From ff20eff6ad7e86f890f7de7fb3779e313d9b66ee Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 1 May 2018 19:59:57 +0000
Subject: Removed all code related to using GEMMA with PLINK input files

---
 wqflask/wqflask/marker_regression/gemma_mapping.py | 144 ++++++++-------------
 .../wqflask/marker_regression/marker_regression.py |   6 +-
 .../new/javascript/show_trait_mapping_tools.js     |  32 -----
 .../templates/show_trait_mapping_tools.html        | 107 +--------------
 4 files changed, 64 insertions(+), 225 deletions(-)

diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 5242ec05..dc13afc3 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -8,7 +8,7 @@ from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMP
 import utility.logger
 logger = utility.logger.getLogger(__name__ )
 
-def run_gemma(this_dataset, samples, vals, covariates, method, use_loco):
+def run_gemma(this_dataset, samples, vals, covariates, use_loco):
     """Generates p-values for each marker using GEMMA"""
 
     if this_dataset.group.genofile != None:
@@ -16,7 +16,7 @@ def run_gemma(this_dataset, samples, vals, covariates, method, use_loco):
     else:
         genofile_name = this_dataset.group.name
 
-    gen_pheno_txt_file(this_dataset, genofile_name, vals, method)
+    gen_pheno_txt_file(this_dataset, genofile_name, vals)
 
     if not os.path.isfile("{}{}_output.assoc.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, genofile_name)):
         open("{}{}_output.assoc.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, genofile_name), "w+")
@@ -32,73 +32,58 @@ def run_gemma(this_dataset, samples, vals, covariates, method, use_loco):
     if covariates != "":
         gen_covariates_file(this_dataset, covariates)
 
-    if method == "gemma_plink":
-        gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.cXX.txt -lmm 2 -maf 0.1' % (flat_files('mapping'),
-                                                                                        this_dataset.group.name,
-                                                                                        flat_files('mapping'),
-                                                                                        this_dataset.group.name)
+    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'),
+                                                                                        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 %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'),
+                                                                                        genofile_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 -outdir %s -o %s_output' % (flat_files('mapping'),
-                                                                                   this_dataset.group.name,
-                                                                                   webqtlConfig.GENERATED_IMAGE_DIR,
-                                                                                   this_dataset.group.name)
+            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'),
+                                                                                                                                     this_dataset.group.name,
+                                                                                                                                     flat_files('genotype/bimbam'),
+                                                                                                                                     genofile_name,
+                                                                                                                                     TEMPDIR,
+                                                                                                                                     gwa_output_filename)
         else:
-            #gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.sXX.txt -lmm 2 -maf 0.1 -o %s_output' % (flat_files('mapping'),
-            gemma_command += ' -outdir %s -o %s_output' % (webqtlConfig.GENERATED_IMAGE_DIR,
-                                                           this_dataset.group.name)
+            gemma_command += ' -a %s/%s_snps.txt -lmm 2 -maf 0.1 -debug > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
+                                                                                                             genofile_name,
+                                                                                                             TEMPDIR,
+                                                                                                             gwa_output_filename)
+
     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 > %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 %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'),
-                                                                                            genofile_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 2 -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 2 -maf 0.1 -debug > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
-                                                                                                                 genofile_name,
-                                                                                                                 TEMPDIR,
-                                                                                                                 gwa_output_filename)
+        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'),
+                                                                                        genofile_name,
+                                                                                        flat_files('genotype/bimbam'),
+                                                                                        genofile_name,
+                                                                                        flat_files('genotype/bimbam'),
+                                                                                        genofile_name,
+                                                                                        flat_files('genotype/bimbam'),
+                                                                                        genofile_name)
 
+        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,
+                                                                                                         genofile_name)
         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'),
-                                                                                            genofile_name,
-                                                                                            flat_files('genotype/bimbam'),
-                                                                                            genofile_name,
-                                                                                            flat_files('genotype/bimbam'),
-                                                                                            genofile_name,
-                                                                                            flat_files('genotype/bimbam'),
-                                                                                            genofile_name)
-
-            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,
-                                                                                                             genofile_name)
-            else:
-                gemma_command += ' -outdir %s -debug -o %s_output' % (webqtlConfig.GENERATED_IMAGE_DIR,
-                                                                      genofile_name)
+            gemma_command += ' -outdir %s -debug -o %s_output' % (webqtlConfig.GENERATED_IMAGE_DIR,
+                                                                  genofile_name)
 
     logger.debug("gemma_command:" + gemma_command)
     os.system(gemma_command)
@@ -110,31 +95,16 @@ def run_gemma(this_dataset, samples, vals, covariates, method, use_loco):
 
     return marker_obs
 
-def gen_pheno_txt_file(this_dataset, genofile_name, vals, method):
+def gen_pheno_txt_file(this_dataset, genofile_name, vals):
     """Generates phenotype file for GEMMA"""
 
-    if method == "gemma_plink":
-        current_file_data = []
-        with open("{}/{}.fam".format(flat_files('mapping'), this_dataset.group.name), "r") as outfile:
-            for i, line in enumerate(outfile):
-                split_line = line.split()
-                current_file_data.append(split_line)
-
-        with open("{}/{}.fam".format(flat_files('mapping'), this_dataset.group.name), "w") as outfile:
-            for i, line in enumerate(current_file_data):
-                if vals[i] == "x":
-                    this_val = -9
-                else:
-                    this_val = vals[i]
-                outfile.write("0" + " " + line[1] + " " + line[2] + " " + line[3] + " " + line[4] + " " + str(this_val) + "\n")
-    else:
-        current_file_data = []
-        with open("{}/{}_pheno.txt".format(flat_files('genotype/bimbam'), genofile_name), "w") as outfile:
-            for value in vals:
-                if value == "x":
-                    outfile.write("NA\n")
-                else:
-                    outfile.write(value + "\n")
+    current_file_data = []
+    with open("{}/{}_pheno.txt".format(flat_files('genotype/bimbam'), genofile_name), "w") as outfile:
+        for value in vals:
+            if value == "x":
+                outfile.write("NA\n")
+            else:
+                outfile.write(value + "\n")
 
 def gen_covariates_file(this_dataset, covariates):
     covariate_list = covariates.split(",")
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index a3631462..033fa2a4 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -174,11 +174,11 @@ class MarkerRegression(object):
             self.genofile_string = start_vars['genofile']
             self.dataset.group.genofile = self.genofile_string.split(":")[0]
         self.dataset.group.get_markers()
-        if self.mapping_method == "gemma" or self.mapping_method == "gemma_bimbam":
+        if self.mapping_method == "gemma":
             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, self.use_loco)
+                marker_obs = gemma_mapping.run_gemma(self.dataset, self.samples, self.vals, self.covariates, self.use_loco)
             results = marker_obs
         elif self.mapping_method == "rqtl_plink":
             results = self.run_rqtl_plink()
@@ -289,7 +289,7 @@ class MarkerRegression(object):
                 export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path, self.mapping_scale, self.score_type)
 
             with Bench("Trimming Markers for Figure"):
-                if len(self.qtl_results) > 20000:
+                if len(self.qtl_results) > 30000:
                     self.qtl_results = trim_markers_for_figure(self.qtl_results)
 
             with Bench("Trimming Markers for Table"):
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index 4d98f5d8..81123de7 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -208,41 +208,10 @@
     };
   })(this));
 
-  $("#plink_compute").on("click", (function(_this) {
-    return function() {
-      var form_data, url;
-      //$("#static_progress_bar_container").modal();
-      url = "/loading";
-      $('input[name=method]').val("plink");
-      $('input[name=maf]').val($('input[name=maf_plink]').val());
-      form_data = $('#trait_data_form').serialize();
-      console.log("form_data is:", form_data);
-      return submit_special(url);
-      //return do_ajax_post(url, form_data);
-    };
-  })(this));
-
   $("#gemma_compute").on("click", (function(_this) {
     return function() {
       var form_data, url;
       console.log("RUNNING GEMMA");
-      //$("#static_progress_bar_container").modal();
-      url = "/loading";
-      $('input[name=method]').val("gemma");
-      $('input[name=genofile]').val($('#genofile_gemma').val());
-      $('input[name=maf]').val($('input[name=maf_gemma]').val());
-      form_data = $('#trait_data_form').serialize();
-      console.log("form_data is:", form_data);
-      return submit_special(url);
-      //return do_ajax_post(url, form_data);
-    };
-  })(this));
-
-  $("#gemma_bimbam_compute").on("click", (function(_this) {
-    return function() {
-      var form_data, url;
-      console.log("RUNNING GEMMA");
-      //$("#static_progress_bar_container").modal();
       url = "/loading";
       $('input[name=method]').val("gemma_bimbam");
       $('input[name=num_perm]').val(0);
@@ -251,7 +220,6 @@
       form_data = $('#trait_data_form').serialize();
       console.log("form_data is:", form_data);
       return submit_special(url);
-      //return do_ajax_post(url, form_data);
     };
   })(this));
 
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index d40a7bd6..3d31797a 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -35,7 +35,6 @@
             </ul>
 
             <div class="tab-content">
-                {% if dataset.group.mapping_id == "1" %}
                 <div class="tab-pane active" id="gemma">
                     <div style="padding-top: 20px;" class="form-horizontal">
                         {% if genofiles and genofiles|length>0 %}
@@ -88,13 +87,14 @@
                         <div class="mapping_method_fields form-group">
                           <label class="col-xs-3 control-label"></label>
                           <div style="margin-left:20px;" class="col-xs-6">
-                            <button id="gemma_bimbam_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
+                            <button id="gemma_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
                                 Compute
                             </button>
                           </div>
                         </div>
                     </div>
                 </div>
+                {% if dataset.group.mapping_id == "1" %}
                 <div class="tab-pane" id="interval_mapping">
                     <div style="margin-top: 20px" class="form-horizontal">
                         {% if genofiles and genofiles|length>0 %}
@@ -164,8 +164,6 @@
                             </div>
                         </div>
 -->
-
-
                         <div class="mapping_method_fields form-group">
                             <label style="text-align: right;" class="col-xs-3 control-label">Marker<br>Regression</label>
                             <div style="margin-left:20px;" class="col-xs-6 controls">
@@ -187,11 +185,9 @@
                               </button>
                             </div>
                         </div>
-                        <!--<div id="alert_placeholder"></div>-->
                     </div>
                 </div>
                 <div class="tab-pane" id="rqtl_geno">
-
                     <div style="margin-top: 20px" class="form-horizontal">
                         {% if genofiles and genofiles|length>0 %}
                         <div class="mapping_method_fields form-group">
@@ -320,117 +316,22 @@
                     </div>
                 </div>
                 {% endif %}
-                {% for mapping_method in dataset.group.mapping_names %}
-                {% if mapping_method == "GEMMA" %}
-                <div class="tab-pane active" id="gemma_plink">
-                    <div style="padding-top: 10px;" class="form-horizontal">
-                        {% if genofiles and genofiles|length>0 %}
-                        <div class="mapping_method_fields form-group">
-                            <label style="text-align:right;" class="col-xs-3 control-label">Genotypes</label>
-                            <div style="margin-left: 20px;" class="col-xs-4 controls">
-                                <select id="genofile_gemma" class="form-control">
-                                    {% for item in genofiles %}
-                                    <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
-                                    {% endfor %}
-                                </select>
-                            </div>
-                        </div>
-                        {% endif %}
-                        <div class="mapping_method_fields form-group">
-                            <label style="text-align:right;" class="col-xs-3 control-label">MAF</label>
-                            <div style="margin-left: 20px;" class="col-xs-4 controls">
-                                <input name="maf_gemma" value="0.01" type="text" class="form-control">
-                            </div>
-                        </div>
-                        <div class="mapping_method_fields form-group">
-                            <label style="text-align: right;" class="col-xs-3 control-label">Use LOCO</label>
-                            <div style="margin-left:20px;" class="col-xs-6 controls">
-                                <label class="radio-inline">
-                                    <input type="radio" name="use_loco" value="True" checked="">
-                                    Yes
-                                </label>
-                                <label class="radio-inline">
-                                    <input type="radio" name="use_loco" value="False">
-                                    No
-                               </label>
-                            </div>
-                        </div>
-                        <div class="mapping_method_fields form-group">
-                            <label style="text-align: right;" class="col-xs-3 control-label">Covariates</label>
-                            <div style="margin-left:20px;" class="col-xs-7">
-                              {% if g.user_session.user_ob and (g.user_session.user_ob.display_num_collections() == "") %}
-                              No collections available. Please add traits to a collection to use them as covariates.
-                              {% elif g.cookie_session.display_num_collections() == "" %}
-                              No collections available. Please add traits to a collection to use them as covariates.
-                              {% else %}
-                              <div style="margin-bottom: 10px;" class="btn-group" role="group">
-                                <button type="button" id="select_covariates" class="btn btn-default">Select</button>
-                                <button type="button" id="remove_covariates" class="btn btn-default">Remove</button>
-                              </div>
-                              <textarea rows="3" cols="20" readonly placeholder="No covariates selected" style="overflow-y: scroll; resize: none;" class="selected_covariates"></textarea>
-                              {% endif %}
-                            </div>
-                        </div>
-                        <div class="mapping_method_fields form-group">
-                          <label class="col-xs-3 control-label"></label>
-                          <div style="margin-left:20px;" class="col-xs-6">
-                            <button id="gemma_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
-                                Compute
-                            </button>
-                          </div>
-                        </div>
-                    </div>
-                </div>
-                {% elif mapping_method == "PLINK" %}
-                <div class="tab-pane" id="plink">
-                    <div style="padding: 20px" class="form-horizontal">
-                        <div class="mapping_method_fields form-group">
-                            <label style="text-align: right;" class="col-xs-3 control-label">MAF</label>
-                            <div style="margin-left: 20px;" class="col-xs-4 controls">
-                                <input name="maf_plink" value="0.01" type="text" class="form-control">
-                            </div>
-                        </div>
-                    </div>
-
-                    <div class="form-group">
-                        <label style="text-align: right;" class="col-xs-3 control-label"></label>
-                        <div style="margin-left:20px;" class="col-xs-6 controls">
-                            <button id="plink_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
-                                Compute
-                            </button>
-                        </div>
-                    </div>
-                </div>
-                {% endif %}
-                {% endfor %}
             </div>
         </div>
     </div>
     <div class="col-xs-5">
-        {% if dataset.group.mapping_id == "1" %}
         <dl>
              <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).</dd>
+             {% if dataset.group.mapping_id == "1" %}
              <dt>Interval Mapping</dt>
              <dd>Interval mapping is a process in which the statistical significance of a hypothetical QTL is evaluated at regular points across a chromosome, even in the absence of explicit genotype data at those points.</dd>
              <dt>R/qtl</dt>
              <dd>R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTL) in experimental crosses.</dd>
              <dt>pyLMM</dt>
              <dd>pyLMM is a fast and lightweight linear mixed-model (LMM) solver for use in genome-wide association studies (GWAS).</dd>
+             {% endif %}
         </dl>
-        {% else %}
-        <dl>
-            {% if mapping_method == "GEMMA" %}
-            <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>
-            </dd>
-            {% elif mapping_method == "PLINK" %}
-            <dt>PLINK</dt>
-            <dd>PLINK is a free, open-source whole genome association analysis toolset.</dd>
-            {% endif %}
-        </dl>
-        {% endif %}
     </div>
     <div id="mapping_result_holder_wrapper" style="display:none;">
         <div id="mapping_result_holder"></div>
-- 
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