def setUp(self):
self.missing = "tests/bedfiles/ped_missing"
self.missing_bed = resource_filename("libgwas",
"%s.bed" % (self.missing))
self.missing_bim = resource_filename("libgwas",
"%s.bim" % (self.missing))
self.missing_fam = resource_filename("libgwas",
"%s.fam" % (self.missing))
self.genotypes = [[0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
[1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1],
[0, 2, 1, 1, 0, 0, 0, 2, 1, 1, 0, 0],
[0, 1, 2, 1, 1, 0, 0, 1, 2, 1, 1, 0],
[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]]
self.nonmissing = "tests/bedfiles/ped_nomiss"
self.nonmissing_bed = resource_filename("libgwas",
"%s.bed" % (self.nonmissing))
self.nonmissing_bim = resource_filename("libgwas",
"%s.bim" % (self.nonmissing))
self.nonmissing_fam = resource_filename("libgwas",
"%s.fam" % (self.nonmissing))
self.genotypes_w_missing = [[0, 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.nonmissing_mapdata = libgwas.get_lines(self.nonmissing_bim,
split=True)
self.missing_mapdata = libgwas.get_lines(self.missing_bim, split=True)
self.phenotypes = [
0.1, 0.4, 1.0, 0.5, 0.9, 1.0, 0.1, 0.4, 1.0, 0.5, 0.9, 1.0
]
self.sex = [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 1, 1]
self.chrom = BoundaryCheck.chrom
self.boundary = DataParser.boundary
self.min_maf = DataParser.min_maf
self.max_maf = DataParser.max_maf
self.snp_miss_tol = DataParser.snp_miss_tol
self.ind_miss_tol = DataParser.ind_miss_tol
self.sex_as_covar = PhenoCovar.sex_as_covariate
self.has_sex = DataParser.has_sex
self.has_pheno = DataParser.has_pheno
self.has_parents = DataParser.has_parents
self.has_fid = DataParser.has_fid
self.has_liability = DataParser.has_liability
DataParser.boundary = BoundaryCheck()
def testPedWithMissingMxIndExclusionsToo(self):
pc = PhenoCovar()
DataParser.ind_exclusions = ["2:2", "3:3"]
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 = libgwas.get_lines(self.miss_tped_filename, split=True)
genotypes_w_missing = [[0, -1, -1, -1, -1, -1, -1, -1, -1, 1],
[1, 0, 0, 1, 1, 1, 0, 0, 0, 1],
[0, 1, 0, 0, 0, 2, 1, 1, 0, 0],
[0, 1, 1, 0, 0, 1, 2, 1, 1, 0],
[1, 1, 0, 0, 1, 2, 0, 1, 0, 0],
[1, 0, 0, 0, 0, 0, 1, 0, 0, 0],
[0, 0, 0, 0, 0, 1, 1, 0, 0, 0]]
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 testCmdLinePedigreeWithLiability(self):
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()
cmds = "--file %s --liability" % (self.ped_filename.split(".")[0])
app = mvtest.MVTestApplication()
ped_parser, pc, args = app.LoadCmdLine(cmds.split(" "))
mapdata = libgwas.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 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 setUp(self):
self.WriteTestFiles()
self.ped = get_lines(self.ped_filename)
self.phenotypes = [
0.1, 0.4, 1.0, 0.5, 0.9, 1.0, 0.1, 0.4, 1.0, 0.5, 0.9, 1.0
]
self.sex = [1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 1, 1]
self.chrom = BoundaryCheck.chrom
self.boundary = DataParser.boundary
DataParser.boundary = BoundaryCheck()
self.min_maf = DataParser.min_maf
self.max_maf = DataParser.max_maf
self.snp_miss_tol = DataParser.snp_miss_tol
self.ind_miss_tol = DataParser.ind_miss_tol
DataParser.ind_exclusions = []
DataParser.ind_inclusions = []
self.sex_as_covar = PhenoCovar.sex_as_covariate
self.has_sex = DataParser.has_sex
self.has_pheno = DataParser.has_pheno
self.has_parents = DataParser.has_parents
self.has_fid = DataParser.has_fid
self.has_liability = DataParser.has_liability
self.sex_as_covariate = PhenoCovar.sex_as_covariate
self.standardizer = libgwas.standardizer.get_standardizer()
libgwas.standardizer.set_standardizer(
libgwas.standardizer.NoStandardization)
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 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 testPedCmdLineMIND2(self):
cmds = "--ped %s --map %s --mind=0.10" % (self.ped_filename_missing,
self.map_filename)
app = mvtest.MVTestApplication()
dataset, vars, args = app.LoadCmdLine(cmds.split(" "))
genotypes = [[0, 0, 1, 0], [1, 0, 0, 1], [0, 1, 0, 0], [0, 1, 1, 0],
[0, 1, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0]]
mapdata = libgwas.get_lines(self.map_filename, split=True)
index = 0
for snp in dataset:
snp_filter = numpy.ones(snp.missing_genotypes.shape[0]) == 1
try:
genodata = snp.get_genotype_data(snp_filter)
self.assertEqual(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)
index += 1
except TooMuchMissing as e:
pass
except InvalidFrequency as e:
skipped += 1
except TooMuchMissingpPhenoCovar as e:
pass
self.assertEqual(5, index) # Last two are fixed
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 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 testTPedNoParentsPheno(self):
f = open(self.tfam_filename, "w")
f.write("""1 1 1
2 2 1
3 3 2
4 4 2
5 5 1
6 6 1
7 7 1
8 8 1
9 9 2
10 10 2
11 11 1
12 12 1""")
f.close()
DataParser.has_parents = False
DataParser.has_pheno = False
pc = PhenoCovar()
ped_parser = TransposedPedigreeParser(self.tfam_filename,
self.tped_filename)
ped_parser.load_tfam(pc)
ped_parser.load_genotypes()
mapdata = libgwas.get_lines(self.tped_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 testCmdLinePedigreeNoFamSexOrParents(self):
f = open(self.ped_filename, "w")
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""")
f.close()
cmds = "--file %s --no-parents --no-fid --no-sex" % (
self.ped_filename.split(".")[0])
app = mvtest.MVTestApplication()
ped_parser, pc, args = app.LoadCmdLine(cmds.split(" "))
mapdata = libgwas.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 testTPedNoFamIDSex(self):
f = open(self.tfam_filename, "w")
f.write("""1 0 0 0.1
2 0 0 0.4
3 0 0 1.0
4 0 0 0.5
5 0 0 0.9
6 0 0 1.0
7 0 0 0.1
8 0 0 0.4
9 0 0 1.0
10 0 0 0.5
11 0 0 0.9
12 0 0 1.0""")
f.close()
DataParser.has_fid = False
DataParser.has_sex = False
pc = PhenoCovar()
ped_parser = TransposedPedigreeParser(self.tfam_filename,
self.tped_filename)
ped_parser.load_tfam(pc)
ped_parser.load_genotypes()
mapdata = libgwas.get_lines(self.tped_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 testTPedLiability(self):
f = open(self.tfam_filename, "w")
f.write("""1 1 0 0 1 0.1 1
2 2 0 0 1 0.4 1
3 3 0 0 2 1.0 1
4 4 0 0 2 0.5 1
5 5 0 0 1 0.9 1
6 6 0 0 1 1.0 1
7 7 0 0 1 0.1 1
8 8 0 0 1 0.4 1
9 9 0 0 2 1.0 1
10 10 0 0 2 0.5 1
11 11 0 0 1 0.9 1
12 12 0 0 1 1.0 1""")
f.close()
DataParser.has_liability = True
pc = PhenoCovar()
ped_parser = TransposedPedigreeParser(self.tfam_filename,
self.tped_filename)
ped_parser.load_tfam(pc)
ped_parser.load_genotypes()
mapdata = libgwas.get_lines(self.tped_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 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 = libgwas.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:
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 = libgwas.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)
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 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 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 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 testCmdLineNoExternalVars(self):
cmds = "--file %s --sex" % (self.ped_filename.split(".")[0])
app = mvtest.MVTestApplication()
ped_parser, pc, args = app.LoadCmdLine(cmds.split(" "))
mapdata = libgwas.get_lines(self.map_filename, split=True)
c = pc.covariate_data
y = pc.phenotype_data
self.assertEqual(["SEX"], pc.covariate_labels)
self.assertEqual(["Pheno-1"], pc.phenotype_names)
for i in range(0, len(y[0])):
self.assertAlmostEqual(self.dummy_pheno[i], y[0][i])
self.assertAlmostEqual(1, c[0][i])
def testPedNegativePositions(self):
pc = PhenoCovar()
ped_parser = TransposedPedigreeParser(self.tfam_filename,
self.misssnp_tped_filename)
ped_parser.load_tfam(pc)
ped_parser.load_genotypes()
mapdata = libgwas.get_lines(self.misssnp_tped_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 = 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 testPedComplete(self):
pc = PhenoCovar()
ped_parser = TransposedPedigreeParser(self.tfam_filename,
self.tped_filename)
ped_parser.load_tfam(pc)
ped_parser.load_genotypes()
self.assertEqual(12, ped_parser.ind_count)
mapdata = libgwas.get_lines(self.tped_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 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 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 testCmdLinePhenoWithNames(self):
cmds = "--file %s --pheno %s --pheno-names=BMI --covar %s --covar-names SEX,AGE" % (
self.ped_filename.split(".")[0], self.pheno_covar,
self.pheno_covar)
app = mvtest.MVTestApplication()
ped_parser, pc, args = app.LoadCmdLine(cmds.split(" "))
mapdata = libgwas.get_lines(self.map_filename, split=True)
c = pc.covariate_data
y = pc.phenotype_data
self.assertEqual(["SEX", "AGE"], pc.covariate_labels)
self.assertEqual(["BMI"], pc.phenotype_names)
for i in range(0, len(y[0])):
self.assertAlmostEqual(self.phenotype_data[i], y[0][i])
self.assertAlmostEqual(self.covariate_data[0][i], c[0][i])
self.assertAlmostEqual(self.covariate_data[1][i], c[1][i])
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 testTPedPhenoComplete(self):
PhenoCovar.sex_as_covariate = True
pc = PhenoCovar()
ped_parser = TransposedPedigreeParser(self.tfam_filename,
self.tped_filename)
ped_parser.load_tfam(pc)
ped_parser.load_genotypes()
self.assertEqual(12, len(pc.covariate_data[0]))
self.assertEqual(12, len(pc.phenotype_data[0]))
self.assertEqual(1, len(pc.phenotype_names))
mapdata = libgwas.get_lines(self.tped_filename, split=True)
index = 0
self.assertEqual(7, ped_parser.locus_count)
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 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)