1 files changed, 94 insertions, 0 deletions
diff --git a/gn3/base/mrna_assay_tissue_data.py b/gn3/base/mrna_assay_tissue_data.py
new file mode 100644
index 0000000..0f51ade
--- /dev/null
+++ b/gn3/base/mrna_assay_tissue_data.py
@@ -0,0 +1,94 @@
+
+# pylint: disable-all
+import collections
+
+from flask import g
+
+from gn3.utility.db_tools import create_in_clause
+from gn3.utility.db_tools import escape
+from gn3.utility.bunch import Bunch
+
+
+# from utility.logger import getLogger
+# logger = getLogger(__name__ )
+
+class MrnaAssayTissueData(object):
+
+    def __init__(self, gene_symbols=None):
+        self.gene_symbols = gene_symbols
+        if self.gene_symbols == None:
+            self.gene_symbols = []
+
+        self.data = collections.defaultdict(Bunch)
+
+        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
+                        where TissueProbeSetFreezeId=1 and '''
+
+        # Note that inner join is necessary in this query to get distinct record in one symbol group
+        # with highest mean value
+        # 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)
+                as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol
+                and t.Mean = x.maxmean;
+                    '''
+        else:
+            in_clause = 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
+            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 = []
+        for gene_symbol in gene_symbols:
+            if gene_symbol != None:
+                lower_symbols.append(gene_symbol.lower())
+
+        for result in results:
+            symbol = result[0]
+            if symbol.lower() in lower_symbols:
+                symbol = symbol.lower()
+
+                self.data[symbol].gene_id = result.GeneId
+                self.data[symbol].data_id = result.DataId
+                self.data[symbol].chr = result.Chr
+                self.data[symbol].mb = result.Mb
+                self.data[symbol].description = result.description
+                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,
+    #        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!
+    ###########################################################################
+
+    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:
+            query = """SELECT TissueProbeSetXRef.Symbol, TissueProbeSetData.value
+                       FROM TissueProbeSetXRef, TissueProbeSetData
+                       WHERE TissueProbeSetData.Id IN {} and
+                             TissueProbeSetXRef.DataId = TissueProbeSetData.Id""".format(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)
+
+        return symbol_values_dict