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authorLei Yan2014-08-21 18:56:29 +0000
committerLei Yan2014-08-21 18:56:29 +0000
commit7ff0dcda04dc853620bb5162180f18db596f1574 (patch)
tree0d4c0160607badcc800e6ee27cc32d5a4bbbd04c
parent41fb705cc57c94276573fd19b50c91c095fe76a9 (diff)
downloadgenenetwork2-7ff0dcda04dc853620bb5162180f18db596f1574.tar.gz
Committer: Lei Yan <lei@penguin.uthsc.edu>
On branch master
-rwxr-xr-xwqflask/base/data_set.py4
-rwxr-xr-xwqflask/base/trait.py8
-rwxr-xr-xwqflask/wqflask/correlation/show_corr_results.py6
-rwxr-xr-xwqflask/wqflask/templates/correlation_page.html8
4 files changed, 8 insertions, 18 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index c2a05c90..3fb7203d 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -579,10 +579,10 @@ class DataSet(object):
""".format(*mescape(self.type, self.type, self.type, self.type,
self.name, dataset_type, self.type, self.type, dataset_type))
- print("trait data query: ", query)
+ #print("trait data query: ", query)
results = g.db.execute(query).fetchall()
- print("query results:", results)
+ #print("query results:", results)
trait_sample_data.append(results)
trait_count = len(trait_sample_data[0])
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 2bbd1f2a..71691899 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -315,7 +315,7 @@ class GeneralTrait(object):
ProbeSet.Name = '%s'
""" % (escape(display_fields_string),
escape(self.dataset.name),
- escape(self.name))
+ escape(str(self.name)))
trait_info = g.db.execute(query).fetchone()
#XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name
# to avoid the problem of same marker name from different species.
@@ -340,10 +340,6 @@ class GeneralTrait(object):
""" % (string.join(self.dataset.display_fields,','),
self.dataset.type, self.name)
trait_info = g.db.execute(query).fetchone()
-
-
- #self.cursor.execute(query)
- #trait_info = self.cursor.fetchone()
if trait_info:
self.haveinfo = True
@@ -440,8 +436,6 @@ class GeneralTrait(object):
PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
PublishFreeze.Id =%s
""", (self.name, self.dataset.id)).fetchone()
- #self.cursor.execute(query)
- #trait_qtl = self.cursor.fetchone()
if trait_qtl:
self.locus, self.lrs = trait_qtl
else:
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 06cf1915..f35fe075 100755
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -164,7 +164,7 @@ class CorrelationResults(object):
for _trait_counter, trait in enumerate(self.correlation_data.keys()[:self.return_number]):
print("trait name:", trait)
- trait_object = GeneralTrait(dataset=self.dataset, name=trait, get_qtl_info=True)
+ trait_object = GeneralTrait(dataset=self.target_dataset, name=trait, get_qtl_info=True)
(trait_object.sample_r,
trait_object.sample_p,
@@ -474,10 +474,6 @@ class CorrelationResults(object):
this_trait_vals.append(sample_value)
target_vals.append(target_sample_value)
- # print("trait:", trait)
- print("this_trait_vals: %s" % this_trait_vals)
- print("target_vals: %s" % target_vals)
-
this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(
this_trait_vals, target_vals)
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 88f6d65a..fc5aca42 100755
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -24,7 +24,7 @@
<table id="corr_results" class="table table-hover table-striped table-bordered">
<thead>
<tr>
- {% if dataset.type == 'ProbeSet' %}
+ {% if target_dataset.type == 'ProbeSet' %}
<th>Trait</th>
<th>Symbol</th>
<th>Description</th>
@@ -47,7 +47,7 @@
<th>Tissue rho</th>
<th>Tissue p(rho)</th>
{% endif %}
- {% elif dataset.type == "Publish" %}
+ {% elif target_dataset.type == "Publish" %}
<th>Record ID</th>
<th>Phenotype</th>
<th>Authors</th>
@@ -67,7 +67,7 @@
<tbody>
{% for trait in correlation_results %}
<tr>
- {% if dataset.type == 'ProbeSet' %}
+ {% if target_dataset.type == 'ProbeSet' %}
<td><a href="/show_trait?trait_id={{trait.name}}&amp;dataset={{trait.dataset.name}}">{{ trait.name }}</a></td>
<td>{{ trait.symbol }}</td>
<td>{{ trait.description }} <br><br> <b>Aliases</b>: {{ trait.alias }}</td>
@@ -81,7 +81,7 @@
<td>{{'%0.3f'|format(trait.lit_corr)}}</td>
<td>{{'%0.3f'|format(trait.tissue_corr)}}</td>
<td>{{'%0.3e'|format(trait.tissue_pvalue)}}</td>
- {% elif dataset.type == "Publish" %}
+ {% elif target_dataset.type == "Publish" %}
<td><a href="/show_trait?trait_id={{trait.name}}&amp;dataset={{trait.dataset.name}}">{{ trait.name }}</a></td>
<td>{{ trait.post_publication_description }}</td>
<td>{{ trait.authors }}</td>