[Bioperl-l] Bio::SearchIO::blast

[Brian Osborne]

Josh,

Forgive me for asking but why do you need the
Bio::Search::Result::BlastResult object? I ask because sometimes people
don't realize what can be done with the generic objects.

Brian O.


-----Original Message-----
From: bioperl-l-bounces at bioperl.org [mailto:bioperl-l-bounces at bioperl.org]On
Behalf Of Josh Lauricha
Sent: Wednesday, April 09, 2003 2:21 PM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] Bio::SearchIO::blast

I have the following code:

...
my $searchio = new Bio::SearchIO(-format => 'blast', -file => 'blast.out')
   or die "couldn't open blast.out";

print $searchio, "\n"; # print type...
while(my $result = $searchio->next_result() ) {
        print $result, "\n"; # print type
...

I need to be able to access the Bio::Search::Result::BlastResult object,
however, $searchio->next_result appears to be returning a
Bio::Search::Result::GenericResult, how can I access the additional
fields?

Also, since that gives the GenericResult, next_hit and next_hsp return
GenericHit and GenericHSP, respectivly.


Thanks
Josh Lauricha
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