Script to split a provided interval list into contigs. Excesses will be dropped into the last provided file. Works like splitIntervals.sh. This is for Queue.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3895 348d0f76-0448-11de-a6fe-93d51630548a

python/splitIntervalsByContig.py

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+import sys
+input_file = sys.argv[1]
+file_index = 1
+
+headerLines = list()
+intervals = open(input_file)
+prevContig = None
+outFile = None
+
+def parseContig(line):
+    if( line.find("-") > -1 ): ## format is chr:start-stop
+        return line.split(":")[0]
+    else:
+        return line.split("\t")[0]
+
+for line in open(input_file).readlines():
+    if ( line.startswith("@") ):
+        headerLines.append(line)
+    else:
+        thisContig = parseContig(line)
+        if ( thisContig != prevContig ):
+            file_index += 1
+            try:
+                newOutFile = open(sys.argv[file_index],'w')
+                if ( outFile != None):
+                    outFile.close()
+                outFile = newOutFile
+                for headerline in headerLines:
+                    outFile.write(headerline)
+            except IndexError:
+                print("Error: fewer output files than contigs. Writing remainder to final file.")
+            prevContig = thisContig
+        outFile.write(line)