1 files changed, 0 insertions, 94 deletions
diff --git a/gn3/base/mrna_assay_tissue_data.py b/gn3/base/mrna_assay_tissue_data.py
deleted file mode 100644
index 0f51ade..0000000
--- a/gn3/base/mrna_assay_tissue_data.py
+++ /dev/null
@@ -1,94 +0,0 @@
-
-# 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