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 ) )