adding batch id to record id in parse

snakecnv/bin/parse.py

@@ -19,7 +19,7 @@ tool_to_writer = {"pindel": PindelWriter, "delly": DellyWriter,
 def convert_svtool_to_vcf(reference, inputfile, gaps, outputfile,
                           toolname, svtype,
                           minlen=50, maxlen=5000000,
-                          doNotFilter=False):
+                          batch=None, doNotFilter=False):
 
     # The reference handle
     reference_handle = Fastafile(reference) if reference else None
@@ -57,19 +57,18 @@ def convert_svtool_to_vcf(reference, inputfile, gaps, outputfile,
 
     eprint("Now writing the records")
     for record in records:
+        record.addbatch2Id(batch)
         SVWriter.write(record)
     SVWriter.close()
     eprint("%d records" % (len(records)))
 
-    # Removed, this is done by SVWriter.close()
-    # tabix_index(outputfile, force=True, preset='vcf')
 
-
-def parsing(reference, tooloutput, gaps, parseoutput, tool, svtype, doNotFilter):
+def parsing(reference, tooloutput, gaps, parseoutput, tool, svtype,
+            doNotFilter, batch):
     #print("\n".join([reference, tooloutput, gaps, parseoutput, tool, svtype]))
 
     convert_svtool_to_vcf(reference, tooloutput, gaps, parseoutput,
-                          tool, svtype, doNotFilter=doNotFilter)
+                          tool, svtype, batch=batch, doNotFilter=doNotFilter)
 
 
 if __name__ == "__main__":
@@ -90,6 +89,8 @@ if __name__ == "__main__":
                         help="Tool name")
     parser.add_argument("-s", "--sv-type", required=True,
                         help="Type of variant")
+    parser.add_argument("-b", "--batch", default=None,
+                        help="the batch")
     parser.add_argument("-f", "--nofilter", action="store_true", default=False,
                         help="Filter false : do not filter during parse")
 
@@ -101,4 +102,6 @@ if __name__ == "__main__":
             parseoutput=args.output_vcf,
             tool=args.tool,
             svtype=args.sv_type,
-            doNotFilter=args.nofilter)
+            batch=args.batch,
+            doNotFilter=args.nofilter
+            )

snakecnv/detection.snk

@@ -193,6 +193,7 @@ rule parsing:
     shell:
         "parse.py -r {input.reference} -i {input.tooloutput} -g {input.gaps} "
         "-o {output.parseoutput} -t {wildcards.tool} -s {wildcards.svtype} "
+        "-b {wildcards.batch} "
         "1>{log.stdout} 2>{log.stderr}"
 
 if "no_detection_index" not in config or not config["no_detection_index"]: