This is the two field key comparison script. Here I also am trying to exclude those records that contain some binary (corrupted) data. Look for the "next unless" lines. Tell me please what you think about it. The script worked fine until I tryied to add this feature. I'm screwing it up now, since the diffs are bigger than expected. (sorry for posting this undebugged version)

#!/usr/bin/perl 
my ($prefijo, $n1, $n2)=@ARGV;
my ($endOfFile1,$endOfFile2)=(0,0);

open FILE1, "<".("0"x(8-length($n1)))."$n1"."\/$prefijo".".txt";
open FILE2, "<".("0"x(8-length($n2)))."$n2"."\/$prefijo".".txt";
open OUTPUTF1, ">$prefijo$n1"."NoEn$n2";
open OUTPUTF2, ">$prefijo$n2"."NoEn$n1";
open OUTPUTR1, ">repetidos\-$prefijo$n1"."NoEn$n2";
open OUTPUTR2, ">repetidos\-$prefijo$n2"."NoEn$n1";

my $recordf1=<FILE1> or $endOfFile1=1;
my $recordf2=<FILE2> or $endOfFile2=1;
my $key1, $key2;
my $keyDos1, $keyDos2;
my $firstpass=1;
my $prevkey1, $prevkey2;
my $prevkeyDos1, $prevkeyDos2;

while ( !$endOfFile1 && !$endOfFile2 ) {
  unless ($recordf1 =~ /^[ -\~]*\n$/) {
    $recordf1=<FILE1> or $endOfFile1=1;
    next;
  }
  unless ($recordf2 =~ /^[ -\~]*\n$/) {
    $recordf2=<FILE1> or $endOfFile2=1;
    next;
  }
  if ($recordf1=~/^ *([0-9]+)\,/) {
    $prevkey1=$key1;
    $key1=$1;
  } else {
    undef $key1;
  }

  if ($recordf2=~/^ *([0-9]+)\,/) {
    $prevkey2=$key2;
    $key2=$1;
  } else {
    undef $key2;
  }

  if ( $key1 < $key2 ) {

    if (($key1 eq $prevkey1) && !$firstpass)
      { print OUTPUTR1 $recordf1 if $key1;}
    else
      { print OUTPUTF1 $recordf1 if $key1;}

    $recordf1=<FILE1> or $endOfFile1=1;
    
  } elsif ( $key1 > $key2 ) {
  
    if (($key2 eq $prevkey2) && !$firstpass)
      { print OUTPUTR2 $recordf2 if $key2;}
    else
      { print OUTPUTF2 $recordf2 if $key2;}

    $recordf2=<FILE2> or $endOfFile2=1;

  } else {
 
    if ($recordf1=~/\, *([0-9]+)\,/) {
        $prevkeyDos1=$keyDos1;
        $keyDos1=$1;
    } else {
      undef $keyDos1;
    }

    if ($recordf2=~/\, *([0-9]+)\,/) {
        $prevkeyDos2=$keyDos2;
        $keyDos2=$1;
    } else {
      undef $keyDos2;
    }

    if ( $keyDos1 < $keyDos2 ) {
 
      if (($keyDos1 eq $prevkeyDos1) && !$firstpass)
        { print OUTPUTR1 $recordf1 if $key1;}
      else
        { print OUTPUTF1 $recordf1 if $key1;}
 
      $recordf1=<FILE1> or $endOfFile1=1;
 
    } elsif ( $keyDos1 > $keyDos2 ) {
 
      if (($keyDos2 eq $prevkeyDos2) && !$firstpass)
        { print OUTPUTR2 $recordf2 if $key2;}
      else
        { print OUTPUTF2 $recordf2 if $key2;}
 
      $recordf2=<FILE2> or $endOfFile2=1;
 
    } else {
      $recordf1=<FILE1> or $endOfFile1=1;
      $recordf2=<FILE2> or $endOfFile2=1;
    }
  }
  $firstpass=0 if ($firstpass);
}

while ( !$endOfFile1 ) {
  unless ($recordf1 =~ /^[ -\~]*\n$/) {
    $recordf1=<FILE1> or $endOfFile1=1;
    next;
  }
  if ($recordf1=~/^ *([0-9]+)\, *([0-9]+)\,/) {
    $prevkey1=$key1;
    $prevkeyDos1=$keyDos1;
    $key1=$1;
    $keyDos1=$2;
  } else {
    undef $key1;
    undef $keyDos1;
  }

  if (($key1 eq $prevkey1) && ($keyDos1 eq $prevkeyDos1) && !$firstpas
+s)
    { print OUTPUTR1 $recordf1 if $key1;}
  else
    { print OUTPUTF1 $recordf1 if $key1;}
    
  $recordf1=<FILE1> or $endOfFile1=1;
  $firstpass=0 if ($firstpass);
}

while ( !$endOfFile2 ) {
  unless ($recordf2 =~ /^[ -\~]*\n$/) {
    $recordf2=<FILE1> or $endOfFile1=1;
    next;
  }
  if ($recordf2=~/^ *([0-9]+)\, *([0-9]+)\,/) {
    $prevkey2=$key2;
    $prevkeyDos2=$keyDos2;
    $key2=$1;
    $keyDos2=$2;
  } else {
    undef $key2;
    undef $keyDos2;
  }

  if (($key2 eq $prevkey2) && ($keyDos2 eq $prevkeyDos2) && !$firstpas
+s)
    { print OUTPUTR2 $recordf2 if $key2;}
  else
    { print OUTPUTF2 $recordf2 if $key2;}
 
  $recordf2=<FILE2> or $endOfFile2=1;
  $firstpass=0 if ($firstpass);
}

close FILE1;
close FILE2;
close OUTPUTF1;
close OUTPUTF2;
close OUTPUTR1;
close OUTPUTR2;
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