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| author | zsloan | 2018-09-17 11:15:24 -0500 |
|---|---|---|
| committer | GitHub | 2018-09-17 11:15:24 -0500 |
| commit | b2a7886df64073042a89b466cc103f9bbf06827a (patch) | |
| tree | ba05604bd7908b1ed1123e3e35ac266fa950833b /wqflask | |
| parent | ec45dcbd4b61d51eff27e67d437bcdfad126580f (diff) | |
| parent | 0b88b9afd30a4afec910ae057f8d9dbfddd5c83b (diff) | |
| download | genenetwork2-b2a7886df64073042a89b466cc103f9bbf06827a.tar.gz | |
Merge pull request #342 from pjotrp/gemma-20180915
Gemma optimized for production
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/marker_regression/gemma_mapping.py | 22 |
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 |