[BioRuby] BlastXML parser outputs RDF/JSON etc.

[Joachim Baran]

Hi!

  The use of ERBs is pretty wicked! So, it would absolutely be possible to
have JSON-LD output too, right?

Thanks,

Kim


On 6 September 2014 05:08, Pjotr Prins <pjotr.public14 at thebird.nl> wrote:

> Hi all,
>
> One of my oldest gems gets a new life :)
>
> I revamped the bioblastxml parser to produce any type of RDF, JSON,
> csv etc. All that needs to be done is write (or use an existing) ERB
> template. JSON example:
>
>
> https://github.com/pjotrp/blastxmlparser/blob/master/template/blast2json.erb
>
> Also the bioblastxml parser makes use of multicore parallelism.
> It is probably one of the fastest BLAST XML parser around.
>
> The strategy of a command line interface, lazy parsing, parallelism
> throuth the Parallel gem and flexible output with ERB I consider core
> strategies for bioinformatics gems. The good news is that it is
> surprisingly easy to do!
>
> Have a look at the source code:
>
>   https://github.com/pjotrp/blastxmlparser/blob/master/bin/blastxmlparser
>
> and the README
>
>   https://github.com/pjotrp/blastxmlparser
>
> When the Parallel gem is not found the parser defaults to single thread.
>
> I'll add these features to the bio-vcf and bio-table gems too in the
> near future. With releases to match.
>
> Pj.
>
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