diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/gemma_mapping.py | 26 |
1 files changed, 15 insertions, 11 deletions
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 3bf9fdd5..fa7f0beb 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -7,7 +7,7 @@ import json from base import webqtlConfig from base.trait import create_trait from base.data_set import create_dataset -from utility.tools import flat_files +from utility.tools import flat_files, assert_file from utility.tools import GEMMA_WRAPPER_COMMAND from utility.tools import TEMPDIR from utility.tools import WEBSERVER_MODE @@ -55,22 +55,26 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, if covariates != "": covar_filename = gen_covariates_file(this_dataset, covariates, samples) if str(use_loco).lower() == "true": + bimbam_dir = flat_files('genotype/bimbam') + geno_filepath = assert_file( + f"{bimbam_dir}/{genofile_name}_geno.txt") + pheno_filepath = assert_file(f"{TEMPDIR}/gn2/{pheno_filename}.txt") + snps_filepath = assert_file( + f"{bimbam_dir}/{genofile_name}_snps.txt") + k_json_output_filepath = f"{TEMPDIR}/gn2/{k_output_filename}.json" generate_k_command = (f"{GEMMA_WRAPPER_COMMAND} --json --loco " f"{chr_list_string} -- {GEMMAOPTS} " - f"-g {flat_files('genotype/bimbam')}/" - f"{genofile_name}_geno.txt -p " - f"{TEMPDIR}/gn2/{pheno_filename}.txt -a " - f"{flat_files('genotype/bimbam')}/" - f"{genofile_name}_snps.txt -gk > " - f"{TEMPDIR}/gn2/{k_output_filename}.json") + f"-g {geno_filepath} -p " + f"{pheno_filepath} -a " + f"{snps_filepath} -gk > " + f"{k_json_output_filepath}") os.system(generate_k_command) gemma_command = (f"{GEMMA_WRAPPER_COMMAND} --json --loco " - f"--input {TEMPDIR}/gn2/{k_output_filename}.json " + f"--input {k_json_output_filepath} " f"-- {GEMMAOPTS} " - f"-g {flat_files('genotype/bimbam')}/" - f"{genofile_name}_geno.txt " - f"-p {TEMPDIR}/gn2/{pheno_filename}.txt ") + f"-g {geno_filepath} " + f"-p {pheno_filepath} ") if covariates != "": gemma_command += (f"-c {flat_files('mapping')}/" f"{covar_filename}.txt " |