I have worked with Text::CSV in the past. I have only slight issue with it, which I am not sure if I am not getting how to use it correctly. Here is the following code:

my $csv = Text::CSV->new();

open (CSV,"<", "Merged_CSVfiles.csv") || die "File not found\n"; 

    while (<CSV>) {            # While Loop Open Bracket

        next if ($. == 1);
        
        if ($csv->parse($_)) {        #If Open Bracket
        
            my @columns = $csv->fields();
                
                #__ Assigning $columns[0]-$columns[26] to variables
                

                    
                    my @Sample_Ids_m = $columns[16];
                    print ($Sample_Ids_m[0]);        
                    
    
        } else {                    # If Closed Bracket
                                            # Else Open Bracket
        
            my $err = $csv-> error_input; 
            print "Failed to parse line: $err";
            
            close CSV;

        } # Closed Else Bracket
    }#Closed While Loop Bracket
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All the ID are loaded into the first element of the array @Sample_Ids_m. This would be a problem but arrays can be different lengths and there are no rules current for constructing Sample ID numbers. It is a random sort of thing.

If there was some uniformity I could use the substr function and a for loop and extract our individual id's but I dont seem to be able too. I will play around with it for a bit more

The script below is based upon the Text::CSV documentation:

use Modern::Perl;
use Text::CSV;

my @Sample_Ids_m;
my $csv = Text::CSV->new( { binary => 1 } )    # should set binary att
+ribute.
  or die "Cannot use CSV: " . Text::CSV->error_diag();


while ( my $row = $csv->getline(*DATA) ) {
    push @Sample_Ids_m, $row->[6];            # Element 6 is the ID
}

say for @Sample_Ids_m;                         # Print the collected I
+Ds

__DATA__
John Doe,G building,05-Aug-2012,08-Aug-2012,"New York City, NY",ABC234
+5,UCD23467, 
John Moe,H building,05-Aug-2012,08-Aug-2012,New York City,DEF2345,UCD8
+0645,
John Slo,I building,05-Aug-2012,08-Aug-2012,New York City,GHI2345,UCD7
+6765,
John Hor,j building,05-Aug-2012,08-Aug-2012,New York City,JKL2345,UCD8
+7111,
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Output:

UCD23467
UCD80645
UCD76765
UCD87111
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Adapted for your csv file (untested):

use Modern::Perl;
use Text::CSV;

my @Sample_Ids_m;
my $csv = Text::CSV->new( { binary => 1 } )    # should set binary att
+ribute.
  or die "Cannot use CSV: " . Text::CSV->error_diag();

open my $fh, "<", "Merged_CSVfiles.csv" or die "Merged_CSVfiles.csv: $
+!";
while ( my $row = $csv->getline($fh) ) {

    push @Sample_Ids_m, $row->[16];            # Element 16 is the ID
}
$csv->eof or $csv->error_diag();
close $fh;

say for @Sample_Ids_m;                         # Print the collected I
+Ds
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From your code above, it looks like the ID is the 16th element in @columns, and the $row->[16] notation grabs it after parsing a csv line. See if this may assist your scripting...

Thanks again Kenosis and thanks to everyone who replied. I was able to fix my program finally. I made a lot of modifications from my original program. Using the CSV module was a much better strategy for getting out the total number of sample_ids. I did find it very helpful to go back and check that all my arrays and hashes were storing what they in fact were storing.Thanks again for all your suggestion

I made a hash table with the sample_Id as keys and the line of text from the Merged_File with the sample id as a value. I used dumpvalue to display my hash contents and used a hash slice to print out the specific values I needed. Thanks to everyone dave

use Dumpvalue;


%id_lookup_table = map { ($Merged_Ids[$_], $merged_array[$_]) } 0..$#M
+erged_Ids;

    my $dumper = Dumpvalue -> new;        
    $dumper -> dumpValue(\%id_lookup_table);

        open(ERRORREPORT,"+<","reported_list.csv") or die "reported_li
+st.csv: $!";    
            print ERRORREPORT @id_lookup_table{(@sample_ids)};
        close ERRORREPORT;

'UCD12-00242-P' => "\"Joe Schmie\",ABD032,12-Feb-12,23-Feb-12,\"Whale 
+Tail Island, Fictitious Place\",USA,California,etc
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