diff novo_sort.py @ 7:2f3d4c867e1d draft default tip

planemo upload for repository https://github.com/zipho/novo_sort commit 4db125fcd73327813d7bd511852bbe9ffc68a25c
author sanbi-uwc
date Mon, 09 Jan 2017 08:19:31 -0500
parents e35fbd921b6b
children
line wrap: on
line diff
--- a/novo_sort.py	Fri Apr 01 10:26:19 2016 -0400
+++ b/novo_sort.py	Mon Jan 09 08:19:31 2017 -0500
@@ -7,6 +7,7 @@
 import logging
 log = logging.getLogger( __name__ )
 
+
 def novo_sort( bam_filename, output_filename ):
     cmdline_str = "novosort -c 8 -m 8G -s -f {} -o {}".format( bam_filename, output_filename )
     cmdline = newSplit(cmdline_str)
@@ -15,6 +16,7 @@
     except CalledProcessError:
         print("Error running the nova-sort", file=sys.stderr)
 
+
 def newSplit(value):
     lex = shlex.shlex(value)
     lex.quotes = '"'
@@ -22,12 +24,15 @@
     lex.commenters = ''
     return list(lex)
 
+
 def main():
     parser = argparse.ArgumentParser(description="Re-sorting aligned files by read position")
     parser.add_argument('output_filename')
     parser.add_argument('--bam_filename')
     args = parser.parse_args()
-   
+
     novo_sort(args.bam_filename, args.output_filename)
 
-if __name__ == "__main__": main()
+
+if __name__ == "__main__":
+    main()