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

8 files changed, 64 insertions, 1 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 04436a2e..06e02b02 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -279,6 +279,7 @@ class DatasetGroup(object):
         self.incparentsf1 = False
         self.allsamples = None
         self._datasets = None
+        self.genofile = None
 
     def get_accession_id(self):
         results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where
@@ -423,7 +424,10 @@ class DatasetGroup(object):
         genotype_1 = reaper.Dataset()
 
         # reaper barfs on unicode filenames, so here we ensure it's a string
-        full_filename = str(locate(self.name+'.geno','genotype'))
+        if self.genofile:
+            full_filename = str(locate(self.genofile, 'genotype'))
+        else:
+            full_filename = str(locate(self.name + '.geno', 'genotype'))
         genotype_1.read(full_filename)
 
         if genotype_1.type == "group" and self.parlist:
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index fef0d8a0..d9dbd0da 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -165,6 +165,7 @@ class MarkerRegression(object):
             self.mapping_scale = "morgan"
             self.control_marker = start_vars['control_marker']
             self.do_control = start_vars['do_control']
+            self.dataset.group.genofile = start_vars['genofile']
             self.method = start_vars['mapmethod_rqtl_geno']
             self.model = start_vars['mapmodel_rqtl_geno']
             if start_vars['pair_scan'] == "true":
@@ -200,6 +201,7 @@ class MarkerRegression(object):
 
             self.control_marker = start_vars['control_marker']
             self.do_control = start_vars['do_control']
+            self.dataset.group.genofile = start_vars['genofile']
             logger.info("Running qtlreaper")
             results, self.json_data, self.perm_output, self.suggestive, self.significant, self.bootstrap_results = qtlreaper_mapping.gen_reaper_results(self.this_trait,
                                                                                                                                                         self.dataset,
@@ -216,6 +218,7 @@ class MarkerRegression(object):
             #results = self.run_plink()
         elif self.mapping_method == "pylmm":
             logger.debug("RUNNING PYLMM")
+            self.dataset.group.genofile = start_vars['genofile']
             if self.num_perm > 0:
                 self.run_permutations(str(temp_uuid))
             results = self.gen_data(str(temp_uuid))
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index d9617c7c..8aff5482 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -4,6 +4,7 @@ import string
 import os
 import cPickle
 import uuid
+import json as json
 #import pyXLWriter as xl
 
 from collections import OrderedDict
@@ -24,6 +25,7 @@ from basicStatistics import BasicStatisticsFunctions
 from pprint import pformat as pf
 
 from utility.tools import flat_files, flat_file_exists
+from utility.tools import get_setting
 
 from utility.logger import getLogger
 logger = getLogger(__name__ )
@@ -175,6 +177,7 @@ class ShowTrait(object):
             else:
                 return False
 
+        self.genofiles = get_genofiles(self.this_trait)
         self.use_plink_gemma = check_plink_gemma()
         self.use_pylmm_rqtl = check_pylmm_rqtl()
 
@@ -1261,6 +1264,15 @@ def get_nearest_marker(this_trait, this_db):
         return result[0][0]
         #return result[0][0], result[1][0]
 
+def get_genofiles(this_trait):
+    jsonfile = "%s/%s.json" % (webqtlConfig.GENODIR, this_trait.dataset.group.name)
+    try:
+        f = open(jsonfile)
+    except:
+        return None
+    jsondata = json.load(f)
+    return jsondata['genofile']
+
 def get_trait_table_width(sample_groups):
     table_width = 35
     if sample_groups[0].se_exists():
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 e9db0a12..e7df9228 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -168,6 +168,7 @@
       //$("#progress_bar_container").modal();
       url = "/marker_regression";
       $('input[name=method]').val("pylmm");
+      $('input[name=genofile').val($('#genofile_pylmm').val());
       $('input[name=num_perm]').val($('input[name=num_perm_pylmm]').val());
       $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_pylmm]:checked').val());
       form_data = $('#trait_data_form').serialize();
@@ -183,6 +184,7 @@
       //$("#progress_bar_container").modal();
       url = "/marker_regression";
       $('input[name=method]').val("rqtl_geno");
+      $('input[name=genofile').val($('#genofile_rqtl_geno').val());
       $('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val());
       $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_rqtl]:checked').val());
       $('input[name=control_marker]').val($('input[name=control_rqtl_geno]').val());
@@ -242,6 +244,7 @@
       //$("#progress_bar_container").modal();
       url = "/marker_regression";
       $('input[name=method]').val("reaper");
+      $('input[name=genofile').val($('#genofile_reaper').val());
       $('input[name=num_perm]').val($('input[name=num_perm_reaper]').val());
       $('input[name=control_marker]').val($('input[name=control_reaper]').val());
       $('input[name=do_control]').val($('input[name=do_control_reaper]:checked').val());
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index 7454b650..c6112edb 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -14,6 +14,9 @@
         <input type="hidden" name="temp_uuid" value="{{ temp_uuid }}">
         <input type="hidden" name="trait_id" value="{{ this_trait.name }}">
         <input type="hidden" name="dataset" value="{{ dataset.name }}">
+        {% if mapping_method == "reaper" %}
+        <input type="hidden" name="genofile" value="{{ dataset.group.genofile }}">
+        {% endif %}
         <input type="hidden" name="method" value="{{ mapping_method }}">
         {% for sample in samples %}
         <input type="hidden" name="value:{{ sample }}" value="{{ vals[loop.index - 1] }}">
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 59e0185e..d76e8af8 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -39,6 +39,7 @@
         </div>
 
         <input type="hidden" name="temp_uuid" id="temp_uuid" value="{{ temp_uuid }}">
+        <input type="hidden" name="genofile" value="">
 
         <div class="container">
             <div class="panel-group" id="accordion">
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 0f293942..149ad864 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -32,6 +32,18 @@
                 {% if use_pylmm_rqtl and not use_plink_gemma and dataset.group.species != "human" %}
                 <div class="tab-pane active" id="interval_mapping">
                     <div style="margin-top: 20px" class="form-horizontal">
+                        {% if genofiles and genofiles|length>0 %}
+                        <div class="mapping_method_fields form-group">
+                            <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
+                            <div style="margin-left: 20px;" class="col-xs-8 controls">
+                                <select id="genofile_reaper" class="form-control">
+                                    {% for item in genofiles %}
+                                    <option value="{{item['location']}}">{{item['title']}}</option>
+                                    {% endfor %}
+                                </select>
+                            </div>
+                        </div>
+                        {% endif %}
                         <div class="mapping_method_fields form-group">
                             <label for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
                             <div style="margin-left: 20px;" class="col-xs-4 controls">
@@ -114,6 +126,18 @@
                 </div>
                 <div class="tab-pane" id="pylmm">
                     <div style="margin-top: 20px" class="form-horizontal">
+                        {% if genofiles and genofiles|length>0 %}
+                        <div class="mapping_method_fields form-group">
+                            <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
+                            <div style="margin-left: 20px;" class="col-xs-8 controls">
+                                <select id="genofile_pylmm" class="form-control">
+                                    {% for item in genofiles %}
+                                    <option value="{{item['location']}}">{{item['title']}}</option>
+                                    {% endfor %}
+                                </select>
+                            </div>
+                        </div>
+                        {% endif %}
                         <div class="mapping_method_fields form-group">
                             <label for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
                             <div style="margin-left: 20px;" class="col-xs-4 controls">
@@ -169,6 +193,18 @@
                 <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">
+                            <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
+                            <div style="margin-left: 20px;" class="col-xs-8 controls">
+                                <select id="genofile_rqtl_geno" class="form-control">
+                                    {% for item in genofiles %}
+                                    <option value="{{item['location']}}">{{item['title']}}</option>
+                                    {% endfor %}
+                                </select>
+                            </div>
+                        </div>
+                        {% endif %}
                         <div class="mapping_method_fields form-group">
                             <label for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
                             <div style="margin-left: 20px;" class="col-xs-4 controls">
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index ec5035ce..4f6725b3 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -468,6 +468,7 @@ def marker_regression_page():
         'control_marker',
         'control_marker_db',
         'do_control',
+        'genofile',
         'pair_scan',
         'startMb',
         'endMb',