Hi ,

I am a new bioperl user. I made a script to count the nucleotide composition in each column of the alignment. I am able to get the count for the nucleotides, but slice doesn't allow the count of gaps as it seems to exclude them. I would greatly appreciate any suggestions to solve this.

#!/bin/perl -w
use strict;
use warnings;

use List::Util 'max';
use Bio::SimpleAlign; 
use Bio::Align::AlignI;
use Bio::AlignIO;
use Bio::SeqIO;

my $in= Bio::AlignIO->new( -file => "seq.fst", -format => "fasta");

my $align = $in->next_aln();

print "column\tA's\tT'st\C's\tG's\n";

for (my $i = 1; $i <= $align->length; $i++) {
    my %count;
    my $seqs = $align->slice($i,$i);
    my $gap_char = $seqs->gap_char();       
    my $count_A=0;
    my $count_C=0;
    my $count_T=0;
    my $count_G=0;
    my $count_N=0;
    my $count_gap=0;
    foreach my $seq ($seqs->each_seq) {
        my $col=$seq->seq;
        if ($col eq 'A') {
            $count_A++;
        } elsif ($col eq 'C'){
            $count_C++;
        } elsif ($col eq 'T'){
            $count_T++;
        } elsif ($col eq 'G'){
            $count_G++;
        } elsif ( $col eq 'N'){
            $count_N++;
        } elsif ($col =~ m/^\Q$gap_char\E$/){
            $count_gap++;
        }
        $count{$seq->seq} += 1;
    }
    print"$i\t$count_A\t$count_T\t$count_C\t$count_G\n";
}

I get a warning like this: MSG: Slice [5-5] of sequence [3/1-6] contains no residues. Sequence excluded from the new alignment". and doesn't seem to count the gaps in the column.