[Bioperl-l] Determining strand orientation from bl2seq report

[Ewan Birney]

On Thu, 23 Jan 2003, Dave Arenillas wrote:

> I'm trying to figure out if there is any way to determine the strand
> orientation (Plus / Plus or Plus / Minus) of an HSP from the blast report
> created by running bl2seq.
>
> ex.
> my @params = ('program' => 'blastn',
>                 'outfile' => "$BlastFile");
> my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
> my $report = $factory->bl2seq($seq1, $seq2);
>
> while (my $hsp = $report->next_feature) {
> 	#
> 	# get orientation info from $hsp???
> 	#
> }
>
> Apparently Bio::Tools::BPlite::HSP objects have no methods to return this
> information. I (incorrectly) assumed that I could test
> $hsp->hit->start > $hsp->hit->end
> but start is always less than end even for Plus / Minus orientation.
>

look at $hsp->hit->strand()