[Biojava-dev] Should I write a new blast parser?

[mark.schreiber at group.novartis.com]

You may find this tutorial of interest if you do make a custom parser. 
Usually you don't need to completely reinvent the wheel. You can probably 
get away with making your own SearchContentHandler and leaving the rest as 
is.

http://www.biojava.org/docs/bj_in_anger/blastecho.htm





"Ji Xuwo" <jixw at mail.cbi.pku.edu.cn>
Sent by: biojava-dev-bounces at portal.open-bio.org
12/13/2004 08:53 PM

 
        To:     <biojava-dev at biojava.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-dev] Should I write a new blast parser?


Hi everyone,

I have ran blastp and planned to parse the result and to extract those hit
sequences' stretches, which are accurately identical to some stretches of
the query sequence. In other words, I need those hsp without any gap or
substitution.

I search the tutorial and API documents. It seemed that I need to write a
new parser for my task,isn't it? I hope to confirm this point. If I should
write this parser, I hope anyone give some suggestion, such as how to make
new parser general and what I can study from the current
"BlastLikeSAXParser". Any suggestion will be appreciated. Thanks in 
advance.
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