[Biojava-l] status? Blast parser?

[Jared Nedzel]

Simon:

Sorry for the delayed response.  Yes, I want a Blast parser.
I want to be able to give the parser a Blast output file.
I want to be able to get:

  - all the hits
  - the best hit

For each hit, get the set of consistent HSPs. For the hsps,
get the P and E values and the bases, the ranges (query and
subject), the gaps, etc.

At this point, I don't need or want html or xml.  Instead,
I want objects (hits, hsps, etc.).

Jared
nedzel@mpi.com



Simon Brocklehurst wrote:
> 
> Dear All,
> 
> Having previously posted that CAT wouldn't be contributing to biojava,
> I'm happy to say that we now have the OK to contribute code that we
> regard as precompetetive.  Parsers for things like Blast and Hmmer
> certainly fall into that category.
> 
> We'd be happy contribute this functionality to biojava (our systems
> extract essentially all the information from the output of these type of
> common bioinformatics software).  Before we release any code, however ,
> I'd like to see some feedback on the list about:
> 
> a) Do people actually want parsers for Blast, Hmmer etc?
> 
> If the answer is yes:
> 
> b) What do people want to use them for - we'd like to make them work out
> of the box for people if possible.  What we could go with pretty much
> right away (subject to finding the time to package it all up in a
> suitable form for biojava) are classes for getting all the information
> out that you can use in your own systems, and classes designed to
> produce marked up HTML etc.
> 
> It would be good to have some use cases from people out there (Jared?)
> 
> Simon
> --
> Simon M. Brocklehurst, Ph.D.
> Head of Bioinformatics
> Cambridge Antibody Technology
> The Science Park, Melbourn, Cambridgeshire, UK
> http://www.CambridgeAntibody.com/
> mailto:simon.brocklehurst@CambridgeAntibody.com