note
Cristoforo
Here is a solution to counting the letters taken from the [http://www.bioperl.org/wiki/Main_Page|BioPerl] webpage, the 'HOWTO:Beginners' link on the opening page, then link 17 - (Obtaining basic sequence statistics). That led to the docs on [mod://Bio::Tools::SeqStats].
<p>
<c>#!/usr/bin/perl
use strict;
use warnings;
use Bio::SeqIO;
use Bio::Tools::SeqStats;
my @prot = qw/ A C D E F G H I K L M N P Q R S T V W Y /;
my $outputfile = "countaa";
open my $OUT, ">", $outputfile
or die "Can't open file \"$outputfile\" to write to $!\n\n";
my $proteinio=Bio::SeqIO->new (-file=>"ec 1.1.1.fasta",-format=>'fasta');
while(my $seq = $proteinio->next_seq() ) {
my $seq_stats = Bio::Tools::SeqStats->new(-seq => $seq);
my $count = $seq_stats->count_monomers();
print $OUT join(' ', map {$_ || 0} @$count{ @prot }), "\n";
}
close $OUT or die $!;
</c>
<p> Hope this is of some help,
<p>Chris
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