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-rwxr-xr-x[-rw-r--r--]wqflask/base/mrna_assay_tissue_data.py11
1 files changed, 9 insertions, 2 deletions
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index be5df657..1a05fce7 100644..100755
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -19,6 +19,8 @@ class MrnaAssayTissueData(object):
if self.gene_symbols == None:
self.gene_symbols = []
+ print("self.gene_symbols:", self.gene_symbols)
+
self.data = collections.defaultdict(Bunch)
#self.gene_id_dict ={}
@@ -28,7 +30,7 @@ class MrnaAssayTissueData(object):
#self.desc_dict = {}
#self.probe_target_desc_dict = {}
- query = '''select t.Symbol, t.GeneId, t.DataId,t.Chr, t.Mb, t.description, t.Probe_Target_Description
+ query = '''select t.Symbol, t.GeneId, t.DataId, t.Chr, t.Mb, t.description, t.Probe_Target_Description
from (
select Symbol, max(Mean) as maxmean
from TissueProbeSetXRef
@@ -53,6 +55,7 @@ class MrnaAssayTissueData(object):
'''.format(in_clause)
results = g.db.execute(query).fetchall()
+
for result in results:
symbol = result[0]
if symbol in gene_symbols:
@@ -66,7 +69,7 @@ class MrnaAssayTissueData(object):
self.data[symbol].description = result.description
self.data[symbol].probe_target_description = result.Probe_Target_Description
- #print("self.data: ", pf(self.data))
+ print("self.data: ", pf(self.data))
###########################################################################
#Input: cursor, symbolList (list), dataIdDict(Dict)
@@ -79,6 +82,8 @@ class MrnaAssayTissueData(object):
def get_symbol_values_pairs(self):
id_list = [self.data[symbol].data_id for symbol in self.data]
+ print("id_list:", id_list)
+
symbol_values_dict = {}
query = """SELECT TissueProbeSetXRef.Symbol, TissueProbeSetData.value
@@ -86,6 +91,8 @@ class MrnaAssayTissueData(object):
WHERE TissueProbeSetData.Id IN {} and
TissueProbeSetXRef.DataId = TissueProbeSetData.Id""".format(db_tools.create_in_clause(id_list))
+ print("TISSUE QUERY:", query)
+
results = g.db.execute(query).fetchall()
for result in results:
if result.Symbol.lower() not in symbol_values_dict: