misc

Author: Dan-RAI

python/PascalX/genescorer.py

@@ -2053,4 +2053,40 @@ def score(self,gene,parallel=1,unloadRef=False,method='saddle',mode='auto',reqac
             self._SCORES[X[0]] = float(X[1])
 
 
-        return R
+        return R
+    
+    
+    def _getMinSNP(self,cr,gene,REF):
+        
+        RID = self._getSNPs(cr,gene,REF)
+        
+        minp = 1
+        
+        for R in RID:
+            p = self._GWAS[R]
+            
+            if p < minp:
+                minp = p
+            
+        return minp
+    
+    def getMinSNPs(self):
+        """
+        Returns dictionary with minimal GWAS p-value for gene
+        """
+        RET = {}
+        REF = {}
+        for gid in self._GENEID:
+            cr = self._GENEID[gid][0]
+    
+            # Load Reference panel
+            if not cr in REF:
+                REF = {}
+                REF[cr] = self._ref.load_pos_reference(cr)
+
+            minp = self._getMinSNP(cr,gid,REF)
+            
+            RET[self._GENEID[gid][4]] = minp
+        
+        return RET
+    

python/PascalX/pathway.py

@@ -53,7 +53,7 @@ def set_genescorer(self,S):
         """
         self._genescorer = S
 
-    def load_modules(self,file,ncol=0,fcol=2):    
+    def load_modules(self,file,ncol=0,fcol=2,symbol=True):    
         """
         Load modules from tab separated file
 
@@ -62,7 +62,7 @@ def load_modules(self,file,ncol=0,fcol=2):
             file(string): path/filename
             ncol(int): Column with name of module
             fcol(int): Column with first gene (symbol) in module. Remaining genes have to follow tab (\t) separated
-        
+            symbol(bool): Genes are given as gene symbols (False requires genome to be set in genescorer)
         """
         F = []
 
@@ -72,7 +72,16 @@ def load_modules(self,file,ncol=0,fcol=2):
 
             L = line.rstrip('\n').split("\t")
 
-            F.append([L[ncol],L[fcol:]])
+            if symbol:
+                F.append([L[ncol],L[fcol:]])
+            else:
+                G = L[fcol:]
+                R = []
+                for x in G:
+                    if x in self._genescorer._GENEID:
+                        R.append(self._genescorer._GENEID[x][-1])
+                
+                F.append([L[ncol],R])
 
         f.close()