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-rwxr-xr-xwqflask/base/data_set.py12
-rwxr-xr-xwqflask/base/trait.py26
2 files changed, 26 insertions, 12 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index cd8c1ac1..8296adea 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -318,12 +318,17 @@ class DatasetGroup(object):
#determine default genotype object
if self.incparentsf1 and genotype_1.type != "intercross":
- self.genotype = genotype_2
+ #self.genotype = genotype_2
+ genotype = genotype_2
else:
self.incparentsf1 = 0
- self.genotype = genotype_1
+ #self.genotype = genotype_1
+ genotype = genotype_1
- self.samplelist = list(self.genotype.prgy)
+ #self.samplelist = list(self.genotype.prgy)
+ self.samplelist = list(genotype.prgy)
+
+ return genotype
#class DataSets(object):
@@ -1084,6 +1089,7 @@ class MrnaAssayDataSet(DataSet):
Strain.Name
""" % (escape(trait), escape(self.name))
results = g.db.execute(query).fetchall()
+ print("RETRIEVED RESULTS HERE:", results)
return results
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 731f99eb..74bc07bb 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -154,7 +154,7 @@ class GeneralTrait(object):
result.append(None)
return result
- def export_informative(self, incVar=0):
+ def export_informative(self, include_variance=0):
"""
export informative sample
mostly used in qtl regression
@@ -163,12 +163,12 @@ class GeneralTrait(object):
samples = []
vals = []
the_vars = []
- for sample, value in self.data.items():
- if value.val != None:
- if not incVar or value.var != None:
- samples.append(sample)
- vals.append(value.val)
- the_vars.append(value.var)
+ for sample_name, sample_data in self.data.items():
+ if sample_data.value != None:
+ if not include_variance or sample_data.variance != None:
+ samples.append(sample_name)
+ vals.append(sample_data.value)
+ the_vars.append(sample_data.variance)
return samples, vals, the_vars
@@ -235,11 +235,19 @@ class GeneralTrait(object):
# Todo: is this necessary? If not remove
self.data.clear()
+ if self.dataset.group.parlist:
+ all_samples_ordered = (self.dataset.group.parlist +
+ self.dataset.group.f1list +
+ self.dataset.group.samplelist)
+ elif self.dataset.group.f1list:
+ all_samples_ordered = self.dataset.group.f1list + self.dataset.group.samplelist
+ else:
+ all_samples_ordered = self.dataset.group.samplelist
+
if results:
for item in results:
- #name, value, variance, num_cases = item
+ name, value, variance, num_cases = item
if not samplelist or (samplelist and name in samplelist):
- name = item[0]
self.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases)
#def keys(self):