[BioRuby] BlastXML parser outputs RDF/JSON etc.

[Pjotr Prins]

Yup, any textual output is possible, including LaTeX, XML and HTML. It
took me a long time to figure out what I needed for these tools, but
this is it :). It makes perfect sense for linked data.

ERB's are a bit slow, but with multi-core that is not a problem.

Pj.

On Sat, Sep 06, 2014 at 08:57:48AM -0700, Joachim Baran wrote:
>    Hi!
>    Â  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 <[1]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:
> 
>      Â
>      [2]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:
> 
>      Â
>      [3]https://github.com/pjotrp/blastxmlparser/blob/master/bin/blastxmlparser
> 
>      and the README
> 
>      Â  [4]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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> References
> 
>    Visible links
>    1. mailto:pjotr.public14 at thebird.nl
>    2. https://github.com/pjotrp/blastxmlparser/blob/master/template/blast2json.erb
>    3. https://github.com/pjotrp/blastxmlparser/blob/master/bin/blastxmlparser
>    4. https://github.com/pjotrp/blastxmlparser
>    5. http://www.bioruby.org/
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