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-rw-r--r--wqflask/wqflask/marker_regression/marker_regression.py12
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression_gn1.py16
-rw-r--r--wqflask/wqflask/templates/marker_regression_gn1.html22
-rw-r--r--wqflask/wqflask/views.py1
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',