diff parseSnpEffVcf.py @ 48:a38cc72edd75

xena header

--- a/parseSnpEffVcf.py	Thu Aug 13 23:26:33 2015 -0700
+++ b/parseSnpEffVcf.py	Fri Aug 14 00:04:41 2015 -0700
@@ -436,7 +436,13 @@
 
     myVcf = vcf(sys.stdin)
 
-    fout =open(args.ID,'w')
+    tmpOutput = "file_"+args.ID
+    fout =open(tmpOutput, 'w')
+
+    if args.ID[-4:]==".vcf":
+        sampleID = args.ID[:-4]
+    else:
+        sampleID = args.ID
 
     for row in myVcf.read():
         #total =total+1
@@ -460,7 +466,7 @@
                 AA_Change = row.effectPerGene[gene]["Amino_Acid_Change"]
                 if AA_Change !="" and AA_Change[:2]!="p.":
                     AA_Change="p."+AA_Change
-                fout.write(string.join([args.ID, row.chr, str(row.start),
+                fout.write(string.join([sampleID, row.chr, str(row.start),
                                         str(row.end), row.reference, row.alt,
                                         gene,row.effectPerGene[gene]["effect"],
                                         str(row.DNA_AF), str(row.RNA_AF),AA_Change
@@ -470,7 +476,7 @@
             gene =""
             AA_Change=""
             effect =""
-            fout.write(string.join([args.ID, row.chr, str(row.start),
+            fout.write(string.join([sampleID, row.chr, str(row.start),
                                     str(row.end), row.reference, row.alt,
                                     gene,effect,
                                     str(row.DNA_AF), str(row.RNA_AF),AA_Change
@@ -478,10 +484,10 @@
                                     ],"\t")+"\n")
     fout.close()
 
-    os.system("cat "+args.ID+" >> "+args.output)
-    os.system("rm -f "+args.ID)
+    os.system("cat "+tmpOutput+" >> "+args.output)
+    os.system("rm -f "+tmpOutput)
 
 if __name__ == '__main__':
-        main()
+    main()