[Bioperl-l] seq_inds with the conserved argument prints all residues

[Anders Stegmann]

Bioperl,

I am trying to print out the positions of the residues that are conserved between the two proteins I am blasting against each other.

This subrutine prints out all residue positions in the query seq that are conserved and identical?? between the compared seq's:


sub query_seq_alignment_conserved_residues {		

	my ($hsp_obj) = @_;
	
	my @query_string = split "", $$hsp_obj->query_string;

	print "protein conserved positions in query sequence are:","\n";

	foreach ($$hsp_obj->seq_inds('query', 'conserved')) {

		print $_, "\n";

		#push my @conserved, $query_string[$_ -1];

	}

}	


According to Bio::Search HOWTO, it should only print out i.e. a S->A substitution position.

As the following subrutine works, it should not be the subrutine code that is wrong:

sub query_seq_alignment_nomatch_residues {		

	my ($hsp_obj) = @_;
	
	my @query_string = split "", $$hsp_obj->query_string;

	print "protein mismatch positions i query seq are:","\n";

	foreach ($$hsp_obj->seq_inds('query', 'nomatch')) {

		print $_, "\n";

		#push my @nomatch, $query_string[$_ -1];

	}

}	

It prints out the one nomatch position I have made in the seq. As you can see, the query_seq_alignment_conserved_residues subrutine is a copy of the query_seq_alignment_nomatch_residues with a few modifications. 

What's wrong?

Regards Anders.