From 08849a27af933340fc14decf8dfdd62e3d65b3b3 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 3 Aug 2016 16:35:13 +0000
Subject: Fixed issue with certain sample names (for example BXD48a, BXD72a,
 etc) that caused single chromosome mapping to not work

Disabled bootstrap for mapping unil issue causing wrong results is fixed

Added header to first column of basic statistics table and increased width to avoid rows spilling over to second line
---
 wqflask/wqflask/marker_regression/marker_regression.py     | 4 +++-
 wqflask/wqflask/marker_regression/marker_regression_gn1.py | 5 +++--
 wqflask/wqflask/static/new/javascript/show_trait.js        | 2 +-
 wqflask/wqflask/templates/marker_regression_gn1.html       | 2 +-
 wqflask/wqflask/templates/show_trait_statistics.html       | 2 +-
 5 files changed, 9 insertions(+), 6 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 510b26af..a8324442 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -57,7 +57,9 @@ class MarkerRegression(object):
         self.samples = [] # Want only ones with values
         self.vals = []
 
-        #for sample in self.this_trait.data.keys():
+        all_samples_ordered = self.dataset.group.all_samples_ordered()
+        primary_sample_names = list(all_samples_ordered)
+
         for sample in self.dataset.group.samplelist:
             in_trait_data = False
             for item in self.this_trait.data:
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 9573a9de..d0509c75 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -169,6 +169,7 @@ class MarkerRegression(object):
         self.species = start_vars['species']
 
         #Needing for form submission when doing single chr mapping or remapping after changing options
+        self.samples = start_vars['samples']
         self.vals = start_vars['vals']
         self.mapping_method = start_vars['mapping_method']
         if self.mapping_method == "rqtl_geno":
@@ -801,8 +802,8 @@ class MarkerRegression(object):
         plotXScale = self.drawGraphBackground(canvas, gifmap, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
 
         #draw bootstap
-        if self.bootChecked and not self.multipleInterval:
-            self.drawBootStrapResult(canvas, self.nboot, drawAreaHeight, plotXScale, offset=newoffset)
+        #if self.bootChecked and not self.multipleInterval:
+        #    self.drawBootStrapResult(canvas, self.nboot, drawAreaHeight, plotXScale, offset=newoffset)
 
         # Draw clickable region and gene band if selected
         if self.plotScale == 'physic' and self.selectedChr > -1:
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 419aa7a2..feaaac30 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -173,7 +173,7 @@
     };
     make_table = function() {
       var header, key, row, row_line, table, the_id, the_rows, value, _i, _len, _ref, _ref1;
-      header = "<thead><tr><th>&nbsp;</th>";
+      header = "<thead><tr><th>Statistic</th>";
       _ref = js_data.sample_group_types;
       for (key in _ref) {
         if (!__hasProp.call(_ref, key)) continue;
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index 978ea55f..5389978a 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -15,7 +15,7 @@
         <input type="hidden" name="trait_id" value="{{ this_trait.name }}">
         <input type="hidden" name="dataset" value="{{ dataset.name }}">
         <input type="hidden" name="method" value="{{ mapping_method }}">
-        {% for sample in dataset.group.samplelist %}
+        {% for sample in samples %}
         <input type="hidden" name="value:{{ sample }}" value="{{ vals[loop.index - 1] }}">
         {% endfor %}
         <input type="hidden" name="maf">
diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html
index 3ee8bdea..62d6dcfd 100644
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/wqflask/wqflask/templates/show_trait_statistics.html
@@ -26,7 +26,7 @@
             <div class="tab-content">
                 <div class="tab-pane active" id="stats_tab">
                     <div style="padding: 20px" class="form-horizontal">
-                            <table border="1" id="stats_table" style="width: 300px; float: left;" class="table table-hover table-striped cell-border"></table>
+                            <table border="1" id="stats_table" style="width: 450px; float: left;" class="table table-hover table-striped cell-border"></table>
                     </div>
                 </div>   
                 <div class="tab-pane" id="histogram_tab">
-- 
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