From 63300e26ec4a8dab60cc9a80a6c4204c2c156e22 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 19 Sep 2022 09:07:11 +0300
Subject: Check paths before running gemma command
* Check that the required file paths exist
* Check the bimbam directory path only once
---
wqflask/wqflask/marker_regression/gemma_mapping.py | 26 +++++++++++++---------
1 file 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 "
--
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