 0.9 A C G G A A C G C C G G T T
6 0 0 1 1.0 A A G T A A G G C C G G T T
7 0 0 1 0.1 A A G T A A G G C T G G T T
8 0 0 1 0.4 A C G T G G C G T T G G C T
9 0 0 2 1.0 A A G G A G C C C C G T C T
10 0 0 2 0.5 A A G G A G C G C T G G T T
11 0 0 1 0.9 A C G G A A C G C C G G T T
12 0 0 1 1.0 A A G T A A G G C C G G T T""")
f.close()
pc = PhenoCovar()
ped_parser = PedigreeParser(self.map_filename, self.ped_filename)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
mapdata = [x.strip().split() for x in open(self.map_filename).readlines()]
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(self.genotypes[index], list(snp.genotype_data))
index += 1
self.assertEqual(7, index)
def testForInvariant(self):
prefix = "__test_pedigree"
self.pheno_file = "%s_mch.txt" % (prefix)
with open(self.pheno_file, "w") as f:
f.write("""FID\tIID\tBMI\tIBM\tMSA
1\t1\t0.1\t1.0\t1.0
2\t2\t0.2\t0.5\t1.0
3\t3\t0.3\t0.6\t1.0
4\t4\t0.4\t0.5\t1.0
5\t5\t0.5\t1.0\t1.0
6\t6\t0.6\t0.1\t1.0
17\t7\t0.1\t1.0\t1.0
8\t8\t0.2\t0.5\t1.0
9\t9\t0.3\t0.6\t1.0
10\t10\t0.4\t0.5\t1.0
11\t11\t0.5\t1.0\t1.0
12\t12\t0.6\t0.1\t1.0""")
PhenoCovar.sex_as_covariate = True
pc = PhenoCovar()
ped_parser = PedigreeParser(self.map_filename, self.ped_filename)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
with open(self.pheno_file) as f2:
pc.load_phenofile(f2, indices=[3])
index = 0
mapdata = get_lines(self.map_filename, split=True)
with self.assertRaises(InvariantVar):
for snp in ped_parser:
for y in pc:
non_missing = numpy.ones(len(snp.genotype_data),
dtype=bool)
(pheno, covariates, nonmissing) = y.get_variables(
numpy.invert(non_missing))
def testPedigreeNoFamSexOrParents(self):
DataParser.has_fid = False
DataParser.has_sex = False
DataParser.has_parents = False
with open(self.ped_filename, "w") as f:
f.write("""1 0.1 A A G T A A G G C T G T T T
2 0.4 A C G T G G C G T T G G C T
3 1.0 A A G G A G C C C C G T C T
4 0.5 A A G G A G C G C T G G T T
5 0.9 A C G G A A C G C C G G T T
6 1.0 A A G T A A G G C C G G T T
7 0.1 A A G T A A G G C T G G T T
8 0.4 A C G T G G C G T T G G C T
9 1.0 A A G G A G C C C C G T C T
10 0.5 A A G G A G C G C T G G T T
11 0.9 A C G G A A C G C C G G T T
12 1.0 A A G T A A G G C C G G T T""")
pc = PhenoCovar()
ped_parser = PedigreeParser(self.map_filename, self.ped_filename)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
mapdata = get_lines(self.map_filename, split=True)
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(self.genotypes[index], list(snp.genotype_data))
index += 1
self.assertEqual(7, index)
def testPedigreeIndExclusionsMissingIndThresh(self):
pc = PhenoCovar()
DataParser.ind_exclusions = ["11:11", "12:12"]
DataParser.ind_miss_tol = 0.5 # We should only lose 1
ped_parser = PedigreeParser(self.map_filename, self.ped_filename_missing)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
mapdata = [x.strip().split() for x in open(self.map_filename).readlines()]
genotypes = [
[1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
[-1, -1, -1, -1, 1, -1, -1, -1, 0, 0, 1],
[2, 1, 1, 0, 0, 0, 2, 1, 1, 0, 0],
[1, 0, 1, 1, 2, 2, 1, 0, 1, 1, 2],
[2, 0, 1, 0, 0, 1, 2, 0, 1, 0, 0],
[0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0],
[1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0],
]
index = 0
map_idx = 0
for snp in ped_parser:
self.assertEqual(int(mapdata[map_idx][0]), snp.chr)
self.assertEqual(int(mapdata[map_idx][3]), snp.pos)
self.assertEqual(mapdata[map_idx][1], snp.rsid)
self.assertEqual(genotypes[index][0:9], list(snp.genotype_data))
index += 1
map_idx += 1
self.assertEqual(7, index)
def testPedigreeNoPheno(self):
DataParser.has_pheno = False
f = open(self.ped_filename, "w")
f.write(
"""1 1 0 0 1 A A G T A A G G C T G T T T
2 2 0 0 1 A C G T G G C G T T G G C T
3 3 0 0 2 A A G G A G C C C C G T C T
4 4 0 0 2 A A G G A G C G C T G G T T
5 5 0 0 1 A C G G A A C G C C G G T T
6 6 0 0 1 A A G T A A G G C C G G T T
7 7 0 0 1 A A G T A A G G C T G G T T
8 8 0 0 1 A C G T G G C G T T G G C T
9 9 0 0 2 A A G G A G C C C C G T C T
10 10 0 0 2 A A G G A G C G C T G G T T
11 11 0 0 1 A C G G A A C G C C G G T T
12 12 0 0 1 A A G T A A G G C C G G T T"""
)
f.close()
PhenoCovar.sex_as_covariate = True
pc = PhenoCovar()
ped_parser = PedigreeParser(self.map_filename, self.ped_filename)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
mapdata = [x.strip().split() for x in open(self.map_filename).readlines()]
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(self.genotypes[index], list(snp.genotype_data))
index += 1
self.assertEqual(7, index)
def testPedigreeIndExclusionsMissingComplete(self):
DataParser.ind_exclusions = ["11:11", "12:12"]
pc = PhenoCovar()
ped_parser = PedigreeParser(self.map_filename, self.ped_filename_missing)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
mapdata = [x.strip().split() for x in open(self.map_filename).readlines()]
genotypes = [
[0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
[-1, -1, -1, -1, -1, 1, -1, -1, -1, 0, 0, 1],
[-1, 2, 1, 1, 0, 0, 0, 2, 1, 1, 0, 0],
[-1, 1, 0, 1, 1, 2, 2, 1, 0, 1, 1, 2],
[-1, 2, 0, 1, 0, 0, 1, 2, 0, 1, 0, 0],
[-1, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0],
[0, 1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0],
]
index = 0
for snp in ped_parser:
self.assertEqual(genotypes[index][0:10], list(snp.genotype_data))
self.assertEqual(int(mapdata[index][0]), snp.chr)
self.assertEqual(int(mapdata[index][3]), snp.pos)
self.assertEqual(mapdata[index][1], snp.rsid)
index += 1
self.assertEqual(7, index)
def testMissingComplete(self):
pc = PhenoCovar()
ped_parser = PedigreeParser(self.map_filename,
self.ped_filename_missing)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
mapdata = get_lines(self.map_filename, split=True)
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(self.missing_genotypes[index],
list(genodata.genotypes))
self.assertEqual(int(mapdata[index][0]), snp.chr)
self.assertEqual(int(mapdata[index][3]), snp.pos)
self.assertEqual(mapdata[index][1], snp.rsid)
valid += 1
except TooMuchMissing as e:
missing += 1
except InvalidFrequency as e:
pass
index += 1
self.assertEqual(0, missing)
self.assertEqual(7, valid)
def testMissingSnpThresh(self):
pc = PhenoCovar()
DataParser.snp_miss_tol = 0.5 # We should only lose 1
ped_parser = PedigreeParser(self.map_filename,
self.ped_filename_missing)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
#self.assertEqual([0,1,0,0,0,0,0,0,0,0,0,0], list(ped_parser.individual_mask))
mapdata = get_lines(self.map_filename, split=True)
index = 0
missing = 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(self.missing_genotypes[index],
list(genodata.genotypes))
except TooMuchMissing as e:
missing += 1
except InvalidFrequency as e:
pass
index += 1
self.assertEqual(1, missing)
self.assertEqual(7, index)
def testMapFileWithRegionAndSnpExclusion(self):
BoundaryCheck.chrom = 2
DataParser.boundary = BoundaryCheck(bp=[0, 10000])
ped_parser = PedigreeParser(self.map_filename, self.ped_filename)
ped_parser.load_mapfile()
self.assertEqual(2, len(ped_parser.markers))
self.assertEqual(7, len(ped_parser.snp_mask[:, 0]))
self.assertEqual(2, ped_parser.locus_count)
# Masks are filters, so we should have 7 entries, but 4 will be 1
self.assertEqual(5, numpy.sum(ped_parser.snp_mask[:, 0]))
self.assertEqual(0, ped_parser.snp_mask[4, 1])
self.assertEqual(0, ped_parser.snp_mask[5, 0])
def testMapFileWithRegionAndSnpExclusion(self):
BoundaryCheck.chrom = 2
DataParser.boundary = BoundaryCheck(bp=[0, 10000])
ped_parser = PedigreeParser(self.map_filename, self.ped_filename)
ped_parser.load_mapfile()
self.assertEqual(2, len(ped_parser.markers))
self.assertEqual(7, len(ped_parser.snp_mask[:, 0]))
self.assertEqual(2, ped_parser.locus_count)
# Masks are filters, so we should have 7 entries, but 4 will be 1
self.assertEqual(5, numpy.sum(ped_parser.snp_mask[:, 0]))
self.assertEqual(0, ped_parser.snp_mask[4, 1])
self.assertEqual(0, ped_parser.snp_mask[5, 0])
def testMapFileWithSnpBoundary(self):
BoundaryCheck.chrom = 1
DataParser.boundary = SnpBoundaryCheck(snps=["rs0001-rs0003"])
ped_parser = PedigreeParser(self.map_filename, self.ped_filename)
ped_parser.load_mapfile()
self.assertEqual(3, len(ped_parser.markers))
self.assertEqual(7, len(ped_parser.snp_mask))
self.assertEqual(3, ped_parser.locus_count)
# Masks are filters, so we should have 7 entries, but 4 will be 1
self.assertEqual(4, numpy.sum(ped_parser.snp_mask[:, 0]))
self.assertEqual(0, ped_parser.snp_mask[0, 0])
self.assertEqual(0, ped_parser.snp_mask[1, 1])
self.assertEqual(0, ped_parser.snp_mask[2, 1])
def testMapFileWithSnpBoundary(self):
BoundaryCheck.chrom = 1
DataParser.boundary = SnpBoundaryCheck(snps=["rs0001-rs0003"])
ped_parser = PedigreeParser(self.map_filename, self.ped_filename)
ped_parser.load_mapfile()
self.assertEqual(3, len(ped_parser.markers))
self.assertEqual(7, len(ped_parser.snp_mask))
self.assertEqual(3, ped_parser.locus_count)
# Masks are filters, so we should have 7 entries, but 4 will be 1
self.assertEqual(4, numpy.sum(ped_parser.snp_mask[:, 0]))
self.assertEqual(0, ped_parser.snp_mask[0, 0])
self.assertEqual(0, ped_parser.snp_mask[1, 1])
self.assertEqual(0, ped_parser.snp_mask[2, 1])
def testMap3File(self):
ped_parser = PedigreeParser(self.map3_filename, self.ped_filename)
ped_parser.load_mapfile(map3=True)
self.assertEqual(7, len(ped_parser.markers))
self.assertEqual(7, len(ped_parser.snp_mask))
self.assertEqual(7, ped_parser.locus_count)
chrom = [int(a) for a in "1,1,1,1,2,2,2".split(",")]
self.assertEqual(chrom, list(ped_parser.markers[:, 0]))
self.assertEqual("rs0001", ped_parser.rsids[0])
self.assertEqual("rs0005", ped_parser.rsids[4])
self.assertEqual("rs0007", ped_parser.rsids[6])
self.assertEqual([500, 10000, 25000, 45000, 750, 10000, 25000], list(ped_parser.markers[:, 1]))
# Masks are filters, so we should have 7 entries, but none will be 1
self.assertEqual(0, numpy.sum(ped_parser.snp_mask))
def testMap3File(self):
ped_parser = PedigreeParser(self.map3_filename, self.ped_filename)
ped_parser.load_mapfile(map3=True)
self.assertEqual(7, len(ped_parser.markers))
self.assertEqual(7, len(ped_parser.snp_mask))
self.assertEqual(7, ped_parser.locus_count)
chrom = [int(a) for a in "1,1,1,1,2,2,2".split(",")]
self.assertEqual(chrom, list(ped_parser.markers[:, 0]))
self.assertEqual("rs0001", ped_parser.rsids[0])
self.assertEqual("rs0005", ped_parser.rsids[4])
self.assertEqual("rs0007", ped_parser.rsids[6])
self.assertEqual([500, 10000, 25000, 45000, 750, 10000, 25000], list(ped_parser.markers[:, 1]))
# Masks are filters, so we should have 7 entries, but none will be 1
self.assertEqual(0, numpy.sum(ped_parser.snp_mask))
def testPedNegativePositions(self):
pc = PhenoCovar()
ped_parser = PedigreeParser(self.map_miss_filename, self.ped_filename)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
mapdata = get_lines(self.map_filename, split=True)
index = 2
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(self.genotypes[index], list(snp.genotype_data))
index += 1
self.assertEqual(7, index)
def testWithFewIndividuals(self):
pc = PhenoCovar()
ped_parser = PedigreeParser(self.map_filename, self.miniped_filename)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
mapdata = [x.strip().split() for x in open(self.map_filename).readlines()]
genotypes = [[0, 1, 0], [1, 1, 0], [0, 2, 1], [0, 1, 1], [1, 0, 1], [1, 0, 1], [0, 1, 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[index], list(snp.genotype_data))
index += 1
self.assertEqual(7, index)
def testPedNegativePositions(self):
pc = PhenoCovar()
ped_parser = PedigreeParser(self.map_miss_filename, self.ped_filename)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
mapdata = [x.strip().split() for x in open(self.map_filename).readlines()]
index = 2
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(self.genotypes[index], list(snp.genotype_data))
index += 1
self.assertEqual(7, index)
def testMissingComplete(self):
pc = PhenoCovar()
ped_parser = PedigreeParser(self.map_filename, self.ped_filename_missing)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
mapdata = [x.strip().split() for x in open(self.map_filename).readlines()]
index = 0
for snp in ped_parser:
self.assertEqual(self.missing_genotypes[index], list(snp.genotype_data))
self.assertEqual(int(mapdata[index][0]), snp.chr)
self.assertEqual(int(mapdata[index][3]), snp.pos)
self.assertEqual(mapdata[index][1], snp.rsid)
index += 1
self.assertEqual(7, index)
def testPedNegativePositionsLocalChrom(self):
BoundaryCheck.chrom = 1
pc = PhenoCovar()
ped_parser = PedigreeParser(self.map_miss_filename, self.ped_filename)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
mapdata = [x.strip().split() for x in open(self.map_filename).readlines()]
index = 2
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(self.genotypes[index], list(snp.genotype_data))
index += 1
self.assertEqual(4, index)
def testWithFewIndividuals(self):
pc = PhenoCovar()
ped_parser = PedigreeParser(self.map_filename, self.miniped_filename)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
mapdata = get_lines(self.map_filename, split=True)
genotypes = [[0, 1, 0], [1, 1, 0], [0, 2, 1], [0, 1, 1], [1, 0, 1],
[1, 0, 1], [0, 1, 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[index], list(snp.genotype_data))
index += 1
self.assertEqual(7, index)
def testPedigreeIndExclusionsComplete(self):
DataParser.ind_exclusions = ["11:11", "12:12"]
pc = PhenoCovar()
ped_parser = PedigreeParser(self.map_filename, self.ped_filename)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
mapdata = get_lines(self.map_filename, split=True)
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(self.genotypes[index][0:10],
list(snp.genotype_data))
index += 1
self.assertEqual(7, index)
def testPedBoundary(self):
pc = PhenoCovar()
ped_parser = PedigreeParser(self.map_filename, self.ped_filename)
DataParser.boundary = BoundaryCheck()
BoundaryCheck.chrom = 2
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
pedigree = get_lines(self.map_filename, split=True)
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(7, index)
def testPedNegativePosLocalChromMissSNP(self):
BoundaryCheck.chrom = 1
DataParser.boundary.LoadExclusions(snps=["rs0004"])
pc = PhenoCovar()
ped_parser = PedigreeParser(self.map_miss_filename, self.ped_filename)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
mapdata = get_lines(self.map_filename, split=True)
index = 2
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(self.genotypes[index], list(snp.genotype_data))
index += 1
self.assertEqual(3, index)
def testPedNegativePosLocalChromMissSNP(self):
BoundaryCheck.chrom = 1
DataParser.boundary.LoadExclusions(snps=["rs0004"])
pc = PhenoCovar()
ped_parser = PedigreeParser(self.map_miss_filename, self.ped_filename)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
mapdata = [x.strip().split() for x in open(self.map_filename).readlines()]
index = 2
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(self.genotypes[index], list(snp.genotype_data))
index += 1
self.assertEqual(3, index)
def testPedBoundary(self):
pc = PhenoCovar()
ped_parser = PedigreeParser(self.map_filename, self.ped_filename)
DataParser.boundary = BoundaryCheck()
BoundaryCheck.chrom = 2
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
pedigree = [x.split() for x in open(self.map_filename).readlines()]
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(7, index)
def testMissingIndThresh(self):
pc = PhenoCovar()
DataParser.ind_miss_tol = 0.5 # We should only lose 1
ped_parser = PedigreeParser(self.map_filename, self.ped_filename_missing)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
mapdata = [x.strip().split() for x in open(self.map_filename).readlines()]
index = 0
map_idx = 0
for snp in ped_parser:
self.assertEqual(int(mapdata[map_idx][0]), snp.chr)
self.assertEqual(int(mapdata[map_idx][3]), snp.pos)
self.assertEqual(mapdata[map_idx][1], snp.rsid)
self.assertEqual(self.missing_genotypes[index][1:], list(snp.genotype_data))
index += 1
map_idx += 1
self.assertEqual(7, index)
def testMissingSnpThresh(self):
pc = PhenoCovar()
DataParser.snp_miss_tol = 0.5 # We should only lose 1
ped_parser = PedigreeParser(self.map_filename, self.ped_filename_missing)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
# self.assertEqual([0,1,0,0,0,0,0,0,0,0,0,0], list(ped_parser.individual_mask))
mapdata = [x.strip().split() for x in open(self.map_filename).readlines()]
index = 0
for snp in ped_parser:
if index == 1: # This gets dropped due to missingness
index += 1
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(self.missing_genotypes[index], list(snp.genotype_data))
index += 1
self.assertEqual(7, index)
def testPedMultiPheno(self):
PhenoCovar.sex_as_covariate = True
pc = PhenoCovar()
ped_parser = PedigreeParser(self.map_filename, self.ped_filename)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
with open(self.pheno_file) as f:
pc.load_phenofile(f, indices=[2, 3])
mapdata = get_lines(self.map_filename, split=True)
sex = [1, 1, 2, 2, 1, 1, 1, 2, 2, 1, 1]
pheno_data = [[0.1, 0.2, 0.3, 0.4, 0.5, 0.6],
[1.0, 0.5, 0.6, 0.5, 1.0, 0.1],
[0.5, 1.0, 0.1, 0.5, 1.0, 0.2]]
dual_pheno = [[1.0, 0.5, 0.6, 0.5, 1.0, 0.1, 0.5, 0.6, 0.5, 1.0, 0.1],
[0.5, 1.0, 0.1, 0.5, 1.0, 0.2, 1.0, 0.1, 0.5, 1.0, 0.2]]
self.assertEqual(2, len(pc.phenotype_data))
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(self.genotypes[index], list(snp.genotype_data))
idx = 0
for y in pc:
non_missing = numpy.ones(len(snp.genotype_data), dtype=bool)
non_missing[6] = False
(pheno, covariates,
nm_indata) = y.get_variables(numpy.invert(non_missing))
for i in range(0, 11):
self.assertEqual(sex[i], covariates[0][i])
self.assertAlmostEqual(dual_pheno[idx][i], pheno[i])
idx += 1
self.assertEqual(2, idx)
index += 1
self.assertEqual(7, index)
def testMissingIndThresh(self):
pc = PhenoCovar()
DataParser.ind_miss_tol = 0.5 # We should only lose 1
ped_parser = PedigreeParser(self.map_filename, self.ped_filename_missing)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
mapdata = [x.strip().split() for x in open(self.map_filename).readlines()]
index = 0
map_idx = 0
for snp in ped_parser:
self.assertEqual(int(mapdata[map_idx][0]), snp.chr)
self.assertEqual(int(mapdata[map_idx][3]), snp.pos)
self.assertEqual(mapdata[map_idx][1], snp.rsid)
self.assertEqual(self.missing_genotypes[index][1:], list(snp.genotype_data))
index += 1
map_idx += 1
self.assertEqual(7, index)
def testMissingSnpThresh(self):
pc = PhenoCovar()
DataParser.snp_miss_tol = 0.5 # We should only lose 1
ped_parser = PedigreeParser(self.map_filename, self.ped_filename_missing)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
#self.assertEqual([0,1,0,0,0,0,0,0,0,0,0,0], list(ped_parser.individual_mask))
mapdata = [x.strip().split() for x in open(self.map_filename).readlines()]
index = 0
for snp in ped_parser:
if index == 1: # This gets dropped due to missingness
index += 1
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(self.missing_genotypes[index], list(snp.genotype_data))
index += 1
self.assertEqual(7, index)
def testPedMultiPheno(self):
PhenoCovar.sex_as_covariate = True
pc = PhenoCovar()
ped_parser = PedigreeParser(self.map_filename, self.ped_filename)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
pc.load_phenofile(open(self.pheno_file), indices=[2, 3])
mapdata = [x.strip().split() for x in open(self.map_filename).readlines()]
sex = [1, 1, 2, 2, 1, 1, 1, 2, 2, 1, 1]
pheno_data = [[0.1, 0.2, 0.3, 0.4, 0.5, 0.6], [1.0, 0.5, 0.6, 0.5, 1.0, 0.1], [0.5, 1.0, 0.1, 0.5, 1.0, 0.2]]
dual_pheno = [
[1.0, 0.5, 0.6, 0.5, 1.0, 0.1, 0.5, 0.6, 0.5, 1.0, 0.1],
[0.5, 1.0, 0.1, 0.5, 1.0, 0.2, 1.0, 0.1, 0.5, 1.0, 0.2],
]
self.assertEqual(2, len(pc.phenotype_data))
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(self.genotypes[index], list(snp.genotype_data))
idx = 0
for y in pc:
non_missing = numpy.ones(len(snp.genotype_data), dtype=bool)
non_missing[6] = False
(pheno, covariates, nm_indata) = y.get_variables(numpy.invert(non_missing))
for i in range(0, 11):
self.assertEqual(sex[i], covariates[0][i])
self.assertAlmostEqual(dual_pheno[idx][i], pheno[i])
idx += 1
self.assertEqual(2, idx)
index += 1
self.assertEqual(7, index)
def testPedCompleteAlternateIteration(self):
"""Useful if you need to iterate over these in a more controlled manner"""
pc = PhenoCovar()
ped_parser = PedigreeParser(self.map_filename, self.ped_filename)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
mapdata = [x.strip().split() for x in open(self.map_filename).readlines()]
index = 0
snp = ped_parser.__iter__().next()
try:
while True:
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(self.genotypes[index], list(snp.genotype_data))
index += 1
snp.next()
except StopIteration:
pass
self.assertEqual(7, index)
def testPedCompleteAlternateIteration(self):
"""Useful if you need to iterate over these in a more controlled manner"""
pc = PhenoCovar()
ped_parser = PedigreeParser(self.map_filename, self.ped_filename)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
mapdata = get_lines(self.map_filename, split=True)
index = 0
snp = next(ped_parser.__iter__())
try:
while True:
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(self.genotypes[index],
list(snp.genotype_data))
index += 1
next(snp)
except StopIteration:
pass
self.assertEqual(7, index)
def testForInvariant(self):
prefix = "__test_pedigree"
self.pheno_file = "%s_mch.txt" % (prefix)
f = open(self.pheno_file, "w")
f.write(
"""FID\tIID\tBMI\tIBM\tMSA
1\t1\t0.1\t1.0\t1.0
2\t2\t0.2\t0.5\t1.0
3\t3\t0.3\t0.6\t1.0
4\t4\t0.4\t0.5\t1.0
5\t5\t0.5\t1.0\t1.0
6\t6\t0.6\t0.1\t1.0
17\t7\t0.1\t1.0\t1.0
8\t8\t0.2\t0.5\t1.0
9\t9\t0.3\t0.6\t1.0
10\t10\t0.4\t0.5\t1.0
11\t11\t0.5\t1.0\t1.0
12\t12\t0.6\t0.1\t1.0"""
)
f.close()
PhenoCovar.sex_as_covariate = True
pc = PhenoCovar()
ped_parser = PedigreeParser(self.map_filename, self.ped_filename)
ped_parser.load_mapfile()
ped_parser.load_genotypes(pc)
pc.load_phenofile(open(self.pheno_file), indices=[3])
index = 0
mapdata = [x.strip().split() for x in open(self.map_filename).readlines()]
with self.assertRaises(InvariantVar):
for snp in ped_parser:
for y in pc:
non_missing = numpy.ones(len(snp.genotype_data), dtype=bool)
(pheno, covariates, nonmissing) = y.get_variables(numpy.invert(non_missing))