[BioRuby] Made a change in format10.rb
Naohisa GOTO
ngoto at gen-info.osaka-u.ac.jp
Wed May 6 07:56:48 UTC 2009
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
>
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