file1:
0, 4.38336420e+00, -2.47429684e-01, 6.79128885e+00, 1.51447906e+05
1, 4.38336420e+00, -2.78662264e-01, 6.79128885e+00, 1.58727812e+05
2, 4.38336420e+00, -2.78662264e-01, 6.69878864e+00, 1.61132406e+05
3, 4.38336420e+00, -2.47429684e-01, 6.69878864e+00, 1.54500719e+05

file2:
0, 4.38336420e+00, -2.47429684e-01, 6.79128885e+00, 3.43969625e+05
1, 4.38336420e+00, -2.47429684e-01, 6.69878864e+00, 3.29992562e+05
2, 4.38336420e+00, -2.78662264e-01, 6.69878864e+00, 3.30176656e+05
3, 4.38336420e+00, -2.78662264e-01, 6.79128885e+00, 3.42821781e+05

##</code><code>##

#!/usr/bin/perl -w

# Aufruf: test.pl file1_a file2_i fnout

use strict;
use warnings;
no warnings qw/once/;

my (@biga,@bigi);
my (%all);
my ($nr,$x,$y,$z,$p);
my ($tmp);
my ($fna,$fni,$fnout);
my (@allnr);
my ($i);
my (@header);

# Datei 1 (aussen) Datei einlesen
{ open (my $DAT,'<',$ARGV[0])  || do {print STDERR "***error*** during opening $ARGV[0]: $!\n";die;};
(@biga) = <$DAT>;
close $DAT; }
chomp @biga;

# Datei 2 (innen) Datei einlesen
{ open (my $DAT,'<',$ARGV[1])  || do {print STDERR "***error*** during opening $ARGV[1]: $!\n";die;};
(@bigi) = <$DAT>;
close $DAT; }
chomp @bigi;

# die Filenamen
$fna = $ARGV[0];
$fni = $ARGV[1];
$fnout = $ARGV[2];

# in den Hash einsortieren
foreach (@biga) {
   ($nr,$x,$y,$z,$p,undef) =  split(/,/,$_);
   $nr = &trim($nr);
   $x = &trim($x);
   $y = &trim($y);
   $z = &trim($z);
   $p = &trim($p);
   $all{$nr}{'x'} = $x;
   $all{$nr}{'y'} = $y;
   $all{$nr}{'z'} = $z;
   $all{$nr}{'pa'} = $p;
   push (@allnr,$nr);
}

# innen dazusortieren
foreach (@bigi) {
   ($nr,$x,$y,$z,$p,undef) =  split(/,/,$_);
   $nr = &trim($nr);
   $x = &trim($x);
   $y = &trim($y);
   $z = &trim($z);
   $p = &trim($p);

   for $i (0 .. $#allnr) {
      if (($all{$i}{'x'} == $x) && ($all{$i}{'y'} == $y) && ($all{$i}{'z'} == $z)) {
         $all{$i}{'pi'} = $p;
         $all{$i}{'dp'} = $all{$i}{'pa'} - $all{$i}{'pi'};
         next;
      }
   }

}

# Ausgabe schreiben
{ open (my $DAT,'>',$fnout)  || do {print STDERR "***error*** during opening $fnout: $!\n";die;};

for $i (0 .. $#allnr) {
   print $DAT "$i, $all{$i}{'x'}, $all{$i}{'y'}, $all{$i}{'z'}, $all{$i}{'dp'}\n";
}
close $DAT; }

# ################################################
# TRIM A STRING
# http://www.symablog.de/blog/perl-fuhrende-und-nachfolgende-leerzeichen-aus-einem-string-entfernen-trim/
# ################################################
sub trim {
   my $str = $_[0];
   $str =~ s/^\s+|\s+$//g;
   return $str;
}