[Bioperl-l] newbie: BLAST Parsing Question
Thu, 9 Jan 2003 21:50:13 -0000
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.
the frame is 0-2 instead of 1-3.
Check out the HOWTO on SearchIO, its very useful...
hope this helps
----- Original Message -----
From: "E Klee" <firstname.lastname@example.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.
> 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.
> Help STOP SPAM: Try the new MSN 8 and get 2 months FREE*
> Bioperl-l mailing list