[Biojava-l] blast parsing and empty hits

Simon Brocklehurst simon.brocklehurst@CambridgeAntibody.com
Thu, 03 Oct 2002 16:41:33 +0100

Doug Rusch wrote:
> Hi all,
> I am relatively new to the biojava community and I had a question about the blast parser in biojava. While looking at the code and judging from its behavior, the blast parser has no way to deal with empty blast reports (where no hit was found). My questions are : Am I missing something obvious? If not, are people really using this blast parser? If so, how do you handle this behavior? If not, what do people actually use to parse blast output?


Can you be a bit more specific e.g. say what you're trying to do, what
behaviour you're observing by using which classes, which version of
Blast (NCBI Blast, Wu Blast, program version numbers) you're using.

The parser is not designed to do anything interesting with empty blast
reports - what would you *like* to be able to do with them?

Simon M. Brocklehurst, Ph.D.
Director of Informatics & Robotics
Cambridge Antibody Technology
The Science Park, Melbourn, Cambridgeshire, UK