Fixed the mapping figure track that lets you zoom into a smaller range

Fixed the third party mapping figure tracks to refer to the correct chromosome (before it was always 1)

5 files changed, 26 insertions, 10 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index aaea7ec3..6cabadb1 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -166,7 +166,6 @@ class Markers(object):
         for marker in markers:
             if (marker['chr'] != "X") and (marker['chr'] != "Y"):
                 marker['chr'] = int(marker['chr'])
-            print("Mb:", marker['Mb'])
             marker['Mb'] = float(marker['Mb'])
             
         self.markers = markers
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index a6fa5274..37f9351d 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -84,6 +84,8 @@ class MarkerRegression(object):
         self.selected_chr = -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.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 a7b5fad3..56286ee6 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -295,8 +295,11 @@ class MarkerRegression(object):
         self.SNPChecked  = False
         self.draw2X = False
         self.lrsMax = 0
-        self.startMb = -1
-        self.endMb = -1
+        if 'mb_range' in start_vars:
+            self.startMb, self.endMb = [float(x) for x in start_vars['mb_range'].split(',')]
+        else:
+            self.startMb = -1
+            self.endMb = -1
 
         #self.additiveChecked = fd.formdata.getvalue('additiveCheck')
         #self.dominanceChecked = fd.formdata.getvalue('dominanceCheck')
@@ -1597,7 +1600,7 @@ class MarkerRegression(object):
     
                 WEBQTL_COORDS = "%d, %d, %d, %d" % (xBrowse1, paddingTop, xBrowse2, (paddingTop+self.WEBQTL_BAND_HEIGHT))
                 bandWidth = xBrowse2 - xBrowse1
-                WEBQTL_HREF = "javascript:centerIntervalMapOnRange2('%s', %f, %f, document.changeViewForm)" % (currentChromosome, max(0, (calBase-webqtlZoomWidth))/1000000.0, (calBase+webqtlZoomWidth)/1000000.0)
+                WEBQTL_HREF = "javascript:rangeView('%s', %f, %f)" % (self.selectedChr, 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))
@@ -1606,9 +1609,9 @@ class MarkerRegression(object):
     
                 UCSC_COORDS = "%d, %d, %d, %d" %(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.UCSC_BAND_HEIGHT))
                 if self.species == "mouse":
-                    UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=%s/snp/chr%s" % (self._ucscDb, currentChromosome, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases, webqtlConfig.PORTADDR, currentChromosome)
+                    UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=%s/snp/chr%s" % (self._ucscDb, self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases, webqtlConfig.PORTADDR, self.selectedChr)
                 else:
-                    UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d" % (self._ucscDb, currentChromosome, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
+                    UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d" % (self._ucscDb, self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
                 UCSC_TITLE = "Click to view this section of the genome in the UCSC Genome Browser"
                 gifmap.areas.append(HT.Area(shape='rect',coords=UCSC_COORDS,href=UCSC_HREF, title=UCSC_TITLE))
                 canvas.drawRect(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.UCSC_BAND_HEIGHT), edgeColor=self.CLICKABLE_UCSC_REGION_COLOR, fillColor=self.CLICKABLE_UCSC_REGION_COLOR)
@@ -1616,9 +1619,9 @@ class MarkerRegression(object):
     
                 ENSEMBL_COORDS = "%d, %d, %d, %d" %(xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop+self.ENSEMBL_BAND_HEIGHT))
                 if self.species == "mouse":
-                    ENSEMBL_HREF = "http://www.ensembl.org/Mus_musculus/contigview?highlight=&chr=%s&vc_start=%d&vc_end=%d&x=35&y=12" % (currentChromosome, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
+                    ENSEMBL_HREF = "http://www.ensembl.org/Mus_musculus/contigview?highlight=&chr=%s&vc_start=%d&vc_end=%d&x=35&y=12" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
                 else:
-                    ENSEMBL_HREF = "http://www.ensembl.org/Rattus_norvegicus/contigview?chr=%s&start=%d&end=%d" % (currentChromosome, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
+                    ENSEMBL_HREF = "http://www.ensembl.org/Rattus_norvegicus/contigview?chr=%s&start=%d&end=%d" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
                 ENSEMBL_TITLE = "Click to view this section of the genome in the Ensembl Genome Browser"
                 gifmap.areas.append(HT.Area(shape='rect',coords=ENSEMBL_COORDS,href=ENSEMBL_HREF, title=ENSEMBL_TITLE))
                 canvas.drawRect(xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop+self.ENSEMBL_BAND_HEIGHT), edgeColor=self.CLICKABLE_ENSEMBL_REGION_COLOR, fillColor=self.CLICKABLE_ENSEMBL_REGION_COLOR)
@@ -1632,7 +1635,7 @@ class MarkerRegression(object):
             #draw the gray text
             chrFont = pid.Font(ttf="verdana", size=26*zoom, bold=1)
             traitFont = pid.Font(ttf="verdana", size=14, bold=0)
-            chrX = xLeftOffset + plotWidth - 2 - canvas.stringWidth("Chr %s" % currentChromosome, font=chrFont)
+            chrX = xLeftOffset + plotWidth - 2 - canvas.stringWidth("Chr %s" % self.selectedChr, font=chrFont)
             canvas.drawString("Chr %s" % currentChromosome, chrX, ensemblPaddingTop-5, font=chrFont, color=pid.gray)
             traitX = chrX - 28 - canvas.stringWidth("database", font=traitFont)
             # end of drawBrowserClickableRegions
@@ -2752,7 +2755,8 @@ class MarkerRegression(object):
                     geneSymbolNCBI = theGO["GeneSymbol"]
 
                 geneLength = (float(theGO["TxEnd"]) - float(theGO["TxStart"]))
-                geneLengthURL = "javascript:centerIntervalMapOnRange2('%s', %f, %f, document.changeViewForm)" % (theGO["Chromosome"], float(theGO["TxStart"])-(geneLength*0.1), float(theGO["TxEnd"])+(geneLength*0.1))
+                #geneLengthURL = "javascript:centerIntervalMapOnRange2('%s', %f, %f, document.changeViewForm)" % (theGO["Chromosome"], float(theGO["TxStart"])-(geneLength*0.1), float(theGO["TxEnd"])+(geneLength*0.1))
+                geneLengthURL = "javascript:rangeView('%s', %f, %f)" % (theGO["Chromosome"], float(theGO["TxStart"])-(geneLength*0.1), float(theGO["TxEnd"])+(geneLength*0.1))
 
                 avgExprVal = []
                 if avgExprVal != "" and avgExprVal:
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index 9f7dd41f..dd8ae236 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="maf">
         <input type="hidden" name="method" value="{{ mapping_method }}">
         <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 }}">
@@ -145,6 +146,15 @@
             return $('#marker_regression_form').submit();
         };
 
+        rangeView = function(this_chr, start_mb, end_mb) {
+            $('input[name=selected_chr]').val(this_chr)
+            $('input[name=mb_range]').val(start_mb + "," + end_mb)
+            
+            console.log("mb_range:", $('input[name=mb_range]').val())
+            
+            return $('#marker_regression_form').submit();
+        };
+
     </script>
 
 {% endblock %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index b42e0d4c..65b6dae4 100755
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -352,6 +352,7 @@ def marker_regression_page():
         'control_marker_db',
         'do_control',
         'pair_scan',
+        'mb_range',
         'mapmethod_rqtl_geno',
         'mapmodel_rqtl_geno'
     )