[Biojava-l] Blast xml parsing

[bėgantis debesis]

Hi,

I think BlastLikeSAXParser is a parser for ordinary (non XML) blast output
files. It can not recognize xml's.

BlastXMLParserFacade is for XML parsing.

Another question:
does biojava has any support for psi-blast result parsing?

Thanks,
Valdemaras Repšys

On 6/19/06, Jose Duarte <duarte at molgen.mpg.de> wrote:
>
> Jose Duarte wrote:
>
> >mark.schreiber at novartis.com wrote:
> >
> >
> >
> >>Hi -=
> >>
> >>I'm not sure where the percent identity gets sent but you can find out
> by
> >>using the example code
> >>(http://biojava.org/wiki/BioJava:CookBook:Blast:Echo).
> >>
> >>It is also a nice code base for making a custom blast parser that is not
> >>so object heavy.
> >>
> >>
> >Thanks, that sounds good. However I have tried to run the BlastEcho.java
> >code and got following error:
> >
> >Exception in thread "main" org.xml.sax.SAXException: Could not recognise
> >the format of this file as one supported by the framework.
> >    at
> >org.biojava.bio.program.sax.BlastLikeSAXParser.parse(
> BlastLikeSAXParser.java:182)
> >    at BlastEcho.echo(BlastEcho.java:29)
> >    at BlastEcho.main(BlastEcho.java:75)
> >
> >I am pretty sure that my xml file is well formated blast output.
> >Actually I've been parsing it already with code using biojava's
> >BlastXMLParser without problems. My blast version is blastp 2.2.10.
> >
> >Also this is happening despite BlastEcho calling the setModeLazy()
> >method of the parser object. As I understand it shouldn't be checking
> >for versions using this mode.
> >
> >
>
> I think I can answer my question now. I just found out that for some
> reason replacing line 17 in BlastEcho.java:
>
>     BlastLikeSAXParser parser = new BlastLikeSAXParser();
>
> for:
>
>     BlastXMLParserFacade parser = new BlastXMLParserFacade();
>
> it all works fine.
>
> I have no idea what's the difference between the BlastLikeSAXParser and
> the BlastXMLParserFacade classes but it looks as it works as good. I can
> change the code in the wiki if somebody can confirm this is correct.
>
> Cheers
>
> Jose
>
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