diff options
| -rwxr-xr-x | wqflask/wqflask/gsearch.py | 18 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/gsearch_gene.html | 62 |
2 files changed, 46 insertions, 34 deletions
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index 396da4cf..7e647b76 100755 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -16,7 +16,7 @@ class GSearch(object): Species.`Name` AS species_name, InbredSet.`Name` AS inbredset_name, Tissue.`Name` AS tissue_name, - ProbeSetFreeze.FullName AS probesetfreeze_fullname, + ProbeSetFreeze.Name AS probesetfreeze_name, ProbeSet.Name AS probeset_name, ProbeSet.Symbol AS probeset_symbol, ProbeSet.`description` AS probeset_description, @@ -35,10 +35,21 @@ class GSearch(object): AND ( MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol,alias,GenbankId, UniGeneId, Probe_Target_Description) AGAINST ('%s' IN BOOLEAN MODE) ) AND ProbeSet.Id = ProbeSetXRef.ProbeSetId AND ProbeSetXRef.ProbeSetFreezeId=ProbeSetFreeze.Id - ORDER BY species_name, inbredset_name, tissue_name, probesetfreeze_fullname, probeset_name + AND ProbeSetFreeze.public > 0 + ORDER BY species_name, inbredset_name, tissue_name, probesetfreeze_name, probeset_name LIMIT 1000 """ % (self.terms) - self.results = g.db.execute(sql).fetchall() + re = g.db.execute(sql).fetchall() + self.trait_list = [] + for line in re: + dataset = create_dataset(line[3], "ProbeSet") + print("dataset: %s %s %s" % (line[3], dataset.name, dataset.id)) + trait_id = line[4] + this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True) + self.trait_list.append(this_trait) + species = webqtlDatabaseFunction.retrieve_species(dataset.group.name) + dataset.get_trait_info([this_trait], species) + elif self.type == "phenotype": sql = """ SELECT @@ -80,4 +91,3 @@ class GSearch(object): self.trait_list.append(this_trait) species = webqtlDatabaseFunction.retrieve_species(dataset.group.name) dataset.get_trait_info([this_trait], species) - diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html index 3e1cb32e..6cf16c08 100755 --- a/wqflask/wqflask/templates/gsearch_gene.html +++ b/wqflask/wqflask/templates/gsearch_gene.html @@ -24,37 +24,44 @@ <br /> <br /> <table class="table table-hover table-striped" id="trait_table"> - <thead> - <tr> + <thead> + <tr> + <th style="width: 30px;"></th> <th>Index</th> - <th>Symbol</th> - <th>Record</th> - <th>Description</th> <th>Species</th> <th>Group</th> <th>Tissue</th> <th>Dataset</th> - <th>Chr</th> - <th>Mb</th> + <th>Record</th> + <th>Symbol</th> + <th>Description</th> + <th>Location</th> <th>Mean</th> - <th>Max LRS</th> - <th>Locus</th> - <th>Pvalue</th> - <th>Additive</th> - </tr> - </thead> - + <th style="text-align: right;">Max <br>LRS<a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="color:#f00"> ?</sup></a></th> + <th>Max LRS Location</th> + <th style="text-align: right;">Additive<br>Effect<a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th> + </tr> + </thead> <tbody> - {% for this_trait in results %} - <TR> - <td><input type="checkbox">{{ loop.index }}</td> - {% for item in this_trait %} - <TD>{{ item }}</TD> - {% endfor %} - </TR> - {% endfor %} + {% for this_trait in trait_list %} + <TR id="trait:{{ this_trait.name }}:{{ this_trait.dataset.name }}"> + <TD><INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" VALUE="{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) }}"></TD> + <TD>{{ loop.index }}</TD> + <TD>{{ this_trait.dataset.group.species }}</TD> + <TD>{{ this_trait.dataset.group.name }}</TD> + <TD>{{ this_trait.dataset.name }}</TD> + <TD>{{ this_trait.dataset.name }}</TD> + <TD><a href="{{ url_for('show_trait_page', trait_id = this_trait.name, dataset = this_trait.dataset.name)}}">{{ this_trait.name }}</a></TD> + <TD>{{ this_trait.symbol }}</TD> + <TD>{{ this_trait.description_display }}</TD> + <TD>{{ this_trait.location_repr }}</TD> + <TD align="right">{{ '%0.3f' % this_trait.mean|float }}</TD> + <TD align="right">{{ '%0.3f' % this_trait.LRS_score_repr|float }}</TD> + <TD>{{ this_trait.LRS_location_repr }}</TD> + <TD align="right">{{ '%0.3f' % this_trait.additive|float }}</TD> + </TR> + {% endfor %} </tbody> - </table> </div> </div> @@ -123,7 +130,7 @@ console.time("Creating table"); $('#trait_table').DataTable( { "columns": [ - { "type": "natural" }, + { "bSortClasses": false }, { "type": "natural" }, { "type": "natural", "width": "35%" }, { "type": "natural", "width": "15%" }, @@ -136,16 +143,11 @@ { "type": "natural", "width": "15%" }, { "type": "natural" }, { "type": "natural" }, - { "type": "natural" }, - { "type": "cust-txt" } + { "type": "natural" } ], - "sDom": "RJtir", - "iDisplayLength": -1, "autoWidth": true, "bLengthChange": true, "bDeferRender": true, - "bSortClasses": false, - "scrollY": "700px", "scrollCollapse": false, "colResize": { "tableWidthFixed": false, |