How about this? 

#!/usr/bin/perl

use strict;

my $file1 = <<END_FILE2;
334  138  34  39 -  TAT_02  PAS_1 id_nu2  new2
545  154  83  11 +  TAT_03  PAS_2 id_nu3  new3
765  131  21  12 -  TAT_05  PAS_3 id_nu5  new5
END_FILE2

my %hash;
open my $myfile, '<', \$file1 or die "cannot open file";
while (<$myfile>) {
    my (@lines) = split;
    $hash{$lines[5]} = [@lines];
}

while (<DATA>) {
    my (@lines) = split;
    if ( defined( $hash{$lines[5]} ) &&
      $hash{$lines[5]}->[5] eq $lines[5] ) {
        print join "  ", @{ $hash{$lines[5]} } , "\n";
    }
    else {
        print;
    }
}

__DATA__
234  13  4  49 +  TAT_01  id_nu1  explan1
236  123  3  67 +  TAT_02  id_nu2  explan2
534  12  8  13 +  TAT_03  id_nu3  explan3
764  124  9  33 +  TAT_04  id_nu4  explan4
224  153  2  37 +  TAT_05  id_nu5  explan5

[download]

In reply to Re: combining two files based on missing values by bichonfrise74
in thread combining two files based on missing values by sugar

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