#!/usr/bin/env perl

use strict;
use warnings;

my $file1 = "pm-890461-in1.txt";
my $file2 = "pm-890461-in2.txt";

open( MYFILE, '<', $file1 ) or die "cannot open $file1: $!";
open( NEWF,   '<', $file2 ) or die "cannot open $file2: $!";

my @in_values;

while ( <MYFILE> ) {
    chomp;
    my( $index, $value ) = ( split /\s+/ )[4, -1];
    # above line does same thing as next three
    # my @fields = ( split /\s+/ );
    # my $index = $fields[4];
    # my $value = $fields[-1];
    $in_values[ $index ] = $value;
}

close MYFILE;

while ( <NEWF> ) {
    chomp;
    my @fields = ( split /\s+/ );
    my $index = $fields[4];
    $fields[-1] = $in_values[ $index ];
    my $output = join "\t", @fields;
    print "$output\n";
}

close NEWF;