[Bioperl-l] newbie: BLAST Parsing Question

[James Wasmuth]

Methinks you want...

$rframe = $hsp->frame;

The method is found in Bio::Search::HSP::GenericHSP so you'll need to check
in there to make sure, plus loads of other stuff you can do with the HSP.
N.B.
the frame is 0-2 instead of 1-3.

Check out the HOWTO on SearchIO, its very useful...
http://bioperl.org/HOWTOs/html/SearchIO.html

hope this helps
J


----- Original Message -----
From: "E Klee" <klee_17@hotmail.com>
To: <bioperl-l@bioperl.org>
Sent: Thursday, January 09, 2003 9:09 PM
Subject: [Bioperl-l] newbie: BLAST Parsing Question


> I am just starting to play around w/ BioPerl's Blast Parsing capability.
I
> was attempting to implement Bio::SearchIO::psiblast to open a blast output
> file and parse it.  I have had difficulty finding the proper command for
> obtaining the translation reference frame for the query sequence when
> parsing a blastx output.
>
> -E
>
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