def test_one_looc(self):
logging.info("TestSingleSnpLeaveOutOneChrom test_one_looc")
from pysnptools.snpreader import Bed
test_snps = Bed(self.bedbase)
pheno = self.phen_fn
covar = self.cov_fn
output_file = self.file_name("one_looc")
frame = single_snp_leave_out_one_chrom(test_snps, pheno,
covar=covar, mixing=0,
output_file_name=output_file
)
self.compare_files(frame,"one_looc")
def test_one_looc(self):
logging.info("TestSingleSnpLeaveOutOneChrom test_one_looc")
from pysnptools.snpreader import Bed
test_snps = Bed(self.bedbase)
pheno = self.phen_fn
covar = self.cov_fn
output_file = self.file_name("one_looc")
frame = single_snp_leave_out_one_chrom(test_snps,
pheno,
covar=covar,
mixing=0,
output_file_name=output_file)
self.compare_files(frame, "one_looc")
def test_covar_by_chrom_mixing(self):
logging.info("TestSingleSnpLeaveOutOneChrom test_covar_by_chrom_mixing")
from pysnptools.snpreader import Bed
test_snps = Bed(self.bedbase)
pheno = self.phen_fn
covar = self.cov_fn
covar_by_chrom = {}
for chrom in xrange(1,6):
covar_by_chrom[chrom] = covar
output_file = self.file_name("covar_by_chrom_mixing")
frame = single_snp_leave_out_one_chrom(test_snps, pheno,
covar=covar,
covar_by_chrom=covar_by_chrom,
output_file_name=output_file
)
self.compare_files(frame,"covar_by_chrom_mixing")
def test_covar_by_chrom_mixing(self):
logging.info(
"TestSingleSnpLeaveOutOneChrom test_covar_by_chrom_mixing")
from pysnptools.snpreader import Bed
test_snps = Bed(self.bedbase)
pheno = self.phen_fn
covar = self.cov_fn
covar_by_chrom = {}
for chrom in xrange(1, 6):
covar_by_chrom[chrom] = covar
output_file = self.file_name("covar_by_chrom_mixing")
frame = single_snp_leave_out_one_chrom(test_snps,
pheno,
covar=covar,
covar_by_chrom=covar_by_chrom,
output_file_name=output_file)
self.compare_files(frame, "covar_by_chrom_mixing")
