[BioRuby] Made a change in format10.rb
Fredrik Johansson
fredjoha at bioreg.kyushu-u.ac.jp
Mon Mar 9 06:19:22 UTC 2009
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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