[Bioperl-l] How can I acess the alignmet score of the axt file?

Albert Vilella avilella at gmail.com
Mon Jul 25 11:06:53 EDT 2005

El dl 25 de 07 del 2005 a les 10:20 -0300, en/na Alynne Chiromatzo va
> Hi! I'm working with axt files. I need to know how can I acess the
> aligment score from the axt file. I've tried to use the
> $hsp->raw_score but it isn't worked. Anyone can help me?

looking at bioperl-live/t/SearchIO.t it seems that raw_score is for a
$hit, whereas the method for $hsp would be "score":

while( my $hit = $r->next_hit ) {
    my $d = shift @dcompare;
    ok($hit->name, shift @$d);
    ok($hit->length, shift @$d);
    ok($hit->raw_score, shift @$d);
    ok($hit->significance, shift @$d);
    my $hsp = $hit->next_hsp;

so maybe $hsp->score?

Hope it helps,


> Thanks.
> Alynne Oya.
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