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-rw-r--r--wqflask/wqflask/do_search.py26
-rw-r--r--wqflask/wqflask/show_trait/SampleList.py3
-rwxr-xr-xwqflask/wqflask/show_trait/show_trait.py3
-rw-r--r--wqflask/wqflask/templates/show_trait_details.html5
4 files changed, 12 insertions, 25 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 403f1b5e..3ce613e9 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -198,26 +198,6 @@ class PhenotypeSearch(DoSearch):
query = self.compile_final_query(where_clause = self.get_fields_clause())
-# self.query = """SELECT PublishXRef.Id,
-#PublishFreeze.createtime as thistable,
-#Publication.PubMed_ID as Publication_PubMed_ID,
-#Phenotype.Post_publication_description as Phenotype_Name FROM Phenotype,
-#PublishFreeze, Publication, PublishXRef WHERE (Phenotype.Post_publication_description
-#REGEXP "[[:<:]]brain[[:>:]]" OR Phenotype.Pre_publication_description REGEXP "[[:<:]]brain[[:>:]]"
-#OR Phenotype.Pre_publication_abbreviation REGEXP "[[:<:]]brain[[:>:]]"
-#OR Phenotype.Post_publication_abbreviation REGEXP "[[:<:]]brain[[:>:]]"
-#OR Phenotype.Lab_code REGEXP "[[:<:]]brain[[:>:]]"
-#OR Publication.PubMed_ID REGEXP "[[:<:]]brain[[:>:]]"
-#OR Publication.Abstract REGEXP "[[:<:]]brain[[:>:]]"
-#OR Publication.Title REGEXP "[[:<:]]brain[[:>:]]"
-#OR Publication.Authors REGEXP "[[:<:]]brain[[:>:]]"
-#OR PublishXRef.Id REGEXP "[[:<:]]brain[[:>:]]")
-#and PublishXRef.InbredSetId = 1
-#and PublishXRef.PhenotypeId = Phenotype.Id
-#and PublishXRef.PublicationId = Publication.Id
-#and PublishFreeze.Id = 1;"""
-
-
results = self.execute(query)
print("in [df] run results are:", results)
return results
@@ -461,7 +441,8 @@ class CisTransLrsSearch(LrsSearch):
class CisLrsSearch(CisTransLrsSearch):
- """Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values
+ """
+ Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values
A cisLRS search can take 3 forms:
- cisLRS=(min_LRS max_LRS)
@@ -484,9 +465,10 @@ class CisLrsSearch(CisTransLrsSearch):
class TransLrsSearch(CisTransLrsSearch):
"""Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values
- A transLRS search can take 2 forms:
+ A transLRS search can take 3 forms:
- transLRS=(min_LRS max_LRS)
- transLRS=(min_LRS max_LRS mb_buffer)
+ - transLRS>min_LRS
where min/max_LRS represent the range of LRS scores and the mb_buffer is the range around
a particular QTL where its eQTL would be considered "cis". If there is no third parameter,
mb_buffer will default to 5 megabases.
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 0c752617..d98a810a 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -56,7 +56,8 @@ class SampleList(object):
if self.this_trait and self.dataset and self.dataset.type == 'ProbeSet':
sample.extra_attributes = self.get_extra_attribute_values(sample_name)
print("sample.extra_attributes is", pf(sample.extra_attributes))
- self.sample_list.append(sample)
+
+ self.sample_list.append(sample)
print("self.attributes is", pf(self.attributes))
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index d1c60877..0f593216 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -1627,10 +1627,11 @@ class ShowTrait(object):
this_trait=this_trait,
sample_group_type='primary',
header="%s Only" % (self.dataset.group.name))
+ print("primary_samples is: ", pf(primary_samples))
+
other_sample_names = []
for sample in this_trait.data.keys():
- print("hjk - sample is:", sample)
if sample not in all_samples_ordered:
all_samples_ordered.append(sample)
other_sample_names.append(sample)
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 4b3862c7..c3abfc9f 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -12,6 +12,7 @@
</a>
</dd>
+ {% if this_trait.probe_set_specificity %}
<dt>
<a href="/blatInfo.html" target="_blank"
title="Values higher than 2 for the specificity are good">
@@ -19,9 +20,11 @@
</a>
</dt>
<dd>{{ "%.1f" % (this_trait.probe_set_specificity) }}</dd>
-
+ {% endif %}
+ {% if this_trait.probe_set_blat_score %}
<dt>BLAT Score</dt>
<dd>{{ "%i" % (this_trait.probe_set_blat_score) }}</dd>
+ {% endif %}
</dl>