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-rw-r--r--wqflask/wqflask/marker_regression/gemma_mapping.py81
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression.py3
-rw-r--r--wqflask/wqflask/templates/show_trait_mapping_tools.html16
-rw-r--r--wqflask/wqflask/views.py2
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 @@
<input name="maf_gemma" value="0.01" type="text" class="form-control">
</div>
</div>
+ <div class="mapping_method_fields form-group">
+ <label class="col-xs-4 control-label">Use LOCO</label>
+ <div style="margin-left: 20px;" class="col-xs-4 controls">
+ <label class="radio-inline">
+ <input type="radio" name="use_loco" value="True">
+ Yes
+ </label>
+ <label class="radio-inline">
+ <input type="radio" name="use_loco" value="False" checked="">
+ No
+ </label>
+ </div>
+ </div>
</div>
-
<div style="padding-top: 5px; padding-bottom: 5px; padding-left: 20px;" class="form-horizontal">
<div class="mapping_method_fields form-group">
<button type="button" id="select_covariates" class="btn btn-default">
@@ -395,7 +407,7 @@
<dt>GEMMA</dt>
<dd>
GEMMA is software implementing the Genome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model for genome-wide association studies (GWAS).<br>
- <font style="color: red;">Note: There currently exists an issue where GEMMA can't be run on traits from the same group simultaneously. If you recieve an error, please wait a few minutes and try again.</font>
+ Note: There currently exists an issue where GEMMA can't be run on traits from the same group simultaneously. If you receive an error, please wait a few minutes and try again.
</dd>
<dt>PLINK</dt>
<dd>PLINK is a free, open-source whole genome association analysis toolset.</dd>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 2d4fd0f2..f340c954 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -516,6 +516,7 @@ def loading_page():
'LRSCheck',
'covariates',
'maf',
+ 'use_loco',
'manhattan_plot',
'control_marker',
'control_marker_db',
@@ -572,6 +573,7 @@ def marker_regression_page():
'LRSCheck',
'covariates',
'maf',
+ 'use_loco',
'manhattan_plot',
'control_marker',
'control_marker_db',
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 22:23:44 +0000