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authorzsloan2017-11-17 17:02:34 +0000
committerzsloan2017-11-17 17:02:34 +0000
commitf27d2609fa8514d01a91500bf010894f746abeac (patch)
tree4f2e4e90a757a5e229081b8b80503ff125715cc5
parente3b27c18f379e969c06f8e0b79daf8b762d4fc1d (diff)
downloadgenenetwork2-f27d2609fa8514d01a91500bf010894f746abeac.tar.gz
Fixed issue that caused GEMMA LOCO to not work on production
-rw-r--r--wqflask/wqflask/marker_regression/gemma_mapping.py12
1 files changed, 8 insertions, 4 deletions
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index bfcf0ffb..a24e43d4 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -49,17 +49,19 @@ def run_gemma(this_dataset, samples, vals, covariates, method, use_loco):
else:
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 > /home/zas1024/tmp/gn2/%s.json' % (flat_files('genotype/bimbam'),
+ 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'),
genofile_name,
flat_files('genotype/bimbam'),
genofile_name,
flat_files('genotype/bimbam'),
genofile_name,
+ TEMPDIR,
k_output_filename)
logger.debug("k_command:" + generate_k_command)
os.system(generate_k_command)
- gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --loco --input /home/zas1024/tmp/gn2/%s.json -- -g %s/%s_geno.txt -p %s/%s_pheno.txt' % (k_output_filename,
+ gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --loco --input %s/gn2/%s.json -- -g %s/%s_geno.txt -p %s/%s_pheno.txt' % (TEMPDIR,
+ k_output_filename,
flat_files('genotype/bimbam'),
genofile_name,
flat_files('genotype/bimbam'),
@@ -67,14 +69,16 @@ def run_gemma(this_dataset, samples, vals, covariates, method, 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 1 -maf 0.1 -debug > /home/zas1024/tmp/gn2/%s.json' % (flat_files('mapping'),
+ gemma_command += ' -c %s/%s_covariates.txt -a %s/%s_snps.txt -lmm 1 -maf 0.1 -debug > %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 1 -maf 0.1 -debug > /home/zas1024/tmp/gn2/%s.json' % (flat_files('genotype/bimbam'),
+ gemma_command += ' -a %s/%s_snps.txt -lmm 1 -maf 0.1 -debug > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
genofile_name,
+ TEMPDIR,
gwa_output_filename)
else: