diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/plink_mapping.py | 20 |
1 files changed, 10 insertions, 10 deletions
diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py index 8d57d556..5d675c38 100644 --- a/wqflask/wqflask/marker_regression/plink_mapping.py +++ b/wqflask/wqflask/marker_regression/plink_mapping.py @@ -9,11 +9,11 @@ import utility.logger logger = utility.logger.getLogger(__name__ ) def run_plink(this_trait, dataset, species, vals, maf): - plink_output_filename = webqtlUtil.genRandStr("%s_%s_"%(dataset.group.name, this_trait.name)) + plink_output_filename = webqtlUtil.genRandStr(f"{dataset.group.name}_{this_trait.name}_") gen_pheno_txt_file(dataset, vals) - plink_command = PLINK_COMMAND + ' --noweb --bfile %s/%s --no-pheno --no-fid --no-parents --no-sex --maf %s --out %s%s --assoc ' % ( - flat_files('mapping'), dataset.group.name, maf, TMPDIR, plink_output_filename) + + plink_command = f"{PLINK_COMMAND} --noweb --bfile {flat_files('mapping')}/{dataset.group.name} --no-pheno --no-fid --no-parents --no-sex --maf {maf} --out { TMPDIR}{plink_output_filename} --assoc " logger.debug("plink_command:", plink_command) os.system(plink_command) @@ -29,12 +29,12 @@ def gen_pheno_txt_file(this_dataset, vals): """Generates phenotype file for GEMMA/PLINK""" current_file_data = [] - with open("{}/{}.fam".format(flat_files('mapping'), this_dataset.group.name), "r") as outfile: + with open(f"{flat_files('mapping')}/{this_dataset.group.name}.fam", "r") as outfile: for i, line in enumerate(outfile): split_line = line.split() current_file_data.append(split_line) - with open("{}/{}.fam".format(flat_files('mapping'), this_dataset.group.name), "w") as outfile: + with open(f"{flat_files('mapping')}/{this_dataset.group.name}.fam","w") as outfile: for i, line in enumerate(current_file_data): if vals[i] == "x": this_val = -9 @@ -44,8 +44,8 @@ def gen_pheno_txt_file(this_dataset, vals): def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''): ped_sample_list = get_samples_from_ped_file(dataset) - output_file = open("%s%s.txt" % (TMPDIR, pheno_filename), "wb") - header = 'FID\tIID\t%s\n' % this_trait.name + output_file = open(f"{TMPDIR}{pheno_filename}.txt", "wb") + header = f"FID\tIID\t{this_trait.name}\n" output_file.write(header) new_value_list = [] @@ -65,7 +65,7 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''): for i, sample in enumerate(ped_sample_list): j = i+1 value = new_value_list[i] - new_line += '%s\t%s\t%s\n'%(sample, sample, value) + new_line += f"{sample}\t{sample}\t{value}\n" if j%1000 == 0: output_file.write(newLine) @@ -78,7 +78,7 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''): # get strain name from ped file in order def get_samples_from_ped_file(dataset): - ped_file= open("{}{}.ped".format(flat_files('mapping'), dataset.group.name), "r") + ped_file= open(f"{flat_files('mapping')}{dataset.group.name}.ped","r") line = ped_file.readline() sample_list=[] @@ -98,7 +98,7 @@ def parse_plink_output(output_filename, species): threshold_p_value = 1 - result_fp = open("%s%s.qassoc"% (TMPDIR, output_filename), "rb") + result_fp = open(f"{TMPDIR}{output_filename}.qassoc","rb") line = result_fp.readline() |