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-rwxr-xr-xwqflask/base/data_set.py5
-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py3
-rw-r--r--wqflask/wqflask/search_results.py22
-rwxr-xr-xwqflask/wqflask/show_trait/show_trait.py4
-rw-r--r--wqflask/wqflask/templates/index_page.html4
5 files changed, 28 insertions, 10 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 10f047f8..71efc9b2 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -185,9 +185,8 @@ class DataSet(object):
self.group = DatasetGroup(self) # sets self.group and self.group_id and gets genotype
self.species = species.TheSpecies(self)
-
-
-
+
+
def get_desc(self):
"""Gets overridden later, at least for Temp...used by trait's get_given_name"""
return None
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 9278c80d..1a0efcee 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -65,6 +65,9 @@ class MarkerRegression(object):
pheno_vector = np.array([float(val) for val in self.vals if val!="x"])
genotype_matrix = np.array(trimmed_genotype_data).T
+ print("pheno_vector is: ", pf(pheno_vector))
+ print("genotype_matrix is: ", pf(genotype_matrix))
+
t_stats, p_values = lmm.run(
pheno_vector,
genotype_matrix,
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index fde30944..080568f0 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -57,15 +57,18 @@ class SearchResultPage():
# self.dataset_groups = map(lambda x: x[1], results)
# self.dataset_group_ids = map(lambda x: x[2], results)
#else:
- if kw['q']:
+
+ self.results = []
+
+ if 'q' in kw:
self.quick_search = True
self.search_terms = kw['q']
+ self.quick_search()
else:
self.quick_search = False
self.search_terms = kw['search_terms']
self.dataset = create_dataset(kw['dataset'])
-
- self.search()
+ self.search()
self.gen_search_result()
@@ -95,13 +98,24 @@ class SearchResultPage():
self.trait_list.append(this_trait)
self.dataset.get_trait_info(self.trait_list, species)
+
+ def quick_search(self):
+
+ return True
+
+ #search_gene
+ #search_geno
+ #searhch_pheno
+ #search_mrn
+ #searhc_publish
def search(self):
self.search_terms = parser.parse(self.search_terms)
print("After parsing:", self.search_terms)
- self.results = []
+
+
for a_search in self.search_terms:
print("[kodak] item is:", pf(a_search))
search_term = a_search['search_term']
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 12d512b2..5c064359 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -1552,8 +1552,10 @@ class ShowTrait(object):
all_samples_ordered = (self.dataset.group.parlist +
self.dataset.group.f1list +
self.dataset.group.samplelist)
- else:
+ elif self.dataset.group.f1list:
all_samples_ordered = self.dataset.group.f1list + self.dataset.group.samplelist
+ else:
+ all_samples_ordered = self.dataset.group.samplelist
this_trait_samples = set(this_trait.data.keys())
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index 8a05173f..46a307b7 100644
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -34,10 +34,10 @@
</div>
<form method="get" action="/search" name="SEARCHFORM">
<fieldset>
- <label for="tfor">Search:</label>
+ <label for="quick">Search:</label>
<div class="input-append">
<input class="input-xlarge"
- id="tfor" name="q"
+ id="quick" name="q"
type="text" maxlength="500">
<input id="btsearch" type="submit"