#!perl -w
use strict;
use Carp;
# $Id: aacomp.PLS,v 1.5 2006/07/04 22:23:29 mauricio Exp $
use Bio::SeqIO;
use Getopt::Long;
use Bio::SeqUtils;
use Bio::Tools::IUPAC;
my $table = new Bio::SeqUtils;
my @BASES = $table->valid_aa(0);
my %all = $table->valid_aa(2);
my ($file,$format,$help) = ( undef, 'fasta');
GetOptions(
           'i|in:s'  => \$file,
           'f|format:s' => \$format,
           'h|help|?'  => \$help,
           );
my $USAGE = "usage: aacomp [-f format] filename\n\tdefault format is fasta\n";
$file = shift unless $file;
die $USAGE if $help;
my $seqin;
if( defined $file ) {
    print "Could not open file [$file]\n$USAGE" and exit unless -e $file;
    $seqin = new Bio::SeqIO(-format => $format,
                            -file   => $file);
} else {
    $seqin = new Bio::SeqIO(-format => $format,
                            -fh     => \*STDIN);
}
my %composition;
my $total;
foreach my $base ( @BASES ) {
    $composition{$base} = 0;
}
while ( my $seq = $seqin->next_seq ) {
    if( $seq->alphabet ne 'protein' ) {
        confess("Must only provide amino acid sequences to aacomp...skipping this seq");
        next;
    }
    foreach my $base ( split(//,$seq->seq()) ) {
        $composition{uc $base}++;
        $total++;
    }
}
printf("%d aa\n",$total); 
printf("%5s %4s\n", 'aa', '#' );
my $ct = 0;
foreach my $base ( @BASES ) {
    printf(" %s %s %3d\n", $base, $all{$base}, $composition{$base} );
    $ct += $composition{$base};
}
printf( "%6s %s\n", '','-'x5);
printf( "%6s %3d\n", '',$ct);
__END__
=head1 NAME
aacomp - amino acid composition of protein sequences
=head1 SYNOPSIS
  aacomp [-f/--format FORMAT] [-h/--help] filename
  or
  aacomp [-f/--format FORMAT] < filename
  or
  aacomp [-f/--format FORMAT] -i filename
=head1 DESCRIPTION
This scripts prints out the count of amino acids over all protein
sequences from the input file.
=head1 OPTIONS
The default sequence format is fasta.
The sequence input can be provided using any of the three methods:
=over 3
=item unnamed argument
  aacomp filename
=item named argument
  aacomp -i filename
=item standard input
  aacomp < filename
=back
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
  http://bugzilla.open-bio.org/
=head1 AUTHOR - Jason Stajich
Email jason@bioperl.org
=head1 HISTORY
Based on aacomp.c from an old version of EMBOSS
=cut