Mapper improved; version tag added

python/PascalX/__init__.py

@@ -1,2 +1,2 @@
-__version__ = "0.0.3"
+__version__ = "0.0.4"
 

python/PascalX/genescorer.py

@@ -225,7 +225,7 @@ def load_GWAS(self,file,rscol=0,pcol=1,bcol=None,a1col=None,a2col=None,delimiter
                 if log10p:
                     p = 10**(-p)
 
-                if p > 0 and p < 1:
+                if p > 0 and p < 1 and L[rscol][:2]=='rs':
                     self._GWAS[L[rscol]] = p
                 else:
                     continue
@@ -706,12 +706,11 @@ def _calcGeneSNPcorr(self,cr,gene,REF,useAll=False):
         else:
             if gene in self._MAP:
                 P = set(REF[str(cr)][0].getSNPsPos(list(self._MAP[gene].keys())))
-                useAll = True
             else:
                 P = []
 
         DATA = REF[str(cr)][0].get(list(P))
-           
+
         filtered = {}
 
         #use = []
@@ -763,7 +762,6 @@ def _calcGeneSNPcorr_wAlleles(self,cr,gene,REF,useAll=False):
         else:
             if gene in self._MAP:
                 P = set(REF[str(cr)][0].getSNPsPos( list(self._MAP[gene].keys()) ))
-                useAll = True
             else:
                 P = []
 
@@ -809,8 +807,11 @@ def _getChi2Sum_mapper(self,RIDs,gene):
         ps = np.zeros(len(RIDs))
         for i in range(0,len(ps)):
             #ps = chi2.ppf(1- np.array([GWAS[x] for x in RIDs]),1)
-            if RIDs[i] in self._MAP[gene]:
+            if RIDs[i] in self._MAP[gene] and self._MAP[gene][RIDs[i]][0] is not None:
                 ps[i] = tools.chiSquared1dfInverseCumulativeProbabilityUpperTail(self._MAP[gene][RIDs[i]][0])
+            else:
+                ps[i] = tools.chiSquared1dfInverseCumulativeProbabilityUpperTail(self._GWAS[RIDs[i]])
+
         return np.sum(ps)
 
     def _getChi2Sum(self,RIDs):
@@ -942,8 +943,11 @@ def _scoremain(self,gene,unloadRef=False,method='saddle',mode='auto',reqacc=1e-1
 
                     if len(R) == 1:
                         if self._MAP is not None and self._joint == False:
-                            if R[0] in self._MAP[G[i]]:
+                            if R[0] in self._MAP[G[i]] and self._MAP[G[i]][R[0]][0] is not None:
                                 RESULT.append( [self._GENEIDtoSYMB[G[i]],float(self._MAP[G[i]][R[0]][0]),1] )
+                            else:
+                                RESULT.append( [self._GENEIDtoSYMB[G[i]],float(self._GWAS[R[0]]),1] )
+
                         else:
                             RESULT.append( [self._GENEIDtoSYMB[G[i]],float(self._GWAS[R[0]]),1] )
                     else:

python/PascalX/mapper.py

@@ -63,6 +63,7 @@ def load_mapping(self,file,gcol=0,rcol=1,wcol=None,a1col=None,a2col=None,bcol=No
                 f.readline()
 
         c = 0
+        s = 0
         for line in f:
             line = line.rstrip().split(delimiter)
 
@@ -99,5 +100,7 @@ def load_mapping(self,file,gcol=0,rcol=1,wcol=None,a1col=None,a2col=None,bcol=No
                     self._SNPtoGENEID[line[rcol]] = [gid]
                 else:
                     self._SNPtoGENEID[line[rcol]].append(gid)
+
+                s += 1
 
-        print(c,"gene to SNP mappings loaded")
+        print(c,"gene to SNP mappings loaded (# SNPs: "+str(s)+")")