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authorLei Yan2013-10-10 17:09:21 -0500
committerLei Yan2013-10-10 17:09:21 -0500
commit8a09358e98dbf88deb101d13107a40bac371de5c (patch)
tree1aeab22ddcf40985a5e7762caf9c128d9b709cc5 /wqflask
parent5daef1bd5e6e494b477797993bb72488b24dd8b3 (diff)
downloadgenenetwork2-8a09358e98dbf88deb101d13107a40bac371de5c.tar.gz
Almost have correlation working for non-primary strain/group
There's just some issue with parents/f1s not being included if you select non-BXD (or whatever the group is). All Samples, however does work.
Diffstat (limited to 'wqflask')
-rwxr-xr-xwqflask/base/data_set.py17
-rw-r--r--wqflask/wqflask/correlation/show_corr_results.py19
2 files changed, 16 insertions, 20 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 20c9a24f..beb62bd7 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -436,8 +436,13 @@ class DataSet(object):
print("Dataset {} is not yet available in GeneNetwork.".format(self.name))
pass
- def get_trait_data(self):
- self.samplelist = self.group.samplelist + self.group.parlist + self.group.f1list
+ def get_trait_data(self, sample_list=None):
+ if sample_list:
+ self.samplelist = sample_list + self.group.parlist + self.group.f1list
+ else:
+ self.samplelist = self.group.samplelist + self.group.parlist + self.group.f1list
+
+
query = """
SELECT Strain.Name, Strain.Id FROM Strain, Species
WHERE Strain.Name IN {}
@@ -1085,16 +1090,8 @@ class MrnaAssayDataSet(DataSet):
ProbeSetXRef.ProbeSetId=ProbeSet.Id;
""" % (column_name, escape(str(self.id)))
results = g.db.execute(query).fetchall()
- print("in retrieve_genes results {}: {}".format(type(results), results))
return dict(results)
-
- #return {item[0]: item[1] for item in results}
-
- #symbol_dict = {}
- #for item in results:
- # symbol_dict[item[0]] = item[1]
- #return symbol_dict
#def retrieve_gene_symbols(self):
# query = """
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 258dcfa4..a5c80674 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -70,7 +70,7 @@ TISSUE_MOUSE_DB = 1
def print_mem(stage=""):
mem = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss
- print("{}: {}".format(stage, mem/1024))
+ #print("{}: {}".format(stage, mem/1024))
class AuthException(Exception):
@@ -119,10 +119,14 @@ class CorrelationResults(object):
#exclude the primary samples (because they would have been added in the previous
#if statement if the user selected All Samples)
if corr_samples_group != 'samples_primary':
+ if corr_samples_group == 'samples_other':
+ primary_samples = [x for x in primary_samples if x not in (
+ self.dataset.group.parlist + self.dataset.group.f1list)]
+ print("primary_samples:", primary_samples)
self.process_samples(start_vars, self.this_trait.data.keys(), primary_samples)
self.target_dataset = data_set.create_dataset(start_vars['corr_dataset'])
- self.target_dataset.get_trait_data()
+ self.target_dataset.get_trait_data(self.sample_data.keys())
self.correlation_results = []
@@ -180,7 +184,7 @@ class CorrelationResults(object):
if self.corr_type != "tissue":
self.do_tissue_correlation_for_trait_list()
- print("self.correlation_results: ", pf(self.correlation_results))
+ #print("self.correlation_results: ", pf(self.correlation_results))
#XZ, 09/18/2008: get all information about the user selected database.
@@ -241,8 +245,6 @@ class CorrelationResults(object):
#Gets tissue expression values for the primary trait
primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
symbol_list = [self.this_trait.symbol])
-
- print("primary_trait_tissue_vals: ", pf(primary_trait_tissue_vals_dict))
if self.this_trait.symbol.lower() in primary_trait_tissue_vals_dict:
primary_trait_tissue_values = primary_trait_tissue_vals_dict[self.this_trait.symbol.lower()]
@@ -258,8 +260,6 @@ class CorrelationResults(object):
corr_result_tissue_vals_dict= correlation_functions.get_trait_symbol_and_tissue_values(
symbol_list=gene_symbol_list)
- print("corr_result_tissue_vals: ", pf(corr_result_tissue_vals_dict))
-
for trait in self.correlation_results:
if trait.symbol and trait.symbol.lower() in corr_result_tissue_vals_dict:
this_trait_tissue_values = corr_result_tissue_vals_dict[trait.symbol.lower()]
@@ -430,14 +430,14 @@ class CorrelationResults(object):
"""
+ print("len(self.sample_data):", len(self.sample_data))
+
this_trait_vals = []
target_vals = []
for index, sample in enumerate(self.target_dataset.samplelist):
if sample in self.sample_data:
sample_value = self.sample_data[sample]
- print("sample_value:", sample_value)
target_sample_value = target_samples[index]
- print("target_sample_value:", target_sample_value)
this_trait_vals.append(sample_value)
target_vals.append(target_sample_value)
@@ -995,7 +995,6 @@ class CorrelationResults(object):
values_2.append(target_value)
correlation = calCorrelation(values_1, values_2)
self.correlation_data[trait] = correlation
- print ('correlation result: %s %s' % (trait, correlation))
"""
correlations = []