Using more recentish functionality of Text::CSV_XS, you get quite readable code IMHO:

use Text::CSV_XS "csv";

my $hr   = csv (
    in           => "hr.txt",
    key          => "samaccountname",
    keep_headers => \my @keys,
    );

my $aoh = csv (in => "ad.txt", bom => 1, on_in => sub {
    my $sam = $_[1]{samaccountname} or die "No name in AD";
    my $ahr = $hr->{$sam};
    unless ($ahr) {
        warn "I got AD data for $sam, not in HR\n";
        next;
        }
    my @diff = map { [ $_, $ahr->{$_}, $_[1]{$_} ] }
        grep { $ahr->{$_} ne $_[1]{$_} } @keys;
    @diff or return;
    say "Changes for samaccount $sam";
    printf "  %-22s %-27.27s -> %s\n", @$_ for @diff;
    });
[download]

with the two datafiles you provided,

$ perl test.pl
Changes for samaccount barsu991
  mail                   Uttiam.Barski@pulse.org     -> William.Barski
+@pulse.org
  title                  Director of Cooks           -> Chief of Cooks
Changes for samaccount walkl003
  givenname              Lreblemet                   -> Larry
  employeenumber         20178941                    ->
  mail                   Lreblemet.Walker@pulse.org  -> Larry.Walker@p
+ulse.org
  title                  Head Cook                   -> Cook
Changes for samaccount karss001
  givenname              Sovyetk                     -> Steven
  mail                   Sovyetk.Karsten@pulse.org   -> Steven.Karsten
+@pulse.org
  title                  Dishwasher                  -> Dishw
  physicaldeliveryoffice Kitchen of the World        -> Sully's Kitche
+n
  streetaddress          205 Willy B. Temple         -> 48720 Belcard
  st                     WI                          -> IL
  postalcode             50987                       -> 34567
Changes for samaccount zingk072
  givenname              Kovon                       -> Kevin
  employeenumber         20113578                    ->
  symphonyemployeetype   IKP                         ->
  mail                   Kovon.Zingerman@pulse.org   -> Kevin.Zingerma
+n@pulse.org
  manager                cn=manager1,ou=users,ou=Kit ->
Changes for samaccount peizs194
  givenname              Synthia                     -> Samantha
  sn                     Smite                       -> Smith
  mail                   Synthia.Peizer@pulse.org    -> Samantha.Smith
+@pulse.org
  title                  Broiler Man                 -> Man, Broiler
Changes for samaccount hutcy231
  givenname              Yello                       -> Yaren
  mail                   Yello Hutchinson            -> Yaren Hutchins
+on
Changes for samaccount haserz221
  sn                     Haserkrilk                  -> Hasermann
  employeenumber         20125471                    ->
  mail                   Zebediah.Haserkrilk@kit.org -> Zebediah.Haser
+man@pulse.org
  telephonenumber                                    -> 555-555-5555
[download]

It is up to you to mold that into a report of your liking

Update: If you want to store the changes in a CSV file, change it like this:

my @diff;
my $aoh = csv (in => "ad.txt", bom => 1, on_in => sub {
    my $sam = $_[1]{samaccountname} or die "No name in AD";
    my $ahr = $hr->{$sam}           or die "I got AD data for $sam, no
+t in HR\n";
    push @diff, map { [ $sam, $_, $ahr->{$_}, $_[1]{$_} ] }
        grep { $ahr->{$_} ne $_[1]{$_} } @keys;
    });
csv (in => \@diff, out => "diff.csv");
[download]

G'day jzelkowsz,

Here's a solution using Text::CSV (if you have Text::CSV_XS installed it will run faster) and in-memory files (see open). The input data I used is a verbatim copy of what you posted here.

#!/usr/bin/env perl

use strict;
use warnings;

use Text::CSV;

my ($hr_file, $ad_file, $com_file) = qw{hr.txt ad.txt com.txt};

my (@col_index, %hr_record_for);

my $csv = Text::CSV::->new({quote_space => 0})
    or die "Can't instantiate a Text::CSV object: ",
            Text::CSV::->error_diag();

{
    open my $mem_fh, '<', canonicalise_file_in_memory($hr_file)
        or die "Can't read in-memory file: $!";

    @col_index = @{$csv->getline($mem_fh)};

    while (my $row = $csv->getline($mem_fh)) {
        $hr_record_for{$row->[0]} = $row;
    }
}

{
    open my $mem_fh, '<', canonicalise_file_in_memory($ad_file)
        or die "Can't read in-memory file: $!";
    open my $out_fh, '>', $com_file
        or die "Can't write '$com_file': $!";
    
    (undef) = $csv->getline($mem_fh);

    while (my $row = $csv->getline($mem_fh)) {
        for my $i (1 .. $#col_index) {
            if ($hr_record_for{$row->[0]}[$i] ne $row->[$i]) {
                $csv->say($out_fh, [
                    $row->[0], $col_index[$i],
                    $hr_record_for{$row->[0]}[$i]
                ]);
            }
        }
    }
}

sub canonicalise_file_in_memory {
    my ($file) = @_;

    open my $fh, '<', $file or die "Can't read '$file': $!";

    my $canon;

    while (<$fh>) {
        chomp if /,$/;
        $canon .= $_;
    }

    return \$canon;
}
[download]

Output:

$ cat com.txt
barsu991,mail,Uttiam.Barski@pulse.org
barsu991,title,Director of Cooks
walkl003,givenname,Lreblemet
walkl003,employeenumber,20178941
walkl003,mail,Lreblemet.Walker@pulse.org
walkl003,title,Head Cook
karss001,givenname,Sovyetk
karss001,mail,Sovyetk.Karsten@pulse.org
karss001,title,Dishwasher
karss001,physicaldeliveryoffice,Kitchen of the World
karss001,streetaddress,205 Willy B. Temple
karss001,st,WI
karss001,postalcode,50987
zingk072,givenname,Kovon
zingk072,employeenumber,20113578
zingk072,symphonyemployeetype,IKP
zingk072,mail,Kovon.Zingerman@pulse.org
zingk072,manager,"cn=manager1,ou=users,ou=Kitchen,dc=Kitchen,dc=net"
hutcy231,givenname,Yello
hutcy231,mail,Yello Hutchinson
haserz221,sn,Haserkrilk
haserz221,employeenumber,20125471
haserz221,mail,Zebediah.Haserkrilk@kit.org
haserz221,telephonenumber,
[download]

Other monks have posted solutions based on Text::CSV to which I think you should pay close attention. This post is not about the OPed code per se, but about a general approach to debugging code.

Are you using warnings and strict with your code? I suspect not. If not, do so (see example code below), then fix the problems these thinking-aids reveal. These modules are useful for all Perl programmers, but especially for novice Perlers.

After being sure warnings and strict are enabled, the next thing to do is to be sure you are getting the data you think you're getting.

The statement
    ($samaccountnameAD,$givennameAD,...,$managerAD)=split(/,$/);
splits a string on a comma that is at the end of the string. The  $ in the  /,$/ regex is an end-of-string anchor; see perlre, perlretut, and perlrequick. You cannot get more than two fields from this split, but you're trying to get quite a few fields.

c:\@Work\Perl\monks>perl -wMstrict -le
"use warnings;
 use strict;
 ;;
 use Data::Dumper;
 ;;
 $_ = 'vv,WWWW,xxx,YY,zzzz,';
 ;;
 my ($v, $w, $x, $y, $z) = split(/,$/);
 print Dumper($v, $w, $x, $y, $z);
 ;;
 print qq{'$v'  '$w'  '$x'  '$y'  '$z'};
"
$VAR1 = 'vv,WWWW,xxx,YY,zzzz';
$VAR2 = '';
$VAR3 = undef;
$VAR4 = undef;
$VAR5 = undef;

Use of uninitialized value in concatenation (.) or string at -e line 1
+.
Use of uninitialized value in concatenation (.) or string at -e line 1
+.
Use of uninitialized value in concatenation (.) or string at -e line 1
+.
'vv,WWWW,xxx,YY,zzzz'  ''  ''  ''  ''
[download]

The example above uses Data::Dumper. This utility for visualizing data can be a sanity-saver. It is a core module (i.e., has been made a part of the standard Perl distribution; see corelist for getting info on core modules). I prefer Data::Dump, but it is not core.

This post addresses just one, small aspect of debugging; there are many more. Good luck.

To get the data in what I believe is the way it is probably presented, I removed the newline immediately following a comma. That way, the entire employee record is on one line. I did not parse the file using Text::CSV as I probably should've. Your data is as follows:

HR data

samaccountname,givenname,sn,initials,employeenumber,symphonyemployeety
+pe,mail,title,department,company,l,physicaldeliveryoffice,streetaddre
+ss,st,postalcode,telephonenumber,manager
barsu991,Uttiam,Barski,K,20114598,IKP,Uttiam.Barski@pulse.org,Director
+ of Cooks,Day Kitchen,MILIFO,Alpena,Kitchen of the World,400 Baker,WI
+,50987,555-555-5555,"cn=manager1,ou=users,ou=Kitchen,dc=Kitchen,dc=ne
+t"
walkl003,Lreblemet,Walker,J,20178941,IKP,Lreblemet.Walker@pulse.org,He
+ad Cook,Day Kitchen,MILIFO,Alpena,Kitchen of the World,400 Baker,WI,5
+0987,555-555-5551,"cn=manager1,ou=users,ou=Kitchen,dc=Kitchen,dc=net"
karss001,Sovyetk,Karsten,Y,20146598,IKP,Sovyetk.Karsten@pulse.org,Dish
+washer,Day Kitchen,MILIFO,Alpena,Kitchen of the World,205 Willy B. Te
+mple,WI,50987,,"cn=manager1,ou=users,ou=Kitchen,dc=Kitchen,dc=net"
zingk072,Kovon,Zingerman,K,20113578,IKP,Kovon.Zingerman@pulse.org,Bake
+r,Day Kitchen,MILIFO,Alpena,Kitchen of the World,205 Willy B. Temple,
+WI,50987,,"cn=manager1,ou=users,ou=Kitchen,dc=Kitchen,dc=net"
peizs194,Synthia,Smite,B,20134743,IKP,Synthia.Peizer@pulse.org,Broiler
+ Man,Day Kitchen,MILIFO,Alpena,Kitchen of the World,205 Willy B. Temp
+le,WI,50987,,"cn=manager1,ou=users,ou=Kitchen,dc=Kitchen,dc=net"
hutcy231,Yello,Hutchinson,W,20145712,IKP,Yello Hutchinson,@pulse.org,B
+ottle Washer,Day Kitchen,MILIFO,Alpena,Kitchen of the World,400 Baker
+,WI,50987,,"cn=manager1,ou=users,ou=Kitchen,dc=Kitchen,dc=net"
haserz221,Zebediah,Haserkrilk,L,20125471,IKP,Zebediah.Haserkrilk@kit.o
+rg,Purchaser,Day Kitchen,MILIFO,Alpena,Kitchen of the World,400 Baker
+,WI,50987,,"cn=manager1,ou=users,ou=Kitchen,dc=Kitchen,dc=net"
[download]

samaccountname,givenname,sn,initials,employeenumber,symphonyemployeety
+pe,mail,title,department,company,l,physicaldeliveryoffice,streetaddre
+ss,st,postalcode,telephonenumber,manager
barsu991,Uttiam,Barski,K,20114598,IKP,William.Barski@pulse.org,Chief o
+f Cooks,Day Kitchen,MILIFO,Alpena,Kitchen of the World,400 Baker,WI,5
+0987,555-555-5555,"cn=manager1,ou=users,ou=Kitchen,dc=Kitchen,dc=net"
walkl003,Larry,Walker,J,,IKP,Larry.Walker@pulse.org,Cook,Day Kitchen,M
+ILIFO,Alpena,Kitchen of the World,400 Baker,WI,50987,555-555-5551,"cn
+=manager1,ou=users,ou=Kitchen,dc=Kitchen,dc=net"
karss001,Steven,Karsten,Y,20146598,IKP,Steven.Karsten@pulse.org,Dishw,
+Day Kitchen,MILIFO,Alpena,Sully's Kitchen,48720 Belcard,IL,34567,,"cn
+=manager1,ou=users,ou=Kitchen,dc=Kitchen,dc=net"
zingk072,Kevin,Zingerman,K,,,Kevin.Zingerman@pulse.org,Baker,Day Kitch
+en,MILIFO,Alpena,Kitchen of the World,205 Willy B. Temple,WI,50987,,p
+eizs194,Samantha,Smith,B,20134743,IKP,Samantha.Smith@pulse.org,"Man, 
+Broiler",Day Kitchen,MILIFO,Alpena,Kitchen of the World,205 Willy B. 
+Temple,WI,50987,,"cn=manager1,ou=users,ou=Kitchen,dc=Kitchen,dc=net"
hutcy231,Yaren,Hutchinson,W,20145712,IKP,Yaren Hutchinson,@pulse.org,B
+ottle Washer,Day Kitchen,MILIFO,Alpena,Kitchen of the World,400 Baker
+,WI,50987,,"cn=manager1,ou=users,ou=Kitchen,dc=Kitchen,dc=net"
haserz221,Zebediah,Hasermann,L,,IKP,Zebediah.Haserman@pulse.org,Purcha
+ser,Day Kitchen,MILIFO,Alpena,Kitchen of the World,400 Baker,WI,50987
+,555-555-5555,"cn=manager1,ou=users,ou=Kitchen,dc=Kitchen,dc=net"
[download]

#!/usr/bin/perl
use strict;
use warnings;

my $hr_file = 'HR.txt';
open my $fh, '<', $hr_file or die $!;

my (undef, @hdr_hr) = split /,/, <$fh>;
chomp @hdr_hr;

my %hr_data;
while (<$fh>) {
    chomp;
    my ($id, @rest) = split /,/;
    @{ $hr_data{$id} }{@hdr_hr} = @rest;
}
close $fh or die $!;

my $ad_file = 'AD.txt';
open $fh, '<', $ad_file or die $!;

my (undef, @hdr_ad) = split /,/, <$fh>;
chomp @hdr_ad;

@hdr_ad ~~ @hdr_hr or die "Uncompatible headers between HR and AD file
+s\n";

my %ad_data;
while (<$fh>) {
    chomp;
    my ($id, @rest) = split /,/;
    @{ $ad_data{$id} }{@hdr_ad} = @rest;
}
close $fh or die $!;

for my $id (sort keys %hr_data) {
    next unless exists $ad_data{$id};
    for my $hdr (@hdr_hr) {
        my $description_hr = $hr_data{$id}{$hdr};
        my $description_ad = $ad_data{$id}{$hdr};
        print "$id,$hdr,$description_hr\n"
            unless $description_hr eq $description_ad;
    }
}
[download]

barsu991,mail,Uttiam.Barski@pulse.org
barsu991,title,Director of Cooks
haserz221,sn,Haserkrilk
haserz221,employeenumber,20125471
haserz221,mail,Zebediah.Haserkrilk@kit.org
haserz221,telephonenumber,
hutcy231,givenname,Yello
hutcy231,mail,Yello Hutchinson
karss001,givenname,Sovyetk
karss001,mail,Sovyetk.Karsten@pulse.org
karss001,title,Dishwasher
karss001,physicaldeliveryoffice,Kitchen of the World
karss001,streetaddress,205 Willy B. Temple
karss001,st,WI
karss001,postalcode,50987
walkl003,givenname,Lreblemet
walkl003,employeenumber,20178941
walkl003,mail,Lreblemet.Walker@pulse.org
walkl003,title,Head Cook
zingk072,givenname,Kovon
zingk072,employeenumber,20113578
zingk072,symphonyemployeetype,IKP
zingk072,mail,Kovon.Zingerman@pulse.org
zingk072,manager,"cn=manager1
[download]

@hdr_ad ~~ @hdr_hr or die "Uncompatible headers between HR and AD files\n";

The  ~~ smartmatch operator is discouraged from use in production code. | not encouraged for use in production code because it is "experimental." See Terminology in perlpolicy.

---

Give a man a fish:  <%-{-{-{-<