[BioRuby] Bio::Faster plugin

[George Githinji]

++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
>
>
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