use strict;
use warnings;

my @filenames = @ARGV;
my @output;
my (@headers_seqs, %head_seqs, %header_pairs, $destination);

open(IN1, '<', $filenames[0]) or die "Can't read from multifasta file with alternating lines of headers and sequences $_: $! \n";
open(IN2, '<', $filenames[1]) or die "Can't read from tab-delimited header replacement file $_: $! \n";

while(<IN1>){
chomp;
if ($_=~ m/\>/)								#looks for match to the '>' character
	{
	my $header = $_;
#	print $header, "\n";
	$header =~ s/\>//;
	push @headers_seqs, $header;	
#	print "header:", "\t", $header, "\n";
	}
elsif ($_!~ m/\>/)								#looks for match to the '>' character
	{
	my $seq = $_;
#	print "seq:", "\t", $seq, "\n";
	push @headers_seqs, $seq;	
	}
}

print $#headers_seqs, "\n";
%head_seqs = @headers_seqs;


###########################***********************----------------------------------------***********************###########################

my @head_orig_new;

while(<IN2>){
chomp;

my @line_splits = split('\s+',$_);

#print "@line_splits", "\n";
my $orig_header = $line_splits[0];
#print $orig_header, "\n";
my $new_header = $line_splits[1]; 
#print $new_header, "\n";

push @head_orig_new, $orig_header;
push @head_orig_new, $new_header;

}


#print $#head_orig_new, "\n";
%header_pairs = @head_orig_new;

###########################***********************----------------------------------------***********************###########################

foreach(keys %head_seqs)
{
push @output, '>', $header_pairs{$_}, "\n";
push @output, $head_seqs{$_},"\n";
}

###########################***********************----------------------------------------***********************###########################	
	
$destination = $filenames[0].'_headers-replaced.fasta';

open (OUT, '>', $destination) or die "Can't write to file $destination: $!\n";	
print OUT @output;
close IN1;
close IN2;
close OUT;