def test_one(self):
logging.info("TestEpistasis test_one")
from pysnptools.snpreader import Bed
test_snps = Bed(self.bedbase, count_A1=False)
pheno = self.phen_fn
covar = self.cov_fn
output_file = self.file_name("one")
frame = epistasis(
test_snps,
pheno,
G0=test_snps,
covar=covar,
sid_list_0=test_snps.sid[:10], #first 10 snps
sid_list_1=test_snps.sid[5:15], #Skip 5 snps, use next 10
output_file_name=output_file,
count_A1=False)
sid0, sid1, pvalue_list = np.array(frame['SNP0']), np.array(
frame['SNP1']), np.array(frame['PValue'])
#Check the output file
self.compare_files(sid0, sid1, pvalue_list, "one")
#Check the values returned
output_file2 = self.file_name("one_again")
write(sid0, sid1, pvalue_list, output_file2)
self.compare_files(sid0, sid1, pvalue_list, "one")
def test_no_sid_list_1(self):
logging.info("TestEpistasis test_no_sid_list_1")
from pysnptools.snpreader import Bed
test_snps = Bed(self.bedbase)
pheno = self.phen_fn
covar = self.cov_fn
output_file = self.file_name("no_sid_list_1")
frame = epistasis(test_snps, pheno, G0=test_snps,
covar=covar,
sid_list_1=['1_4']
)
sid0,sid1,pvalue_list =np.array(frame['SNP0']),np.array(frame['SNP1']),np.array(frame['PValue'])
write(sid0,sid1,pvalue_list,output_file)
self.compare_files(sid1,sid0,pvalue_list,"no_sid_list_0") #Swap order of sid0 and sid1
def test_one(self):
logging.info("TestEpistasis test_one")
from pysnptools.snpreader import Bed
test_snps = Bed(self.bedbase)
pheno = self.phen_fn
covar = self.cov_fn
output_file = self.file_name("one")
frame = epistasis(test_snps, pheno, G0=test_snps,
covar=covar,
sid_list_0=test_snps.sid[:10], #first 10 snps
sid_list_1=test_snps.sid[5:15], #Skip 5 snps, use next 10
output_file_name=output_file
)
sid0,sid1,pvalue_list =np.array(frame['SNP0']),np.array(frame['SNP1']),np.array(frame['PValue'])
#Check the output file
self.compare_files(sid0,sid1,pvalue_list,"one")
#Check the values returned
output_file2 = self.file_name("one_again")
write(sid0,sid1,pvalue_list,output_file2)
self.compare_files(sid0,sid1,pvalue_list,"one")
