diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression.py | 12 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression_gn1.py | 16 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/marker_regression_gn1.html | 22 | ||||
| -rw-r--r-- | 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: </b></td> @@ -51,13 +50,19 @@ <option value="{{ chr[1] }}">{{ chr[0] }}</option> {% endfor %} </select> - <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: </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: </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', |