diff novo_sort.py @ 0:9b131be2b326 draft

planemo upload for repository https://github.com/zipho/novo_sort commit fbf62dc6b9a1794b07b5189279096b7d4c03ea3b

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/novo_sort.py	Fri Mar 11 02:35:09 2016 -0500
@@ -0,0 +1,32 @@
+#!/usr/bin/env python
+from __future__ import print_function
+import argparse
+from subprocess import check_call, CalledProcessError
+import shlex
+import sys
+import logging
+log = logging.getLogger( __name__ )
+
+def novo_sort( bam_filename ):
+    cmdline_str = "novosort -c 8 -m 8G -s -f {}".format( bam_filename )
+    cmdline = newSplit(cmdline_str)
+    try:
+        check_call(cmdline)
+    except CalledProcessError:
+        print("Error running the nova-sort", file=sys.stderr)
+
+def newSplit(value):
+    lex = shlex.shlex(value)
+    lex.quotes = '"'
+    lex.whitespace_split = True
+    lex.commenters = ''
+    return list(lex)
+
+def main():
+    parser = argparse.ArgumentParser(description="Re-sorting aligned files by read position")
+    parser.add_argument('--bam_filename')
+    args = parser.parse_args()
+   
+    novo_sort(args.bam_filename)
+
+if __name__ == "__main__": main()