[Bioperl-l] BIO::SearchIO HOWTO mistake?

[Anders Stegmann]

Hi! 
 
According to the Bio::SearchIO HOWTO this, 
 
$hsp->seq_inds('hit', 'conserved'); 
 
should fetch ONLY the conserved residues in an alignment (not those
identical). 
 
When I use: 
 
sub subject_seq_alignment_conserved_residues { 
 
my ($hsp_obj) = @_; 
my %subject_conserved_hash = (); 
 
my @subject_string = split , $$hsp_obj->hit_string; 
 
foreach ($$hsp_obj->seq_inds('hit', 'conserved')) { 
 
$subject_conserved_hash{$_} = $subject_string[$_ -1]; 
 
} 
 
return %subject_conserved_hash; 
 
} 
 
 
 
I get all residues in the alignment inclusive those that are identical! 
 
What's wrong? 
 
If the Bio::SearchIO HOWTO is wrong about this, is there an easy way to
fetch only the conserved residues? 
 
Anders.