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-rwxr-xr-xwqflask/base/data_set.py15
-rw-r--r--wqflask/wqflask/correlation/show_corr_results.py65
2 files changed, 67 insertions, 13 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 5d21c901..16f9da5d 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -1078,7 +1078,20 @@ class MrnaAssayDataSet(DataSet):
def retrieve_gene_symbols(self):
query = """
- select ProbeSet.Name, ProbeSet.Symbol
+ select ProbeSet.Name, ProbeSet.Symbol, ProbeSet.GeneId
+ from ProbeSet,ProbeSetXRef
+ where ProbeSetXRef.ProbeSetFreezeId = %s and
+ ProbeSetXRef.ProbeSetId=ProbeSet.Id;
+ """ % (self.id)
+ results = g.db.execute(query).fetchall()
+ symbol_dict = {}
+ for item in results:
+ symbol_dict[item[0]] = item[1]
+ return symbol_dict
+
+ def retrieve_gene_ids(self):
+ query = """
+ select ProbeSet.Name, ProbeSet.GeneId
from ProbeSet,ProbeSetXRef
where ProbeSetXRef.ProbeSetFreezeId = %s and
ProbeSetXRef.ProbeSetId=ProbeSet.Id;
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 42d5acd6..5df2f316 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -133,7 +133,7 @@ class CorrelationResults(object):
if self.corr_type == "tissue":
trait_symbol_dict = self.dataset.retrieve_gene_symbols()
- tissue_corr_data = self.do_tissue_corr_for_all_traits(trait_gene_symbols = trait_symbol_dict)
+ tissue_corr_data = self.do_tissue_correlation_for_all_traits(trait_gene_symbols = trait_symbol_dict)
#print("tissue_corr_data: ", pf(tissue_corr_data))
for trait in tissue_corr_data.keys()[:self.return_number]:
@@ -158,8 +158,12 @@ class CorrelationResults(object):
#self.correlation_data[trait] = [sample_r, sample_p, num_overlap]
elif self.corr_type == "lit":
- trait_symbol_dict = self.dataset.retrieve_gene_symbols()
+ trait_geneid_dict = self.dataset.retrieve_gene_ids()
+ lit_corr_data = self.do_lit_correlation_for_all_traits(trait_gene_ids = trait_geneid_dict)
+ for trait in lit_corr_data.keys()[:self.return_number]:
+ self.get_sample_r_and_p_values(trait = trait, target_samples = self.target_dataset.trait_data[trait])
+
elif self.corr_type == "sample":
for trait, values in self.target_dataset.trait_data.iteritems():
self.get_sample_r_and_p_values(trait = trait, target_samples = values)
@@ -181,13 +185,15 @@ class CorrelationResults(object):
#Get symbol for trait and call function that gets each tissue value from the database (tables TissueProbeSetXRef,
#TissueProbeSetData, etc) and calculates the correlation (cal_zero_order_corr_for_tissue in correlation_functions)
+ # Set some sane defaults
+ trait_object.tissue_corr = 0
+ trait_object.tissue_pvalue = 0
+ trait_object.lit_corr = 0
if self.corr_type == "tissue":
trait_object.tissue_corr = tissue_corr_data[trait][1]
trait_object.tissue_pvalue = tissue_corr_data[trait][2]
- else:
- # Set some sane defaults
- trait_object.tissue_corr = 0
- trait_object.tissue_pvalue = 0
+ elif self.corr_type == "lit":
+ trait_object.lit_corr = lit_corr_data[trait][1]
self.correlation_results.append(trait_object)
@@ -299,7 +305,7 @@ class CorrelationResults(object):
#return self.correlation_results
- def do_tissue_corr_for_all_traits(self, trait_gene_symbols, tissue_dataset_id=1):
+ def do_tissue_correlation_for_all_traits(self, trait_gene_symbols, tissue_dataset_id=1):
#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])
@@ -336,7 +342,7 @@ class CorrelationResults(object):
def do_lit_correlation_for_trait_list(self):
input_trait_mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), self.this_trait.geneid)
-
+
for trait in self.correlation_results:
if trait.geneid:
@@ -350,7 +356,7 @@ class CorrelationResults(object):
FROM LCorrRamin3
WHERE GeneId1='%s' and
GeneId2='%s'
- """ % (escape(trait.mouse_gene_id), escape(self.this_trait.geneid))
+ """ % (escape(trait.mouse_gene_id), escape(input_trait_mouse_gene_id))
).fetchone()
if not result:
result = g.db.execute("""SELECT value
@@ -361,9 +367,7 @@ class CorrelationResults(object):
).fetchone()
if result:
- lit_corr = result.value
-
- if lit_corr:
+ lit_corr = result.value
trait.lit_corr = lit_corr
else:
trait.lit_corr = 0
@@ -371,6 +375,43 @@ class CorrelationResults(object):
trait.lit_corr = 0
+ def do_lit_correlation_for_all_traits(self, trait_gene_ids):
+ input_trait_mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), self.this_trait.geneid)
+
+ lit_corr_data = {}
+ for trait, gene_id in trait_gene_ids.iteritems():
+ mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), gene_id)
+
+ if mouse_gene_id and str(mouse_gene_id).find(";") == -1:
+ print("gene_symbols:", input_trait_mouse_gene_id + " / " + mouse_gene_id)
+ result = g.db.execute(
+ """SELECT value
+ FROM LCorrRamin3
+ WHERE GeneId1='%s' and
+ GeneId2='%s'
+ """ % (escape(mouse_gene_id), escape(input_trait_mouse_gene_id))
+ ).fetchone()
+ if not result:
+ result = g.db.execute("""SELECT value
+ FROM LCorrRamin3
+ WHERE GeneId2='%s' and
+ GeneId1='%s'
+ """ % (escape(mouse_gene_id), escape(input_trait_mouse_gene_id))
+ ).fetchone()
+ if result:
+ print("result:", result)
+ lit_corr = result.value
+ lit_corr_data[trait] = [gene_id, lit_corr]
+ else:
+ lit_corr_data[trait] = [gene_id, 0]
+ else:
+ lit_corr_data[trait] = [gene_id, 0]
+
+ lit_corr_data = collections.OrderedDict(sorted(lit_corr_data.items(),
+ key=lambda t: -abs(t[1][1])))
+
+ return lit_corr_data
+
def convert_to_mouse_gene_id(self, species=None, gene_id=None):
"""If the species is rat or human, translate the gene_id to the mouse geneid