Merge /home/lei/gene

Conflicts:
	wqflask/maintenance/quick_search_table.py

2 files changed, 128 insertions, 71 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index befbd518..9fa7beb3 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -438,8 +438,13 @@ class DataSet(object):
             print("Dataset {} is not yet available in GeneNetwork.".format(self.name))
             pass
         
-    def get_trait_data(self):
-        self.samplelist = self.group.samplelist + self.group.parlist + self.group.f1list
+    def get_trait_data(self, sample_list=None):
+        if sample_list:
+            self.samplelist = sample_list + self.group.parlist + self.group.f1list
+        else:
+            self.samplelist = self.group.samplelist + self.group.parlist + self.group.f1list
+        
+        
         query = """
             SELECT Strain.Name, Strain.Id FROM Strain, Species
             WHERE Strain.Name IN {}
@@ -1057,7 +1062,6 @@ class MrnaAssayDataSet(DataSet):
                 """ % (escape(self.name), escape(self.dataset.name))
         results = g.db.execute(query).fetchone()
         return results[0]
-    
    
     def retrieve_sample_data(self, trait):
         query = """
@@ -1078,6 +1082,47 @@ class MrnaAssayDataSet(DataSet):
                     """ % (escape(trait), escape(self.name))
         results = g.db.execute(query).fetchall()
         return results
+    
+    
+    def retrieve_genes(self, column_name):
+        query = """
+                    select ProbeSet.Name, ProbeSet.%s
+                    from ProbeSet,ProbeSetXRef
+                    where ProbeSetXRef.ProbeSetFreezeId = %s and
+                    ProbeSetXRef.ProbeSetId=ProbeSet.Id;
+                """ % (column_name, escape(str(self.id)))
+        results = g.db.execute(query).fetchall()
+        
+        return dict(results)
+
+    #def retrieve_gene_symbols(self):
+    #    query = """
+    #                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;
+    #            """ % (self.id)
+    #    return process_and_run_query(query)
+    #    results = g.db.execute(query).fetchall()
+    #    symbol_dict = {}
+    #    for item in results:
+    #        symbol_dict[item[0]] = item[1]
+    #    return symbol_dict
+    
+    
 
 
 class TempDataSet(DataSet):
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index a08f3f21..be5df657 100644
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -9,6 +9,8 @@ from utility import Bunch
 
 from MySQLdb import escape_string as escape
 
+from pprint import pformat as pf
+
 class MrnaAssayTissueData(object):
     
     def __init__(self, gene_symbols=None):
@@ -35,14 +37,15 @@ class MrnaAssayTissueData(object):
         # 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.
+        # performance of inner join is acceptable.MrnaAssayTissueData(gene_symbols=symbol_list)
+        #print("len(gene_symbols): ", len(gene_symbols))
         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 = dbtools.create_in_clause(gene_symbols)
+            in_clause = db_tools.create_in_clause(gene_symbols)
             
             query += ''' Symbol in {} group by Symbol)
                 as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol
@@ -51,17 +54,19 @@ class MrnaAssayTissueData(object):
 
         results = g.db.execute(query).fetchall()
         for result in results:
-            symbol = item[0]
-            gene_symbols.append(symbol)
-            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
+            symbol = result[0]
+            if symbol in gene_symbols:
+            #gene_symbols.append(symbol)
+                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
 
+        #print("self.data: ", pf(self.data))
 
     ###########################################################################
     #Input: cursor, symbolList (list), dataIdDict(Dict)
@@ -70,65 +75,72 @@ class MrnaAssayTissueData(object):
     #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_value_pairs(self):
-        
-        id_list = [self.tissue_data[symbol.lower()].data_id for item in self.tissue_data]
-    
-        symbol_value_pairs = {}
-        value_list=[]
     
-        query = """SELECT value, id
-                   FROM TissueProbeSetData
-                   WHERE Id IN {}""".format(create_in_clause(id_list))
-    
-        try :
-            results = g.db.execute(query).fetchall()
-            for result in results:
-                value_list.append(result.value)
-            symbol_value_pairs[symbol] = value_list
-        except:
-            symbol_value_pairs[symbol] = None
-    
-        #for symbol in symbol_list:
-        #    if tissue_data.has_key(symbol):
-        #        data_id = tissue_data[symbol].data_id
-        #
-        #        query = """select value, id
-        #                   from TissueProbeSetData
-        #                   where Id={}""".format(escape(data_id))
-        #        try :
-        #            results = g.db.execute(query).fetchall()
-        #            for item in results:
-        #                item = item[0]
-        #                value_list.append(item)
-        #            symbol_value_pairs[symbol] = value_list
-        #            value_list=[]
-        #        except:
-        #            symbol_value_pairs[symbol] = None
+    def get_symbol_values_pairs(self):
+        id_list = [self.data[symbol].data_id for symbol in self.data]
+
+        symbol_values_dict = {}
+        
+        query = """SELECT TissueProbeSetXRef.Symbol, TissueProbeSetData.value
+                   FROM TissueProbeSetXRef, TissueProbeSetData
+                   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)
+
+        #for symbol in self.data:
+        #    data_id = self.data[symbol].data_id
+        #    symbol_values_dict[symbol] = self.get_tissue_values(data_id)
+        
     
-        return symbol_value_pairs
+        return symbol_values_dict
     
-    ########################################################################################################
-    #input: cursor, symbolList (list), dataIdDict(Dict): key is symbol
-    #output: SymbolValuePairDict(dictionary):one dictionary of Symbol and Value Pair.
-    #        key is symbol, value is one list of expression values of one probeSet.
-    #function: wrapper function for getSymbolValuePairDict function
-    #          build gene symbol list if necessary, cut it into small lists if necessary,
-    #          then call getSymbolValuePairDict function and merge the results.
-    ########################################################################################################
     
-    def get_trait_symbol_and_tissue_values(symbol_list=None):
-        tissue_data = MrnaAssayTissueData(gene_symbols=symbol_list)
+    #def get_tissue_values(self, data_id):
+    #    """Gets the tissue values for a particular gene"""
+    #
+    #    tissue_values=[]
+    #
+    #    query = """SELECT value, id
+    #               FROM TissueProbeSetData
+    #               WHERE Id IN {}""".format(db_tools.create_in_clause(data_id))
+    #
+    #    #try :
+    #    results = g.db.execute(query).fetchall()
+    #    for result in results:
+    #        tissue_values.append(result.value)
+    #    #symbol_values_dict[symbol] = value_list
+    #    #except:
+    #    #    symbol_values_pairs[symbol] = None
+    #
+    #    return tissue_values
     
-        #symbolList,
-        #geneIdDict,
-        #dataIdDict,
-        #ChrDict,
-        #MbDict,
-        #descDict,
-        #pTargetDescDict = getTissueProbeSetXRefInfo(
-        #                    GeneNameLst=GeneNameLst,TissueProbeSetFreezeId=TissueProbeSetFreezeId)
-        
-        if len(tissue_data.gene_symbols):
-            return get_symbol_value_pairs(tissue_data)
+########################################################################################################
+#input: cursor, symbolList (list), dataIdDict(Dict): key is symbol
+#output: SymbolValuePairDict(dictionary):one dictionary of Symbol and Value Pair.
+#        key is symbol, value is one list of expression values of one probeSet.
+#function: wrapper function for getSymbolValuePairDict function
+#          build gene symbol list if necessary, cut it into small lists if necessary,
+#          then call getSymbolValuePairDict function and merge the results.
+########################################################################################################
+
+#def get_trait_symbol_and_tissue_values(symbol_list=None):
+#    tissue_data = MrnaAssayTissueData(gene_symbols=symbol_list)
+#
+#    #symbolList,
+#    #geneIdDict,
+#    #dataIdDict,
+#    #ChrDict,
+#    #MbDict,
+#    #descDict,
+#    #pTargetDescDict = getTissueProbeSetXRefInfo(
+#    #                    GeneNameLst=GeneNameLst,TissueProbeSetFreezeId=TissueProbeSetFreezeId)
+#    
+#    if len(tissue_data.gene_symbols):
+#        return get_symbol_values_pairs(tissue_data)