[Biojava-dev] blast parser

Michael Gang michaelgang at gmail.com
Sun Dec 16 14:53:14 UTC 2007


Dear All,

I have a problem when running the blast parser example from the
cookbook (http://www.biojava.org/wiki/BioJava:CookBook:Blast:Parser)
with my custom blast I get the following error.
org.xml.sax.SAXException: Program ncbi-blastp Version 2.2.16 is not
supported by the biojava blast-like parsing framework
	at org.biojava.bio.program.sax.BlastLikeSAXParser.interpret(BlastLikeSAXParser.java:241)
	at org.biojava.bio.program.sax.BlastLikeSAXParser.parse(BlastLikeSAXParser.java:160)
	at parse.BlastParser.main(BlastParser.java:44)

Does it mean that I just can use the parser for older versions of blast ?

Furthermore, as I understand the parser first parses all the blast
queries and then I can iterate on the results.
Is there a blast parser available where it parses every time just the
next hit (this would save lots of memory).

I searched in google and in the biojava wiki and did not find answers
on these questions.

Can you please help me in this topic ?

Best regards,
Michael



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