[Biojava-l] Blast xml parsing

[Jose Duarte]

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.

Anybody knows what might be wrong here or how could I get around this 
problem?

Thanks in advance

Jose