[Bioperl-l] 65% speedup for Bio::SeqIO::fasta::next_seq test

[Tim Bunce]

On Mon, Sep 30, 2002 at 04:27:45PM +0100, Ewan Birney wrote:
> 
> Cool tim - very cool. You clearly have the magic for understanding how to
> optimise these things.

Kind-of. I'm handicapped by not really knowing the "big picture" so
I can't make deeper more structural changes - but you guys seem to be
well able to do that once someone points a finger as a performance problem.

> I am pretty crap at using patch (perhaps I should start to learn...)

It is worth it. (Patch is one of Larry Wall's creations.)

Just do

	patch < the_file_containing_the_patch

and it'll prompt for the path to each file.

Or, somewhat easier, since the paths in the diff start with a
'bioperl-core-timbo' prefix before the Bio/... you could cd to the
directory above Bio and do

	patch -p1 < the_file_containing_the_patch

The -p1 tells patch to remove one level of path name, ie the
bioperl-core-timbo prefix.  Patch will then find the original files
and patch them (saving backup copies as *.orig files).

[The patch supplied with Solaris is different and worth avoiding.]

> can you just send me the three files directly I will diff, apply by hand and
> commit?

To follow in separate email (off list).

Tim.

p.s. I probably won't have time to tinker with bioperl for some time now.