def test_one(self):
logging.info("TestSnpSet test_one")
fn = "lrt_one_kernel_fixed_mixed_effect_linear_qqfit.N300.txt"
tmpOutfile = self.file_name(fn)
referenceOutfile = self._referenceOutfile(fn)
result_dataframe = snp_set(
test_snps = self.currentFolder+'/../../../tests/datasets/all_chr.maf0.001.N300',
set_list = self.currentFolder+'/../../../tests/datasets/set_input.23.txt',
pheno = self.currentFolder+'/../../../tests/datasets/phenSynthFrom22.23.N300.txt',
output_file_name = tmpOutfile
)
out,msg=ut.compare_files(tmpOutfile, referenceOutfile, tolerance)
self.assertTrue(out, "msg='{0}', ref='{1}', tmp='{2}'".format(msg, referenceOutfile, tmpOutfile))
def test_one(self):
logging.info("TestSnpSet test_one")
fn = "lrt_one_kernel_fixed_mixed_effect_linear_qqfit.N300.txt"
tmpOutfile = self.file_name(fn)
referenceOutfile = self._referenceOutfile(fn)
result_dataframe = snp_set(
test_snps = self.currentFolder+'/../../../tests/datasets/all_chr.maf0.001.N300',
set_list = self.currentFolder+'/../../../tests/datasets/set_input.23.txt',
pheno = self.currentFolder+'/../../../tests/datasets/phenSynthFrom22.23.N300.txt',
output_file_name = tmpOutfile
)
out,msg=ut.compare_files(tmpOutfile, referenceOutfile, tolerance)
self.assertTrue(out, "msg='{0}', ref='{1}', tmp='{2}'".format(msg, referenceOutfile, tmpOutfile))
def main(args):
# command line arguments
genotype, phenotype, file_gene, fileout, file_sets = args
genes = load_file(file_gene)
# Running the method
results_df = snp_set(test_snps=genotype,
G0=None,
set_list=file_sets,
pheno=phenotype,
test='lrt',
nperm=0)
statistics = process_results(results_df, genes)
save_file(fileout, statistics)
return 0
def test_three(self):
logging.info("TestSnpSet test_three")
fn = "sc_davies_one_kernel_linear_qqfit.N300.txt"
tmpOutfile = self.file_name(fn)
referenceOutfile = self._referenceOutfile(fn)
result_dataframe = snp_set(
test_snps = self.currentFolder+'/../../../tests/datasets/all_chr.maf0.001.N300',
set_list = self.currentFolder+'/../../../tests/datasets/set_input.small.txt',
pheno = self.currentFolder+'/../../../tests/datasets/phenSynthFrom22.23.N300.txt',
test = "sc_davies",
output_file_name = tmpOutfile
)
out,msg=ut.compare_files(tmpOutfile, referenceOutfile, tolerance)
self.assertTrue(out,msg)#msg='Files %s and %s are different.' % (tmpOutfile, referenceOutfile))
def test_four(self):
logging.info("TestSnpSet test_four")
fn = "sc_davies_two_kernel_linear_qqfit.N300.noautoselect.txt"
tmpOutfile = self.file_name(fn)
referenceOutfile = self._referenceOutfile(fn)
result_dataframe = snp_set(
test_snps = self.currentFolder+'/../../../tests/datasets/all_chr.maf0.001.N300',
set_list = self.currentFolder+'/../../../tests/datasets/set_input.small.txt',
pheno = self.currentFolder+'/../../../tests/datasets/phenSynthFrom22.23.N300.randcidorder.txt',
G0 = self.currentFolder+'/../../../tests/datasets/all_chr.maf0.001.chr22.23.N300.bed',
test = 'sc_davies',
output_file_name = tmpOutfile
)
out,msg=ut.compare_files(tmpOutfile, referenceOutfile, tolerance)
self.assertTrue(out, "msg='{0}', ref='{1}', tmp='{2}'".format(msg, referenceOutfile, tmpOutfile))
def test_two(self):
logging.info("TestSnpSet test_two")
fn = "lrt_up_two_kernel_mixed_effect_linear_qqfit.N300.fullrank.txt"
tmpOutfile = self.file_name(fn)
referenceOutfile = self._referenceOutfile(fn)
result_dataframe = snp_set(
test_snps = self.currentFolder+'/../../../tests/datasets/all_chr.maf0.001.N300',
set_list = self.currentFolder+'/../../../tests/datasets/set_input.23.txt',
pheno = self.currentFolder+'/../../../tests/datasets/phenSynthFrom22.23.N300.txt',
G0 = self.currentFolder+'/../../../tests/datasets/all_chr.maf0.001.chr22.23.N300.bed',
output_file_name = tmpOutfile,
test="lrt"
)
out,msg=ut.compare_files(tmpOutfile, referenceOutfile, tolerance)
self.assertTrue(out,msg)#msg='Files %s and %s are different.' % (tmpOutfile, referenceOutfile))
def test_four(self):
logging.info("TestSnpSet test_four")
fn = "sc_davies_two_kernel_linear_qqfit.N300.noautoselect.txt"
tmpOutfile = self.file_name(fn)
referenceOutfile = self._referenceOutfile(fn)
result_dataframe = snp_set(
test_snps = self.currentFolder+'/../../../tests/datasets/all_chr.maf0.001.N300',
set_list = self.currentFolder+'/../../../tests/datasets/set_input.small.txt',
pheno = self.currentFolder+'/../../../tests/datasets/phenSynthFrom22.23.N300.randcidorder.txt',
G0 = self.currentFolder+'/../../../tests/datasets/all_chr.maf0.001.chr22.23.N300.bed',
test = 'sc_davies',
output_file_name = tmpOutfile
)
out,msg=ut.compare_files(tmpOutfile, referenceOutfile, tolerance)
self.assertTrue(out, "msg='{0}', ref='{1}', tmp='{2}'".format(msg, referenceOutfile, tmpOutfile))
def test_two(self):
logging.info("TestSnpSet test_two")
fn = "lrt_up_two_kernel_mixed_effect_linear_qqfit.N300.fullrank.txt"
tmpOutfile = self.file_name(fn)
referenceOutfile = self._referenceOutfile(fn)
result_dataframe = snp_set(
test_snps = self.currentFolder+'/../../../tests/datasets/all_chr.maf0.001.N300',
set_list = self.currentFolder+'/../../../tests/datasets/set_input.23.txt',
pheno = self.currentFolder+'/../../../tests/datasets/phenSynthFrom22.23.N300.txt',
G0 = self.currentFolder+'/../../../tests/datasets/all_chr.maf0.001.chr22.23.N300.bed',
output_file_name = tmpOutfile,
test="lrt"
)
out,msg=ut.compare_files(tmpOutfile, referenceOutfile, tolerance)
self.assertTrue(out,msg)#msg='Files %s and %s are different.' % (tmpOutfile, referenceOutfile))
def main(args):
# command line arguments
j, blocksize, genotype, phenotype, outdir = args
# File with the set of SNPs corresponding to the 1-degree neighbourhoods
file_sets = outdir + 'neighborhoods_' + blocksize + '/list_nb1_' + j + '.txt'
# Output dir for the statistics on permuted settings
outdir = outdir + 'statistics_' + blocksize + '/'
if (not os.path.exists(outdir)):
os.makedirs(outdir)
# Running the method
results_df = snp_set(test_snps=genotype,
G0=None,
set_list=file_sets,
pheno=phenotype,
test='lrt',
nperm=0)
statistics = process_results(results_df)
save_file(outdir + 'statistics_' + j + '.pkl', statistics)
return 0