[BioRuby] Bio::Faster plugin

[Francesco Strozzi]

Hi,
I haven't done this comparison, but if you want to run it I will be happy
to put the outputs on the wiki.

Cheers

On Friday, March 2, 2012, Mic <mictadlo at gmail.com> wrote:
> 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
>>
>> _______________________________________________
>> BioRuby Project - http://www.bioruby.org/
>> BioRuby mailing list
>> BioRuby at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioruby
>>
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>

-- 

Francesco