[galaxy-user] fasta_to_tabular.py slowness

18 Jul 2009

Hi Galaxy Team,

I've found that fasta_to_tabular.py is very slow with big sequences, e.g. ~4 minutes for a single 5MB sequence.

The patch below makes the running time go from minutes to seconds for such a sequence. Mind you, this is my first line of python, so there may be a smarter way.

Best regards,
Rasmus Ory Nielsen

--- fasta_to_tabular.py.orig	2009-07-18 16:25:50.896487000 +0200
+++ fasta_to_tabular.py	2009-07-18 17:22:49.544611000 +0200
@@ -34,7 +34,7 @@
             fasta_seq = ''
         else:
             if line:
-                fasta_seq = "%s%s" % ( fasta_seq, line )
+                fasta_seq += line
 
     if fasta_seq:
         out.write( "%s\t%s\n" %( fasta_title[ 1:keep_first ], fasta_seq ) )

    