[Biojava-l] parse blast results

[Howard Ungar]

Jennifer,
It sounds like my Alignment object needs to be expanded to support
multiple hits.  If you can send me an example Blast report which
contains multiple hits within the same sequence I can modify the
BlastHandler and BlastReport to handle this.
Howard
--- Jennifer Pan <jpan@incellico.com> wrote:
> Hello Howard and Hello all, 
> 
> I was trying to parse a ncbi-blast results file,
> using the BlastReport Howard provided. 
> For a hit sequence that has mutiple MSPs, I could only retrieve one 
> start and one end position of one MSP within this hit sequence.  
> --------------------
> for example, I would like to see: 
> Query NM_00000
> >hit1 [1, 300]
>  hit1 [400, 600]
>  hit1 [700, 1000]
> >hit2 [1, 700]
> >hit 3 [200, 500]
> 
> and I've gotten 
> Query NM_00000
> >hit1 [400, 600]
> >hit2 [1, 700]
> >hit 3 [200, 500]
> -----------------------------------------
> 
> Any hint and help here?
> 
> many thanks
> 
> -Jennifer 
> 
> -----Original Message-----
> From: Howard Ungar [mailto:howard_ungar@yahoo.com]
> Sent: Friday, October 19, 2001 11:53 AM
> To: richard cai; biojava-l@biojava.org
> Subject: Re: [Biojava-l] parse blast results
> 
> 
> --- richard cai <cairi1@yahoo.com> wrote:
> > Thanks, Howard.  This is exactly what I need. 
> > 
> > Richard Cai
> > 
> Richard,
> There are four files in the attached zip file:
> BlastSAXParser.java - contains changes to the parser to explicitly
> create a "QueryName" attribute.
> BlastHandler.java - uses the parser to read the QueryName attribute
> BlastReport.java - prints the results.
> Alignment.java - support object to pass data between the handler and
> the report.
> 
> Let me know if you need anything else to get this working.
> 
> --- Keith James <kdj@sanger.ac.uk> wrote:
> > This stems from the fact that the DTD has undergone recent
> > modifications since Simon's group first commited their code. They
> > refined the DTD, while incorporating a couple of suggested changes,
> > one of which was adding QueryId.
> > 
> > This is why the DTD reads, for example:
> > 
> > <!ELEMENT biojava:Header (biojava:RawOutput, QueryId?, DatabaseId?
> )>
> > 
> > so that the new elements (here QueryId and DatabaseId) are not
> (yet)
> > mandatory. This avoids breaking existing code, but leaves
> extraction
> > of this information to the user (it's embedded in the
> > biojava:RawOutput element). See Javadoc in
> > org.biojava.bio.program.ssbind.BlastDBQueryHandler.
> 
> Keith,
> I think I tried to get the QueryId from the RawOutput, but the parser
> was not starting to include data until later in the Blast Report
> file. 
> I don't think my changes will fit into the current DTD as you
> described
> it.  I could modify what I did to create these attributes in the
> rawOutput element if you would like me to.  Or would it be better to
> consider modifying the DTD (and risk breaking existing code).
> Either way, please take a look at what I did and provide some
> feedback
> about how you would like me to proceed.
> 
> Howard
> 
> 
> 
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