[BioRuby] Made a change in format10.rb

[Naohisa GOTO]

Hi,

Thank you for reporting a bug.

I've changed codes to support results containing two or
more query sequences.

http://github.com/bioruby/bioruby/commit/e57349594427ad1a51979c9d4e0c3efcffd160c2
http://github.com/bioruby/bioruby/commit/3d3edc44127f4fd97abcc17a859e36623facdc7c


Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org


On Mon, 09 Mar 2009 15:19:22 +0900
Fredrik Johansson <fredjoha at bioreg.kyushu-u.ac.jp> wrote:

> I found that Bioruby can't handle large amounts of output from Fasta. So 
> I made this change to 
> /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/fasta/format10.rb :
> 
> 6,7c6,8
> <       data.sub!(/(.*)\n\n>>>/m, '')
> <       @list = "The best scores are" + $1
> ---
>  >       border = data.index("\n\n>>>")
>  >       @list = "The best scores are" + data[0...border]
>  >       data = data[border+5..-1]
> 
> 
> The old code reported an error when the output was huge:
> RegexpError: Stack overflow in regexp matcher: /(.*)\n\n>>>/m
> 
> So I thought that maybe these lines of code should be changed in Bioruby.
> 
> Regards,
> Fredrik Johansson
> 
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby