[Bioperl-l] Parsing Tabulated Blast result

[B Enn]

Hi all,

I'm new to Bioperl and trying to parse some tabulted result (-m 9 option)
generated by TBLASTX (Blast 2.2.24).

I wish to know if the top hit comes from the minus strand of the Query
sequence or not. I believe one easy way to
know it if the start_query is greater than end_query.

However I found that,while using Bio::SearchIO, the start(query) is always
reported as smaller than end(query), even if the alignment
shows it in a different manner. I'm trying to find out using
strand('query'). I think if the query sequence match
comes from the complementary strand of the sequnce supplied, it is marked as
-1. Am I doing it correctly?

I'll also be very grateful if someone can provide any pointer/link on how to
know which reading frame the TOP query match belongs
to. For that I possibly need a full BLAST report.

The code(crude) I wrote  is as follows:

use strict;
use Bio::SearchIO;
my $in = new Bio::SearchIO(-format => 'blasttable', -file   => 'test.out');

while( my $result = $in->next_result ) {
          my $hit = $result->next_hit;
        my $hsp = $hit->next_hsp;
        print $hsp->start('query')
,"\t",$hsp->end('query'),"\t",$hsp->strand('query'),"\n";
}

Thanks in advance