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-rwxr-xr-xwqflask/wqflask/gsearch.py18
-rwxr-xr-xwqflask/wqflask/templates/gsearch_gene.html62
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&nbsp;&nbsp;<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,