diff options
| -rw-r--r-- | wqflask/base/trait.py | 42 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression_gn1.py | 46 | ||||
| -rwxr-xr-x | wqflask/wqflask/search_results.py | 4 | ||||
| -rwxr-xr-x | wqflask/wqflask/show_trait/show_trait.py | 9 | ||||
| -rw-r--r--[-rwxr-xr-x] | wqflask/wqflask/static/new/javascript/show_trait.js | 8 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/marker_regression_gn1.html | 11 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/show_trait.html | 14 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/show_trait_statistics.html | 1 |
8 files changed, 105 insertions, 30 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 0bc10b97..af22b5a1 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -308,6 +308,7 @@ class GeneralTrait(object): if isinstance(trait_info[i], basestring): holder = unicode(trait_info[i], "utf8", "ignore") setattr(self, field, holder) +<<<<<<< HEAD description_string = unicode(str(self.description).strip(codecs.BOM_UTF8), 'utf-8') target_string = unicode(str(self.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8') @@ -345,6 +346,8 @@ class GeneralTrait(object): self.location_repr = 'Chr%s: %.6f' % (self.chr, float(self.mb)) self.location_value = trait_location_value +======= +>>>>>>> e0c5c1aae3aaaa1d81bcec36835a97e169dcc2e2 if self.dataset.type == 'Publish': self.confidential = 0 @@ -379,8 +382,8 @@ class GeneralTrait(object): if self.pubmed_id: self.pubmed_link = webqtlConfig.PUBMEDLINK_URL % self.pubmed_id + self.homologeneid = None - if self.dataset.type == 'ProbeSet' and self.dataset.group and self.geneid: #XZ, 05/26/2010: From time to time, this query get error message because some geneid values in database are not number. #XZ: So I have to test if geneid is number before execute the query. @@ -408,6 +411,43 @@ class GeneralTrait(object): if result: self.homologeneid = result[0] + + description_string = unicode(str(self.description).strip(codecs.BOM_UTF8), 'utf-8') + target_string = unicode(str(self.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8') + + if len(description_string) > 1 and description_string != 'None': + description_display = description_string + else: + description_display = self.symbol + + if (len(description_display) > 1 and description_display != 'N/A' and + len(target_string) > 1 and target_string != 'None'): + description_display = description_display + '; ' + target_string.strip() + + # Save it for the jinja2 template + self.description_display = description_display + + #XZ: trait_location_value is used for sorting + trait_location_repr = 'N/A' + trait_location_value = 1000000 + + if self.chr and self.mb: + #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y") + #This is so we can convert the location to a number used for sorting + trait_location_value = convert_location_to_value(self.chr, self.mb) + #try: + # trait_location_value = int(self.chr)*1000 + self.mb + #except ValueError: + # if self.chr.upper() == 'X': + # trait_location_value = 20*1000 + self.mb + # else: + # trait_location_value = (ord(str(self.chr).upper()[0])*1000 + + # self.mb) + + #ZS: Put this in function currently called "convert_location_to_value" + self.location_repr = 'Chr%s: %.6f' % (self.chr, float(self.mb)) + self.location_value = trait_location_value + if get_qtl_info: #LRS and its location diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py index 63f62411..01303b0f 100644 --- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py +++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py @@ -2007,6 +2007,7 @@ class MarkerRegression(object): previous_chr = 1 previous_chr_as_int = 0 + lineWidth = 1 oldStartPosX = 0 startPosX = xLeftOffset for i, qtlresult in enumerate(self.qtlresults): @@ -2015,6 +2016,41 @@ class MarkerRegression(object): thisLRSColor = self.colorCollection[0] if qtlresult['chr'] != previous_chr and self.selectedChr == -1: + if self.manhattan_plot != True: + canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + + if not self.multipleInterval and self.additiveChecked: + plusColor = self.ADDITIVE_COLOR_POSITIVE + minusColor = self.ADDITIVE_COLOR_NEGATIVE + for k, aPoint in enumerate(AdditiveCoordXY): + if k > 0: + Xc0, Yc0 = AdditiveCoordXY[k-1] + Xc, Yc = aPoint + if (Yc0-yZero)*(Yc-yZero) < 0: + if Xc == Xc0: #genotype , locus distance is 0 + Xcm = Xc + else: + Xcm = (yZero-Yc0)/((Yc-Yc0)/(Xc-Xc0)) +Xc0 + if Yc0 < yZero: + canvas.drawLine(Xc0, Yc0, Xcm, yZero, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + canvas.drawLine(Xcm, yZero, Xc, yZero-(Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + else: + canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xcm, yZero, color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + canvas.drawLine(Xcm, yZero, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + elif (Yc0-yZero)*(Yc-yZero) > 0: + if Yc < yZero: + canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + else: + canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + else: + minYc = min(Yc-yZero, Yc0-yZero) + if minYc < 0: + canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + else: + canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + + LRSCoordXY = [] + AdditiveCoordXY = [] previous_chr = qtlresult['chr'] previous_chr_as_int += 1 @@ -2032,7 +2068,6 @@ class MarkerRegression(object): else: this_chr = str(self.ChrList[self.selectedChr][1]+1) if self.selectedChr == -1 or str(qtlresult['chr']) == this_chr: - #LRSCoordXY = [] #AdditiveCoordXY = [] #DominanceCoordXY = [] #for k, _locus in enumerate(_chr): @@ -2087,10 +2122,11 @@ class MarkerRegression(object): # Yc = yZero - qtlresult['dominance']*DominanceHeightThresh/dominanceMax # DominanceCoordXY.append((Xc, Yc)) m += 1 - #canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - lineWidth = 1 + if self.manhattan_plot != True: + canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + if not self.multipleInterval and self.additiveChecked: plusColor = self.ADDITIVE_COLOR_POSITIVE minusColor = self.ADDITIVE_COLOR_NEGATIVE @@ -2120,6 +2156,7 @@ class MarkerRegression(object): canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) else: canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) + if not self.multipleInterval and INTERCROSS and self.dominanceChecked: plusColor = self.DOMINANCE_COLOR_POSITIVE minusColor = self.DOMINANCE_COLOR_NEGATIVE @@ -2151,9 +2188,6 @@ class MarkerRegression(object): canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - if self.manhattan_plot != True: - canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)) - ###draw additive scale if not self.multipleInterval and self.additiveChecked: additiveScaleFont=pid.Font(ttf="verdana",size=16*zoom,bold=0) diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index fb03f027..a57bfffe 100755 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -119,9 +119,9 @@ class SearchResultPage(object): #### Excel file needs to be generated #### - print("foo locals are:", locals()) + #print("foo locals are:", locals()) trait_id = result[0] - this_trait = GeneralTrait(dataset=self.dataset, name=trait_id, get_qtl_info=True) + this_trait = GeneralTrait(dataset=self.dataset, name=trait_id, get_qtl_info=True, get_sample_info=False) self.trait_list.append(this_trait) self.dataset.get_trait_info(self.trait_list, species) diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 3cc6121f..2d4c952a 100755 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -152,10 +152,11 @@ class ShowTrait(object): self.trait_table_width = get_trait_table_width(self.sample_groups) - js_data = dict(sample_group_types = self.sample_group_types, - sample_lists = sample_lists, - attribute_names = self.sample_groups[0].attributes, - temp_uuid = self.temp_uuid) + js_data = dict(dataset_type = self.dataset.type, + sample_group_types = self.sample_group_types, + sample_lists = sample_lists, + attribute_names = self.sample_groups[0].attributes, + temp_uuid = self.temp_uuid) self.js_data = js_data def get_mapping_methods(self): diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index 8d5982b7..9e249c28 100755..100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -174,7 +174,6 @@ make_table = function() { var header, key, row, row_line, table, the_id, the_rows, value, _i, _len, _ref, _ref1; header = "<thead><tr><th> </th>"; - console.log("js_data.sample_group_types:", js_data.sample_group_types); _ref = js_data.sample_group_types; for (key in _ref) { if (!__hasProp.call(_ref, key)) continue; @@ -186,14 +185,15 @@ the_rows = "<tbody>"; for (_i = 0, _len = Stat_Table_Rows.length; _i < _len; _i++) { row = Stat_Table_Rows[_i]; - console.log("rowing"); + if ((row.vn == "range_fold" || row.vn == "range") && js_data.dataset_type == "Publish"){ + continue; + } row_line = "<tr>"; if (row.url != null) { row_line += "<td id=\"" + row.vn + "\"><a href=\"" + row.url + "\">" + row.pretty + "</a></td>"; } else { row_line += "<td id=\"" + row.vn + "\">" + row.pretty + "</td>"; } - console.log("box - js_data.sample_group_types:", js_data.sample_group_types); _ref1 = js_data.sample_group_types; for (key in _ref1) { if (!__hasProp.call(_ref1, key)) continue; @@ -202,12 +202,10 @@ row_line += "<td id=\"" + the_id + "\">foo</td>"; } row_line += "</tr>"; - console.log("row line:", row_line); the_rows += row_line; } the_rows += "</tbody>"; table = header + the_rows; - console.log("table is:", table); return $("#stats_table").append(table); }; process_id = function() { diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html index d7950754..f3f33fad 100644 --- a/wqflask/wqflask/templates/marker_regression_gn1.html +++ b/wqflask/wqflask/templates/marker_regression_gn1.html @@ -87,8 +87,8 @@ </td> </tr> </table> - </div> - <div class="col-xs-4" style="padding: 0px;"> + </div> + <div class="col-xs-4" style="padding: 0px;"> {% if (mapping_method == "reaper" or mapping_method == "rqtl_geno") and nperm > 0 %} <input type="checkbox" name="permCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if permChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Permutation Test <a href="http://genenetwork.org/glossary.html#Permutation" target="_blank"> @@ -121,7 +121,10 @@ {% if plotScale != "morgan" %} <input type="checkbox" name="haplotypeAnalystCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if haplotypeAnalystChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Haplotype Analyst </span> <span style="color:red;">*</span> {% endif %} - </div> + </div> + <div class="col-xs-12" align="center" style="padding: 5px;"> + <span style="color:red;">*</span> <span style="font-size: 12px;">only apply to single chromosome physical mapping</span> + </div> </div> </div> @@ -162,6 +165,7 @@ </div> </form> + {% if selectedChr == -1 %} <div style="width:48%;"> <h2> Results @@ -219,6 +223,7 @@ </tbody> </table> </div> + {% endif %} </div> <!-- End of body --> diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index 62a08d85..7429cd5f 100755 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -257,12 +257,10 @@ console.log("SAMPLE GROUP TYPES:", js_data.sample_group_types) if (Object.keys(js_data.sample_group_types).length > 1) { $('#stats_table').DataTable( { - "columns": [ - { "bSortable": false }, - { "bSortable": false }, - { "bSortable": false }, - { "bSortable": false } + "columnDefs": [ + { "orderable": false, "targets": [0, 1, 2, 3] } ], + "order": [], "sDom": "tr", "iDisplayLength": -1, "autoWidth": false, @@ -274,10 +272,10 @@ } else { $('#stats_table').DataTable( { - "columns": [ - { "bSortable": false }, - { "bSortable": false } + "columnDefs": [ + { "orderable": false, "targets": [0, 1] } ], + "order": [], "sDom": "tr", "iDisplayLength": -1, "autoWidth": false, diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html index 2183dd30..9c5c94b2 100755 --- a/wqflask/wqflask/templates/show_trait_statistics.html +++ b/wqflask/wqflask/templates/show_trait_statistics.html @@ -27,7 +27,6 @@ <div class="tab-pane active" id="stats_tab"> <div style="padding: 20px" class="form-horizontal"> <table id="stats_table" style="width: 300px; float: left;" class="table table-hover table-striped"></table> - </div> </div> <div class="tab-pane" id="histogram_tab"> |