From 04d0803abc543df0afc50d7a1bcafe797cb1bf67 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 23 Mar 2016 22:26:27 +0000
Subject: You can now select chromosome and an Mb range from the top menu and
 remap

The track in the single chromosome view to zoom into smaller intervals now works correctly again
---
 .../wqflask/marker_regression/marker_regression.py | 12 ++++++++----
 .../marker_regression/marker_regression_gn1.py     | 16 ++++++++--------
 .../wqflask/templates/marker_regression_gn1.html   | 22 ++++++++++++++++------
 wqflask/wqflask/views.py                           |  1 +
 4 files changed, 33 insertions(+), 18 deletions(-)

diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 7adc0a2e..09dd7852 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -82,11 +82,15 @@ class MarkerRegression(object):
         self.num_perm = 0
 
         #ZS: This is passed to GN1 code for single chr mapping
-        self.selected_chr = -1        
+        self.selected_chr = -1
+        #if "chromosomes" in start_vars:
+        #    self.selected_chr = int(start_vars['chromosomes']) + 1
         if "selected_chr" in start_vars:
-            self.selected_chr = int(start_vars['selected_chr'])
-        if "mb_range" in start_vars:
-            self.mb_range = start_vars['mb_range']
+            self.selected_chr = int(start_vars['selected_chr']) + 1
+        if "startMb" in start_vars:
+            self.startMb = start_vars['startMb']
+        if "endMb" in start_vars:
+            self.endMb = start_vars['endMb']
  
         self.dataset.group.get_markers()
         if self.mapping_method == "gemma":
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 37e67d71..bb8f7b11 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -297,13 +297,13 @@ class MarkerRegression(object):
         self.SNPChecked  = False
         self.draw2X = False
         self.lrsMax = 0
-        if 'startMb' in start_vars:
-            self.startMb = start_vars['startMb']
-        else:
+        try:
+            self.startMb = float(start_vars['startMb'])
+        except:
             self.startMb = -1
-        if 'endMb' in start_vars:
-            self.endMb = start_vars['endMb']
-        else:
+        try:
+            self.endMb = float(start_vars['endMb'])
+        except:
             self.endMb = -1
 
         #self.additiveChecked = fd.formdata.getvalue('additiveCheck')
@@ -487,7 +487,7 @@ class MarkerRegression(object):
             #StartMb or EndMb
             if self.startMb < 0 or self.endMb < 0:
                 self.startMb = 0
-                self.endMb = self.ChrLengthMbList[self.selectedChr]
+                self.endMb = self.ChrLengthMbList[self.selectedChr - 1]
 
         geneTable = ""
 
@@ -1605,7 +1605,7 @@ class MarkerRegression(object):
     
                 WEBQTL_COORDS = "%d, %d, %d, %d" % (xBrowse1, paddingTop, xBrowse2, (paddingTop+self.WEBQTL_BAND_HEIGHT))
                 bandWidth = xBrowse2 - xBrowse1
-                WEBQTL_HREF = "javascript:rangeView('%s', %f, %f)" % (self.selectedChr, max(0, (calBase-webqtlZoomWidth))/1000000.0, (calBase+webqtlZoomWidth)/1000000.0)
+                WEBQTL_HREF = "javascript:rangeView('%s', %f, %f)" % (self.selectedChr - 1, max(0, (calBase-webqtlZoomWidth))/1000000.0, (calBase+webqtlZoomWidth)/1000000.0)
     
                 WEBQTL_TITLE = "Click to view this section of the genome in WebQTL"
                 gifmap.areas.append(HT.Area(shape='rect',coords=WEBQTL_COORDS,href=WEBQTL_HREF, title=WEBQTL_TITLE))
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index 11989ae7..767befd8 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -20,7 +20,6 @@
         {% endfor %}
         <input type="hidden" name="maf">
         <input type="hidden" name="selected_chr" value="{{ selectedChr }}">
-        <input type="hidden" name="mb_range" value="{{ startMb|string + "," + endMb|string }}">
         <input type="hidden" name="manhattan_plot">
         <input type="hidden" name="num_perm">
         <input type="hidden" name="do_control" value="{{ doControl }}">
@@ -41,7 +40,7 @@
               {% endif %}
           </div>
           <div id="gn1_map_options" class="col-xs-5" style="border:2px solid black; padding: 10px; margin: 10px;">
-            <div class="col-xs-7" style="padding-left: 0px;">
+            <div class="col-xs-9" style="padding-left: 0px;">
               <table>
                 <tr>
                   <td><b>Chr:&nbsp;</b></td>
@@ -51,13 +50,19 @@
                         <option value="{{ chr[1] }}">{{ chr[0] }}</option>
                         {% endfor %}
                     </select>&nbsp;
-                    <button type="button" class="btn btn-primary">Remap</button>
+                    <button type="button" class="btn btn-primary" style="padding-bottom: 2px; padding-top: 2px;" onclick="javascript:remap();">Remap</button>
                   </td>
                 </tr>
                 <tr>
                   <td><b>View:&nbsp;</b></td>
                   <td>
-                    <input type="text" name="startMb"
+                    <input type="text" name="startMb" size="10"> to <input type="text" name="endMb" size="10">
+                  </td>
+                </tr>
+                <tr>
+                  <td><b>Width:&nbsp;</b></td>
+                  <td>
+                    <input type="text" name="graphWidth" value="1600" size="5">
                   </td>
                 </tr>
               </table>
@@ -213,10 +218,10 @@
                 $('div#gn1_map_options').show();
             });
 
-            });
+        });
 
         chrView = function(this_chr, chr_mb_list) {
-            $('input[name=selected_chr]').val(this_chr + 1)
+            $('input[name=selected_chr]').val(this_chr)
             $('input[name=chr_mb_list]').val(chr_mb_list)
 
             return $('#marker_regression_form').submit();
@@ -231,6 +236,11 @@
             return $('#marker_regression_form').submit();
         };
 
+        remap = function() { 
+            $('input[name=selected_chr]').val($('select[name=chromosomes]').val());
+            return $('#marker_regression_form').submit(); 
+        };
+
     </script>
 
 {% endblock %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 6f53a950..b5b6fa82 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -343,6 +343,7 @@ def marker_regression_page():
         'method',
         'trimmed_markers',
         'selected_chr',
+        'chromosomes',
         'mapping_scale',
         'score_type',
         'suggestive',
-- 
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