use strict;

my $fasta = $ARGV[0];
my $phylip = $ARGV[1];
my $out = $ARGV[2];

my @ids;
open(F,$fasta) or die "Can not open file $fasta";
while(<F>){
	if (/>(.*)/){
		my $id = $1;
		push(@ids,$id);
	}
}
close(F);

open(O,">$out") or die "Can not open and write into file $out";
open(P,$phylip) or die "Can not open file $phylip";
my $numline = 0;
while(<P>){
	my $line = $_;
	$numline++;
	if (/^([\w\-]+)\s+/ && $numline > 1){
		my $reported_id = $1;
		print "ok"; 
		my $id = $ids[$numline-2];
		$line =~s/$reported_id/$id/g;
		print O $line;
	}
	else{
		print O $line;
	}
}
close(P);
close(O);