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-rw-r--r--wqflask/base/mrna_assay_tissue_data.py38
1 files changed, 22 insertions, 16 deletions
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index f1929518..8f8e2b0a 100644
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -6,12 +6,14 @@ from utility import db_tools
from utility import Bunch
from utility.db_tools import escape
+from gn3.db_utils import database_connector
from utility.logger import getLogger
-logger = getLogger(__name__ )
+logger = getLogger(__name__)
-class MrnaAssayTissueData(object):
+
+class MrnaAssayTissueData:
def __init__(self, gene_symbols=None):
self.gene_symbols = gene_symbols
@@ -20,7 +22,7 @@ class MrnaAssayTissueData(object):
self.data = collections.defaultdict(Bunch)
- 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
@@ -31,29 +33,31 @@ class MrnaAssayTissueData(object):
# Due to the limit size of TissueProbeSetFreezeId table in DB,
# performance of inner join is acceptable.MrnaAssayTissueData(gene_symbols=symbol_list)
if len(gene_symbols) == 0:
- query += '''Symbol!='' and Symbol Is Not Null group by Symbol)
+ query += '''Symbol!='' and Symbol Is Not Null group by Symbol)
as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol
and t.Mean = x.maxmean;
'''
else:
in_clause = db_tools.create_in_clause(gene_symbols)
- #ZS: This was in the query, not sure why: http://docs.python.org/2/library/string.html?highlight=lower#string.lower
+ # ZS: This was in the query, not sure why: http://docs.python.org/2/library/string.html?highlight=lower#string.lower
query += ''' Symbol in {} group by Symbol)
as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol
and t.Mean = x.maxmean;
'''.format(in_clause)
- results = g.db.execute(query).fetchall()
- lower_symbols = []
+ # lower_symbols = []
+ lower_symbols = {}
for gene_symbol in gene_symbols:
+ # lower_symbols[gene_symbol.lower()] = True
if gene_symbol != None:
- lower_symbols.append(gene_symbol.lower())
-
+ lower_symbols[gene_symbol.lower()] = True
+ results = list(g.db.execute(query).fetchall())
for result in results:
symbol = result[0]
- if symbol.lower() in lower_symbols:
+ if symbol is not None and lower_symbols.get(symbol.lower()):
+
symbol = symbol.lower()
self.data[symbol].gene_id = result.GeneId
@@ -64,16 +68,16 @@ class MrnaAssayTissueData(object):
self.data[symbol].probe_target_description = result.Probe_Target_Description
###########################################################################
- #Input: cursor, symbolList (list), dataIdDict(Dict)
- #output: symbolValuepairDict (dictionary):one dictionary of Symbol and Value Pair,
+ # Input: cursor, symbolList (list), dataIdDict(Dict)
+ # output: symbolValuepairDict (dictionary):one dictionary of Symbol and Value Pair,
# key is symbol, value is one list of expression values of one probeSet;
- #function: get one dictionary whose key is gene symbol and value is tissue expression data (list type).
- #Attention! All keys are lower case!
+ # function: get one dictionary whose key is gene symbol and value is tissue expression data (list type).
+ # Attention! All keys are lower case!
###########################################################################
def get_symbol_values_pairs(self):
id_list = [self.data[symbol].data_id for symbol in self.data]
-
+
symbol_values_dict = {}
if len(id_list) > 0:
@@ -82,11 +86,13 @@ class MrnaAssayTissueData(object):
WHERE TissueProbeSetData.Id IN {} and
TissueProbeSetXRef.DataId = TissueProbeSetData.Id""".format(db_tools.create_in_clause(id_list))
+
results = g.db.execute(query).fetchall()
for result in results:
if result.Symbol.lower() not in symbol_values_dict:
symbol_values_dict[result.Symbol.lower()] = [result.value]
else:
- symbol_values_dict[result.Symbol.lower()].append(result.value)
+ symbol_values_dict[result.Symbol.lower()].append(
+ result.value)
return symbol_values_dict