[Bioperl-l] SearchIO , blastn and blastx

David Vilanova danova@urbanet.ch
Wed, 3 Apr 2002 23:57:43 +0200


Hello ,
I've been trying to use SearchIO but I'm getting some problem while
parsing.

I don't reach to retrieve the Frame from a blastn report ???? 
I use $hsp->frame but doesn't return the correct value.

My script launches a blastn using standalone blast from ncbi (2.2.2). I
use read_method = "blast" to parse with BLAST instead of Bplite.
Afterwards I loop each hit and for each hit I loop through every hsp.
Can someone explain how to retrieve the frame or the strand with
SearchIO after running a blastn?

Also ,the strange thing is that $hsp->frame  returns the correct value
if I parse  a blastx report with the same script (just by changing the
database and the program). 
Thanks.

Ps: I can post my script if helps?

David Vilanova