From 1fd25485232b78d13b0fb946c379b55b7e2819e7 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 14 Sep 2017 02:22:46 -0500 Subject: ./bin/genenetwork2: add GEM_PATH for gemma-wrapper --- bin/genenetwork2 | 1 + 1 file changed, 1 insertion(+) diff --git a/bin/genenetwork2 b/bin/genenetwork2 index e07a4e32..5e791885 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -68,6 +68,7 @@ else export PATH=$GN2_PROFILE/bin:$PATH export PYTHONPATH=$GN2_PROFILE/lib/python2.7/site-packages export R_LIBS_SITE=$GN2_PROFILE/site-library + export GEM_PATH=$GN2_PROFILE/lib/ruby/gems/2.4.0 export JS_GUIX_PATH=$GN2_PROFILE/share/genenetwork2/javascript export GUIX_GTK3_PATH="$GN2_PROFILE/lib/gtk-3.0" export GI_TYPELIB_PATH="$GN2_PROFILE/lib/girepository-1.0" -- cgit v1.2.3 From 9016ec7a3e29dbe2275a81337a9cb869366e3416 Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 14 Sep 2017 15:54:46 +0000 Subject: Committing current progress towards implementing LOCO for GEMMA, not done yet --- wqflask/wqflask/marker_regression/gemma_mapping.py | 81 +++++++++++++++++----- .../wqflask/marker_regression/marker_regression.py | 3 +- .../templates/show_trait_mapping_tools.html | 16 ++++- wqflask/wqflask/views.py | 2 + 4 files changed, 81 insertions(+), 21 deletions(-) diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 31e94266..2c99d1fc 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -3,12 +3,12 @@ import os, math from base import webqtlConfig from base.trait import GeneralTrait from base.data_set import create_dataset -from utility.tools import flat_files, GEMMA_COMMAND +from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND import utility.logger logger = utility.logger.getLogger(__name__ ) -def run_gemma(this_dataset, samples, vals, covariates, method): +def run_gemma(this_dataset, samples, vals, covariates, method, use_loco): """Generates p-values for each marker using GEMMA""" print("INSIDE GEMMA_MAPPING") @@ -18,7 +18,13 @@ def run_gemma(this_dataset, samples, vals, covariates, method): if not os.path.isfile("{}{}_output.assoc.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, this_dataset.group.name)): open("{}{}_output.assoc.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, this_dataset.group.name), "w+") - logger.debug("COVARIATES_GEMMA:", covariates) + this_chromosomes = this_dataset.species.chromosomes.chromosomes + chr_list_string = "" + for i in range(this_chromosomes): + if i < (len(this_chromosomes) - 1): + chr_list_string += this_chromosomes[i+1].name + "," + else: + chr_list_string += this_chromosomes[i+1].name if covariates != "": gen_covariates_file(this_dataset, covariates) @@ -35,19 +41,38 @@ def run_gemma(this_dataset, samples, vals, covariates, method): # use GEMMA_RUN in the next one, create a unique temp file else: logger.debug("FLAT FILES:", flat_files('mapping')) - #gemma_command = GEMMA_COMMAND + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -k %s/%s.sXX.txt -lmm 1 -maf 0.1 -c %s/%s_covariates.txt -o %s_output' % (flat_files('genotype/bimbam'), - 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 1 -maf 0.1 -c %s/%s_covariates.txt -outdir %s -debug -o %s_output' % (flat_files('genotype/bimbam'), - this_dataset.group.name, - flat_files('genotype/bimbam'), - this_dataset.group.name, - flat_files('genotype/bimbam'), - this_dataset.group.name, - flat_files('genotype/bimbam'), - this_dataset.group.name, - flat_files('mapping'), - this_dataset.group.name, - webqtlConfig.GENERATED_IMAGE_DIR, - this_dataset.group.name) + if use_loco: + 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/K.json' % (flat_files('genotype/bimbam'), + this_dataset.group.name, + flat_files('genotype/bimbam'), + this_dataset.group.name, + flat_files('genotype/bimbam'), + this_dataset.group.name) + logger.debug("k_command:" + generate_k_command) + os.system(generate_k_command) + + run_loco_command = GEMMA_WRAPPER_COMMAND + ' --json --loco --input /home/zas1024/tmp/gn2/K.json -- -g %s/%s_geno.txt -p %s/%s_pheno.txt -c %s/%s_covariates.txt -a %s/%s_snps.txt -lmm 1 -maf 0.1 -debug > /home/zas1024/tmp/gn2/GWA.json' % (flat_files('genotype/bimbam'), + this_dataset.group.name, + flat_files('genotype/bimbam'), + this_dataset.group.name, + flat_files('mapping'), + this_dataset.group.name, + flat_files('genotype/bimbam'), + this_dataset.group.name) + os.system(run_loco_command) + 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 1 -maf 0.1 -c %s/%s_covariates.txt -outdir %s -debug -o %s_output' % (flat_files('genotype/bimbam'), + this_dataset.group.name, + flat_files('genotype/bimbam'), + this_dataset.group.name, + flat_files('genotype/bimbam'), + this_dataset.group.name, + flat_files('genotype/bimbam'), + this_dataset.group.name, + flat_files('mapping'), + this_dataset.group.name, + webqtlConfig.GENERATED_IMAGE_DIR, + this_dataset.group.name) else: if method == "gemma": #gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.sXX.txt -lmm 1 -maf 0.1 -o %s_output' % (flat_files('mapping'), @@ -58,8 +83,28 @@ def run_gemma(this_dataset, samples, vals, covariates, method): webqtlConfig.GENERATED_IMAGE_DIR, this_dataset.group.name) else: - #gemma_command = GEMMA_COMMAND + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -k %s/%s.sXX.txt -lmm 1 -maf 0.1 -o %s_output' % (flat_files('genotype/bimbam'), - 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 1 -maf 0.1 -outdir %s -debug -o %s_output' % (flat_files('genotype/bimbam'), + if use_loco: + 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/K.json' % (flat_files('genotype/bimbam'), + this_dataset.group.name, + flat_files('genotype/bimbam'), + this_dataset.group.name, + flat_files('genotype/bimbam'), + this_dataset.group.name) + logger.debug("k_command:" + generate_k_command) + os.system(generate_k_command) + + run_loco_command = GEMMA_WRAPPER_COMMAND + ' --json --loco --input /home/zas1024/tmp/gn2/K.json -- -g %s/%s_geno.txt -p %s/%s_pheno.txt -c %s/%s_covariates.txt -a %s/%s_snps.txt -lmm 1 -maf 0.1 -debug > /home/zas1024/tmp/gn2/GWA.json' % (flat_files('genotype/bimbam'), + this_dataset.group.name, + flat_files('genotype/bimbam'), + this_dataset.group.name, + flat_files('mapping'), + this_dataset.group.name, + flat_files('genotype/bimbam'), + this_dataset.group.name) + os.system(run_loco_command) + else: + #gemma_command = GEMMA_COMMAND + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -k %s/%s.sXX.txt -lmm 1 -maf 0.1 -o %s_output' % (flat_files('genotype/bimbam'), + 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 1 -maf 0.1 -outdir %s -debug -o %s_output' % (flat_files('genotype/bimbam'), this_dataset.group.name, flat_files('genotype/bimbam'), this_dataset.group.name, diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 55bbacac..24292c35 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -84,6 +84,7 @@ class MarkerRegression(object): self.manhattan_plot = False self.maf = start_vars['maf'] # Minor allele frequency + self.use_loco = start_vars['use_loco'] self.suggestive = "" self.significant = "" self.pair_scan = False # Initializing this since it is checked in views to determine which template to use @@ -158,7 +159,7 @@ class MarkerRegression(object): self.score_type = "-log(p)" self.manhattan_plot = True with Bench("Running GEMMA"): - marker_obs = gemma_mapping.run_gemma(self.dataset, self.samples, self.vals, self.covariates, self.mapping_method) + marker_obs = gemma_mapping.run_gemma(self.dataset, self.samples, self.vals, self.covariates, self.mapping_method, self.use_loco) results = marker_obs elif self.mapping_method == "rqtl_plink": results = self.run_rqtl_plink() diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index c24a5853..eadc7481 100644 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -302,8 +302,20 @@ +
+ +
+ + +
+
-