diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/gemma_mapping.py | 3 |
1 files changed, 2 insertions, 1 deletions
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 646728ba..8adca6e5 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -27,6 +27,7 @@ def generate_random_n_string(n): def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf=0.01, first_run=True, output_files=None): """Generates p-values for each marker using GEMMA""" + if this_dataset.group.genofile is not None: genofile_name = this_dataset.group.genofile[:-5] else: @@ -53,7 +54,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, chr_list_string = ",".join(this_chromosomes_name) if covariates != "": covar_filename = gen_covariates_file(this_dataset, covariates, samples) - if use_loco == "True": + if str(use_loco).lower() == "true": generate_k_command = (f"{GEMMA_WRAPPER_COMMAND} --json --loco " f"{chr_list_string} -- {GEMMAOPTS} " f"-g {flat_files('genotype/bimbam')}/" |