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-rw-r--r--wqflask/wqflask/marker_regression/gemma_mapping.py22
1 files changed, 13 insertions, 9 deletions
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 5ebab611..cbd0bae5 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -3,11 +3,15 @@ import os, math, string, random, json
from base import webqtlConfig
from base.trait import GeneralTrait
from base.data_set import create_dataset
-from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR
+from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR, WEBSERVER_MODE
import utility.logger
logger = utility.logger.getLogger(__name__ )
+GEMMAOPTS = "-debug"
+if WEBSERVER_MODE == 'PROD':
+ GEMMAOPTS = "-no-check"
+
def run_gemma(this_dataset, samples, vals, covariates, use_loco):
"""Generates p-values for each marker using GEMMA"""
@@ -34,7 +38,7 @@ def run_gemma(this_dataset, samples, vals, covariates, use_loco):
if use_loco == "True":
k_output_filename = this_dataset.group.name + "_K_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
- generate_k_command = GEMMA_WRAPPER_COMMAND + ' --json --loco ' + chr_list_string + ' -- -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -gk -debug > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
+ generate_k_command = GEMMA_WRAPPER_COMMAND + ' --json --loco ' + chr_list_string + ' -- ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -gk > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
genofile_name,
flat_files('genotype/bimbam'),
genofile_name,
@@ -45,7 +49,7 @@ def run_gemma(this_dataset, samples, vals, covariates, use_loco):
logger.debug("k_command:" + generate_k_command)
os.system(generate_k_command)
- gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --loco --input %s/gn2/%s.json -- -g %s/%s_geno.txt -p %s/%s_pheno.txt' % (TEMPDIR,
+ gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --loco --input %s/gn2/%s.json -- '+GEMMAOPTS+' -g %s/%s_geno.txt -p %s/%s_pheno.txt' % (TEMPDIR,
k_output_filename,
flat_files('genotype/bimbam'),
genofile_name,
@@ -54,20 +58,20 @@ def run_gemma(this_dataset, samples, vals, covariates, use_loco):
gwa_output_filename = this_dataset.group.name + "_GWA_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
if covariates != "":
- gemma_command += ' -c %s/%s_covariates.txt -a %s/%s_snps.txt -lmm 2 -maf 0.1 -debug > %s/gn2/%s.json' % (flat_files('mapping'),
+ gemma_command += ' -c %s/%s_covariates.txt -a %s/%s_snps.txt -lmm 2 -maf 0.1 > %s/gn2/%s.json' % (flat_files('mapping'),
this_dataset.group.name,
flat_files('genotype/bimbam'),
genofile_name,
TEMPDIR,
gwa_output_filename)
else:
- gemma_command += ' -a %s/%s_snps.txt -lmm 2 -maf 0.1 -debug > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
+ gemma_command += ' -a %s/%s_snps.txt -lmm 2 -maf 0.1 > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
genofile_name,
TEMPDIR,
gwa_output_filename)
else:
- gemma_command = GEMMA_COMMAND + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -k %s/%s.cXX.txt -lmm 2 -maf 0.1' % (flat_files('genotype/bimbam'),
+ gemma_command = GEMMA_COMMAND + ' ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -k %s/%s.cXX.txt -lmm 2 -maf 0.1' % (flat_files('genotype/bimbam'),
genofile_name,
flat_files('genotype/bimbam'),
genofile_name,
@@ -77,12 +81,12 @@ def run_gemma(this_dataset, samples, vals, covariates, use_loco):
genofile_name)
if covariates != "":
- gemma_command += ' -c %s/%s_covariates.txt -outdir %s -debug -o %s_output' % (flat_files('mapping'),
+ gemma_command += ' -c %s/%s_covariates.txt -outdir %s -o %s_output' % (flat_files('mapping'),
this_dataset.group.name,
webqtlConfig.GENERATED_IMAGE_DIR,
genofile_name)
else:
- gemma_command += ' -outdir %s -debug -o %s_output' % (webqtlConfig.GENERATED_IMAGE_DIR,
+ gemma_command += ' -outdir %s -o %s_output' % (webqtlConfig.GENERATED_IMAGE_DIR,
genofile_name)
logger.debug("gemma_command:" + gemma_command)
@@ -218,4 +222,4 @@ def parse_loco_output(this_dataset, gwa_output_filename):
included_markers.append(line.split("\t")[1])
p_values.append(float(line.split("\t")[9]))
- return marker_obs \ No newline at end of file
+ return marker_obs