[BioRuby] Bio::Faster plugin

[Mic]

Did also compare the speed between biofaster and reading 4 lines (fastq)/2
lines (fasta) at the time?

Cheers,

On Thu, Jan 5, 2012 at 1:20 AM, George Githinji <georgkam at gmail.com> wrote:

> ++1 Sounds cool!
>
>
> On Wed, Jan 4, 2012 at 6:05 PM, Raoul Bonnal <bonnal at ingm.org> wrote:
> > Hi Francesco,
> > It's very cool!
> >
> > And you can access to the seq object/array also in this way:
> > Bio::Faster.parse(File.join(TEST_DATA,"sample.fastq")) do |id, comments,
> > sequence, quality|
> >  puts "#{id} #{comments} #{sequence} #{quality}"
> > end
> >
> > Obviously I like it more than using the raw array :-)
> > I suppose in case of no quality value you get a nil object
> >
> >
> > +1
> >
> >
> > On 04/01/12 10.50, "Francesco Strozzi" <francesco.strozzi at gmail.com>
> wrote:
> >
> >> Hi guys,
> >>
> >> I have created a BioRuby plugin called bio-faster, that implements a
> fast
> >> and simple parser for FastA and FastQ files. It's based on the C library
> >> Kseq written by Heng Li (author of Samtools and BWA). Compared to
> >> Bio::FastQ it is actually 4-5 times faster in parsing large FastQ files.
> >> The code will not create a Bio object for each sequence but it will
> return
> >> a simple array with sequence data and quality values for FastQ (it
> supports
> >> Sanger/Phred format only).
> >> Bio::Faster could be a good choice when you just need to parse huge
> files,
> >> for example to extract information or to store sequence data in a
> database,
> >> and you don't need to create an object for each sequence but you only
> want
> >> to parse the dataset easily and quickly.
> >>
> >> Here is the code: https://github.com/fstrozzi/bioruby-faster
> >> Here is the wiki for more details:
> >> https://github.com/fstrozzi/bioruby-faster/wiki
> >> To get the gem: gem install bio-faster
> >>
> >> Tested with Ruby 1.9 only.
> >>
> >> Any comment or feedback is much appreciated!
> >>
> >> Cheers
> >
> >
> > _______________________________________________
> > BioRuby Project - http://www.bioruby.org/
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
>
>
>
> --
> ---------------
> Sincerely
> George
> Skype: george_g2
> Blog: http://biorelated.wordpress.com/
> Twitter: http://twitter.com/#!/george_l
>
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