Merge branch 'testing' of https://github.com/genenetwork/genenetwork2

7 files changed, 129 insertions, 39 deletions

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"
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 31e94266..f23c390e 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -1,14 +1,14 @@
-import os, math
+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
+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")
@@ -18,62 +18,88 @@ 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(len(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)
-        if method == "gemma":
-            #gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.sXX.txt -lmm 1 -maf 0.1 -c %s/%s_covariates.txt -o %s_output' % (flat_files('mapping'),
-            gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.cXX.txt -lmm 1 -maf 0.1 -c %s/%s_covariates.txt -outdir %s -o %s_output' % (flat_files('mapping'),
-                                                                                            this_dataset.group.name,
-                                                                                            flat_files('mapping'),
-                                                                                            this_dataset.group.name,
-                                                                                            flat_files('mapping'),
-                                                                                            this_dataset.group.name,
-                                                                                            webqtlConfig.GENERATED_IMAGE_DIR,
-                                                                                            this_dataset.group.name)
-            # use GEMMA_RUN in the next one, create a unique temp file
+
+    if method == "gemma":
+        gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.cXX.txt -lmm 1 -maf 0.1' % (flat_files('mapping'),
+                                                                                        this_dataset.group.name,
+                                                                                        flat_files('mapping'),
+                                                                                        this_dataset.group.name)
+        if covariates != "":
+            gemma_command += ' -c %s/%s_covariates.txt -outdir %s -o %s_output' % (flat_files('mapping'),
+                                                                                   this_dataset.group.name,
+                                                                                   webqtlConfig.GENERATED_IMAGE_DIR,
+                                                                                   this_dataset.group.name)
         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'),
+            #gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.sXX.txt -lmm 1 -maf 0.1 -o %s_output' % (flat_files('mapping'),
+            gemma_command += ' -outdir %s -o %s_output' % (webqtlConfig.GENERATED_IMAGE_DIR,
+                                                           this_dataset.group.name)
+    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'),
                                                                                             this_dataset.group.name,
                                                                                             flat_files('genotype/bimbam'),
                                                                                             this_dataset.group.name,
                                                                                             flat_files('genotype/bimbam'),
                                                                                             this_dataset.group.name,
+                                                                                            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,
                                                                                             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'),
-            gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.cXX.txt -lmm 1 -maf 0.1 -outdir %s -o %s_output' % (flat_files('mapping'),
-                                                                                            this_dataset.group.name,
-                                                                                            flat_files('mapping'),
-                                                                                            this_dataset.group.name,
-                                                                                            webqtlConfig.GENERATED_IMAGE_DIR,
+                                                                                            flat_files('genotype/bimbam'),
                                                                                             this_dataset.group.name)
+
+            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'),
+                                                                                                                                         this_dataset.group.name,
+                                                                                                                                         flat_files('genotype/bimbam'),
+                                                                                                                                         this_dataset.group.name,
+                                                                                                                                         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'),
+                                                                                                                 this_dataset.group.name,
+                                                                                                                 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.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'),
+            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' % (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,
-                                                                                            webqtlConfig.GENERATED_IMAGE_DIR,
                                                                                             this_dataset.group.name)
-    logger.debug("gemma_command:" + gemma_command)
 
+            if covariates != "":
+                gemma_command += ' -c %s/%s_covariates.txt -outdir %s -debug -o %s_output' % (flat_files('mapping'),
+                                                                                                             this_dataset.group.name,
+                                                                                                             webqtlConfig.GENERATED_IMAGE_DIR,
+                                                                                                             this_dataset.group.name)
+            else:
+                gemma_command += ' -outdir %s -debug -o %s_output' % (webqtlConfig.GENERATED_IMAGE_DIR,
+                                                                      this_dataset.group.name)
+
+    logger.debug("gemma_command:" + gemma_command)
     os.system(gemma_command)
 
-    marker_obs = parse_gemma_output(this_dataset)
+    if use_loco == "True":
+        marker_obs = parse_loco_output(this_dataset, gwa_output_filename)
+    else:
+        marker_obs = parse_gemma_output(this_dataset)
 
     return marker_obs
 
@@ -172,3 +198,46 @@ def parse_gemma_output(this_dataset):
                 p_values.append(float(line.split("\t")[10]))
 
     return marker_obs
+
+def parse_loco_output(this_dataset, gwa_output_filename):
+
+    output_filelist = []
+    with open("/home/zas1024/tmp/gn2/" + gwa_output_filename + ".json") as data_file:
+       data = json.load(data_file)
+
+    files = data['files']
+    for file in files:
+        output_filelist.append(file[2])
+
+    included_markers = []
+    p_values = []
+    marker_obs = []
+    previous_chr = 0
+
+    for this_file in output_filelist:
+        #with open("/home/zas1024/gene/wqflask/output/{}_output.assoc.txt".format(this_dataset.group.name)) as output_file:
+        with open(this_file) as output_file:
+            for line in output_file:
+                if line.startswith("chr"):
+                    continue
+                else:
+                    marker = {}
+                    marker['name'] = line.split("\t")[1]
+                    if line.split("\t")[0] != "X" and line.split("\t")[0] != "X/Y":
+                        marker['chr'] = int(line.split("\t")[0])
+                    else:
+                        marker['chr'] = line.split("\t")[0]
+                    marker['Mb'] = float(line.split("\t")[2]) / 1000000
+                    marker['p_value'] = float(line.split("\t")[10])
+                    if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
+                        marker['lod_score'] = 0
+                        #marker['lrs_value'] = 0
+                    else:
+                        marker['lod_score'] = -math.log10(marker['p_value'])
+                        #marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61
+                    marker_obs.append(marker)
+
+                    included_markers.append(line.split("\t")[1])
+                    p_values.append(float(line.split("\t")[10]))
+
+    return marker_obs
\ No newline at end of file
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/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 93d75a03..687cfeb5 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -257,6 +257,10 @@ class MarkerRegression(object):
             self.controlLocus = ""
         if 'covariates' in start_vars.keys():
             self.covariates = start_vars['covariates']
+        if 'maf' in start_vars.keys():
+            self.maf = start_vars['maf']
+        if 'use_loco' in start_vars.keys():
+            self.use_loco = start_vars['use_loco']
 
         #try:
         self.selectedChr = int(start_vars['selected_chr'])
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index c6c6bc23..5c457275 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -20,6 +20,7 @@
         <input type="hidden" name="value:{{ sample }}" value="{{ vals[loop.index - 1] }}">
         {% endfor %}
         <input type="hidden" name="maf">
+        <input type="hidden" name="use_loco" value="{{ use_loco }}">
         <input type="hidden" name="selected_chr" value="{{ selectedChr }}">
         <input type="hidden" name="manhattan_plot" value="{{ manhattan_plot }}">
         <input type="hidden" name="num_perm" value="{{ nperm }}">
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',