[Bioperl-l] drawing correct orientations of subject strands

[Rob Edwards]

<snip>

>     my $strand;
>   while( my $hit = $result->next_hit ) {
>     next unless $hit->significance < $eval;
>     $i++;
>     my $feature = Bio::SeqFeature::Generic->new(-score     =>
> $hit->raw_score,
>                                                 -display_name => 
> $hit->name,
>                                                 -strand       => 
> $strand,
>

It looks like at this point $strand is not set to anything. Shouldn't 
you move the while (my $hsp = $hit->next_hsp){ loop above setting 
-strand?

Rob




>                                                 -tag     => {
>                                                              
> description
> =>
> $hit->description
>                                                             },
>                                                );
>     while( my $hsp = $hit->next_hsp ) {
>       $strand=$hsp->sbjct->strand;
>       print "strand is $strand";
>       $feature->add_sub_SeqFeature($hsp,'EXPAND');
>     }
>
>