[galaxy-user] fasta_to_tabular.py slowness

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 ) )