#!/usr/bin/perl -w

#This script takes a fasta file and counts the aminoacids for each protein

print STDOUT "Type fasta file\n";
$infile=<STDIN>;
chomp($infile);
open(FIN, "< $infile") or die;
while($line=<FIN>){
	if($line=~/^>/){
		$line=~/^>(\S+)/;
		$orf_id=$1;
		$line=<FIN>;
		chomp($line);
		$seq=$line;
		$hash{$orf_id}[0]=$seq;
	}
}
close(FIN);
open(FOUT, "> out_aa_freqs");
@array_orfs=sort keys %hash;
foreach $orf (@array_orfs){
	@tmp_array_seq=();
	$count_S=0;
	$count_T=0;
	$count_Y=0;
	$count_seq=0;

	@tmp_array_seq=split(//,$hash{$orf}[0]);
	$count_seq=@tmp_array_seq;
	foreach $aa (@tmp_array_seq){
		if($aa eq 'S'){
			$count_S++;
		}
		if($aa eq 'T'){
			$count_T++;
		}
                if($aa eq 'Y'){
                        $count_Y++;
                }
	}
	print FOUT "$orf\tS:$count_S\tT:$count_T\tY:$count_Y\tlength:$count_seq\n";
}
close(FOUT);