diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/qtlreaper_mapping.py | 46 |
1 files changed, 28 insertions, 18 deletions
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py index 78b1f7b0..505ae295 100644 --- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py +++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py @@ -17,22 +17,29 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo else: genofile_name = this_dataset.group.name - trait_filename = str(this_trait.name) + "_" + str(this_dataset.name) + "_pheno" + trait_filename =f"{str(this_trait.name)}_{str(this_dataset.name)}_pheno" gen_pheno_txt_file(samples, vals, trait_filename) - output_filename = this_dataset.group.name + "_GWA_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + output_filename = (f"{this_dataset.group.name}_GWA_"+ + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + ) bootstrap_filename = None permu_filename = None opt_list = [] if boot_check and num_bootstrap > 0: - bootstrap_filename = this_dataset.group.name + "_BOOTSTRAP_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + bootstrap_filename = (f"{this_dataset.group.name}_BOOTSTRAP_" + + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + ) opt_list.append("-b") - opt_list.append("--n_bootstrap " + str(num_bootstrap)) - opt_list.append("--bootstrap_output " + webqtlConfig.GENERATED_IMAGE_DIR + bootstrap_filename + ".txt") + opt_list.append(f"--n_bootstrap{str(num_bootstrap)}") + opt_list.append(f"--bootstrap_output{webqtlConfig.GENERATED_IMAGE_DIR}{bootstrap_filename}.txt") if num_perm > 0: - permu_filename = this_dataset.group.name + "_PERM_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + permu_filename =("{this_dataset.group.name}_PERM_" + + ''.join(random.choice(string.ascii_uppercase + + string.digits) for _ in range(6)) + ) opt_list.append("-n " + str(num_perm)) opt_list.append("--permu_output " + webqtlConfig.GENERATED_IMAGE_DIR + permu_filename + ".txt") if control_marker != "" and do_control == "true": @@ -40,13 +47,15 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo if manhattan_plot != True: opt_list.append("--interval 1") - reaper_command = REAPER_COMMAND + ' --geno {0}/{1}.geno --traits {2}/gn2/{3}.txt {4} -o {5}{6}.txt'.format(flat_files('genotype'), - genofile_name, - TEMPDIR, - trait_filename, - " ".join(opt_list), - webqtlConfig.GENERATED_IMAGE_DIR, - output_filename) + reaper_command = (REAPER_COMMAND + + ' --geno {0}/{1}.geno --traits {2}/gn2/{3}.txt {4} -o {5}{6}.txt'.format(flat_files('genotype'), + + genofile_name, + TEMPDIR, + trait_filename, + " ".join(opt_list), + webqtlConfig.GENERATED_IMAGE_DIR, + output_filename)) logger.debug("reaper_command:" + reaper_command) os.system(reaper_command) @@ -61,12 +70,13 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo suggestive = permu_vals[int(num_perm*0.37-1)] significant = permu_vals[int(num_perm*0.95-1)] - return marker_obs, permu_vals, suggestive, significant, bootstrap_vals, [output_filename, permu_filename, bootstrap_filename] + return (marker_obs, permu_vals, suggestive, significant, bootstrap_vals, + [output_filename, permu_filename, bootstrap_filename]) def gen_pheno_txt_file(samples, vals, trait_filename): """Generates phenotype file for GEMMA""" - with open("{}/gn2/{}.txt".format(TEMPDIR, trait_filename), "w") as outfile: + with open(f"{TEMPDIR}/gn2/{trait_filename}.txt","w") as outfile: outfile.write("Trait\t") filtered_sample_list = [] @@ -90,7 +100,7 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename): only_cm = False only_mb = False - with open("{}{}.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, gwa_filename)) as output_file: + with open(f"{webqtlConfig.GENERATED_IMAGE_DIR}{gwa_filename}.txt") as output_file: for line in output_file: if line.startswith("ID\t"): if len(line.split("\t")) < 8: @@ -137,13 +147,13 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename): permu_vals = [] if permu_filename: - with open("{}{}.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, permu_filename)) as permu_file: + with open(f"{webqtlConfig.GENERATED_IMAGE_DIR}{permu_filename}.txt") as permu_file: for line in permu_file: permu_vals.append(float(line)) bootstrap_vals = [] if bootstrap_filename: - with open("{}{}.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, bootstrap_filename)) as bootstrap_file: + with open(f"{webqtlConfig.GENERATED_IMAGE_DIR}{bootstrap_filename}.txt") as bootstrap_file: for line in bootstrap_file: bootstrap_vals.append(int(line)) |