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")