#!/usr/bin/perl

$filenameA = $ARGV[0];
$filenameB = $ARGV[1];
$filenameOut = $ARGV[2];

open $FILEA, "< $filenameA" || die "Can't open input file $filenameA.\n";
open $FILEB, "< $filenameB" || die "Can't open input file $filenameB.\n";

my $reformat_file = 'mates_file.txt';

open (OUTFILE, "> $reformat_file") || die "Can't open output file.\n";
my ($name1, $name2);
my (@names1,@names2);
while(<$FILEA>) {
        chomp;
	$name1 = $_;
	$_ = <$FILEA>;

	$name1 =~ tr/^[>]/ /;
        $name1 =~ s/^\s*//;

        @names1 = split(/ /, $name1);
	$name2 = <$FILEB>;
	$_ = <$FILEB>;
	$name2 =~ tr/^[>]/ /;
        $name2 =~ s/^\s*//;
        
        @names2 = split(/ /, $name2);
        print OUTFILE $names1[0]."\t".$names2[0]."\tlibname\n";
}

close OUTFILE;
close FILEA;
close FILEB;