[Biojava-dev] Fwd: [blast-announce] New Version of BLAST XML output

[Andreas Prlic]

On Tue, May 5, 2015 at 1:18 PM, Paolo Pavan <paolo.pavan at gmail.com> wrote:

> I know Indeed. But actually my module is not just a parser, it is part of
> an Input/output system for search results, I think biojava actually lacks
> this.
>

Perhaps others want to chime in if they see the need for this?

As seen in other Bio projects, aside with Sequence IO and Alignment IO
> procedures it could have a Search result IO also.
>

I never understood why other Bio* projects have special Blast modules.
Perhaps XML parsing is not as easy as it is in Java? Please see the code at
the bottom of this message.

There is some limited support for calling Blast (and Hmmer) webservices in
the webservices module (biojava-ws)


The advantage is to define common data structures that models Hsp, Hits,
> Results without taking care (ie. making abstraction) of the underlying
> search program.
>

and the disadvantage is that you constantly need to update them to the
variant of blast plus version of the output file format.



> And all this work is already done.
>

you mean the work has just started :-). Does your module support psiblast,
rpsblast, tblastx and blast+ and what versions?

Take a look at this:

on the command line, create the Java data model with:
xjc -p blast -dtd "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"

and then (slightly shortened)

JAXBContext jc = JAXBContext.newInstance("blast");
Unmarshaller u = jc.createUnmarshaller();
blast.BlastOutput result = (blast.BlastOutput)u.unmarshal(new
File("blastoutputfile");

Do we really need a special BioJava module for wrapping this?

Andreas



-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
RCSB PDB Protein Data Bank
Technical & Scientific Team Lead
University of California, San Diego

Editor Software Section
PLOS Computational Biology

BioJava Project Lead
-----------------------------------------------------------------------
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biojava-dev/attachments/20150505/1adbd022/attachment-0001.html>