def copy_assoc_file(self, assoc_file):
"""
copy assoc file to directory to where program is ran from
"""
#get base extension e.g. qassoc,assoc assoc.linear
base_extention = common.plink_results_extension(assoc_file)
output_number = get_number_of_assoc_file(assoc_file)
assoc_files = []
extentions = ["", ".adjusted"]
for ext in extentions:
if (os.path.exists(assoc_file + ext)):
dest_assoc_file = self.out + "results" + output_number + "." + base_extention + ext
if os.path.exists(dest_assoc_file):
_remove_file(dest_assoc_file)
shutil.copy(assoc_file, dest_assoc_file)
os.path.abspath(os.path.curdir)
log.info("\nResults of PLINK saved as " + dest_assoc_file)
assoc_files.append(dest_assoc_file)
else:
pass
return(assoc_files)
def run_permutation(self, seeds):
"""
performs permutations
"""
permuted_pheno_file = common.create_pheno_permutation_file(self, seeds)
pheno_arg = " --pheno " + str(permuted_pheno_file + " --all-pheno" + " --extract " + self.group)
if self.covar_file:
permuted_covar_file = common.create_covar_permutation_file(self, seeds)
pheno_arg += " --covar " + permuted_covar_file + " --hide-covar"
self.set_plink_arguments("--bfile " + self.bfile + pheno_arg)
else:
self.set_plink_arguments("--bfile " + self.bfile + " --assoc " + pheno_arg)
resultfile = self.run_plink() # run plink
results_extension = common.plink_results_extension(resultfile)
resultfiles = self.point_outputfile_to_phenotype(seeds, resultfile, results_extension)
results = extract_permutated_scores(self.snp_to_group_map, resultfiles, seeds)
os.remove(permuted_pheno_file) #remove permuted pheno file
common.remove_plink_output(resultfile) # remove all output from plink
return results
