#! /usr/bin/perl -w

#Script was written by CSR on 10.27.08
#Input = Sequences in FASTA format.
#Ouput = Sequences (fasta format) with a tag added to the header line.
#Note: Insert a tag between the ID and description, i.e. (id {tag} description). 
#Usage = ./tag_fasta_header1.0.pl -i [input filename] -o [output filename] -t [tag]

use strict;
use Bio::SeqIO;
use Getopt::Std;

my %args;
getopts('i:o:t:', \%args);
my $usage = "Warning, missing information...\nUsage is: ./tag_fasta_filename.pl -i [infile] -o [outfile] -t [tag]\n"; 
my $infile;
my $outfile;
my $tag;

#command line arguments
if ($args{i}) {
    $infile = $args{i};
} else {
    die "$usage";
}
if ($args{o}) {
    $outfile = $args{o};
} else {
    die "$usage";
}
if ($args{t}) {
    $tag = $args{t};
} else {
    die "$usage";
}

#load the input (fasta) file
my $in = Bio::SeqIO-> new(-format => 'fasta' ,
			   -file => $infile);

#open the output file
open (OUTPUT , "> $outfile") or die "COULD NOT OPEN THE OUTPUT FILE\n";

#break each fasta sequence into its parts 
while( my $seqobj = $in->next_seq ) {
    my $id = $seqobj->display_id;
    my $desc = $seqobj->description();
    my $seq = $seqobj->seq;
#add a tag
      	print OUTPUT ">$id {$tag} $desc\n";
	print OUTPUT "$seq\n\n";
    }

close (OUTPUT);