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| author | zsloan | 2017-11-17 17:02:34 +0000 |
|---|---|---|
| committer | zsloan | 2017-11-17 17:02:34 +0000 |
| commit | f27d2609fa8514d01a91500bf010894f746abeac (patch) | |
| tree | 4f2e4e90a757a5e229081b8b80503ff125715cc5 /wqflask | |
| parent | e3b27c18f379e969c06f8e0b79daf8b762d4fc1d (diff) | |
| download | genenetwork2-f27d2609fa8514d01a91500bf010894f746abeac.tar.gz | |
Fixed issue that caused GEMMA LOCO to not work on production
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/marker_regression/gemma_mapping.py | 12 |
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: |