diff novo_align.py @ 12:bfe39c503a40 draft

planemo upload for repository https://github.com/zipho/novo_align commit 896a5a73f2a5f71a7b38dc0403f54afba1f27643

--- a/novo_align.py	Thu Apr 07 09:55:31 2016 -0400
+++ b/novo_align.py	Tue Nov 29 09:18:10 2016 -0500
@@ -3,9 +3,11 @@
 import argparse
 import shlex
 import os
+import sys
 import logging
 log = logging.getLogger( __name__ )
 
+
 def novo_align(output_filename, index_filename, fwd_file, rev_file ):
     param = r'@RG\tID:RG\tSM:$i\tPL:ILLUMINA'
     cmdline_str = "novoalign -c 8 -k -d {} -f {} {} -i PE 250, 100 -o SAM '{}' | samtools view -bS - > {}".format(
@@ -19,6 +21,7 @@
     except:
         print("Error running the nova-align", file=sys.stderr)
 
+
 def newSplit(value):
     lex = shlex.shlex(value)
     lex.quotes = '"'
@@ -26,6 +29,7 @@
     lex.commenters = ''
     return list(lex)
 
+
 def main():
     parser = argparse.ArgumentParser(description="Generate a BAM file from the Novo Align tool")
     parser.add_argument('output_filename')
@@ -33,9 +37,10 @@
     parser.add_argument('--forward_filename')
     parser.add_argument('--reverse_filename')
     args = parser.parse_args()
-   
+
     # a dirty way of referencing the file
     index_file_path = args.index_filename + "/" + args.index_filename.split("/")[-1]
     novo_align(args.output_filename, index_file_path, args.forward_filename, args.reverse_filename)
 
-if __name__ == "__main__": main()
+if __name__ == "__main__":
+    main()