#!perl
#perl "copy of findandreplaceemail2.pl" -d . -i "Reporting Devices_01-
+03-2009-09-00-00.csv" -s "Master Sched.csv" -o "Master Sched(new1).cs
+v"

use Getopt::Long;
use Text::CSV;

&GetOptions('d=s'   => \$baseDir
           ,'i=s'   => \$inFlNm
           ,'s=s'   => \$subFlNm
           ,'o=s'   => \$outFlNm
           ,'h'     => \$hlp
           ,'hlp'   => \$hlp
           ,'help'  => \$hlp);
       
$emailList = "test.csv";
$csv = Text::CSV->new();

# Save substitution data in memory indexed by manager email address
open IN1, "<"."./$baseDir/$subFlNm" or die "Can't open input file >$su
+bFlNm<\n";

open OUT, ">"."$baseDir/$outFlNm" or die "Can't open output file >$out
+FlNm<\n";

while(<IN1>){
    chomp;
    $_ =~ s/\,\,$//;
    $csv->parse($_);
    @subIn = $csv->fields();
    $subRcd{$subIn[2]} = $_;
    #print "@subIn\n";
}
close IN1;

#There's got to be a way to take all of the Master file and use it in 
+the while loop

open IN1, "<"."./$baseDir/$subFlNm" or die "Can't open input file >$su
+bFlNm<\n";

while ($in1 = <IN1>){
    chomp($in1);
    @mainFlds = split(/,/, $in1);
    $mainFlds[2] =~ s/^\s+//; $mainFlds[2] =~ s/\s+$//;
    if($in1 =~ /\d+\.\d+\.\d+\.\d+/){
        open IN2, "<"."$baseDir/$inFlNm" or die "Can't open input file
+ >$inFlNm<\n";
        while ($in2 = <IN2>){
            chomp($in2);
            @subFlds = split(/,/, $in2);
            if($in2 =~ /\d+\.\d+\.\d+\.\d+/){
                $subFlds[1] =~ s/^\s+//; $subFlds[1] =~ s/\s+$//;
                if("$mainFlds[2]" eq "$subFlds[1]" && "$mainFlds[1]" e
+q "$subFlds[0]"){
                    if($in1 =~ /,,$/ || $mainFlds[7] ne '' || $mainFld
+s[8] ne ''){
                        print OUT "$in1,$subFlds[5]\n";
                    }
                    elsif ($mainFlds[6] ne ''){
                        print OUT "$in1,,$subFlds[5]\n";
                    }
                    else {
                        print OUT "$in1,,,$subFlds[5]\n";
                    }
                }
            }
        }
        close IN2;
    }
    elsif(($mainFlds[2] eq '' || $mainFlds[3] eq '') && $mainFlds[5] n
+e '') {
        open IN2, "<"."$baseDir/$inFlNm" or die "Can't open input file
+ >$inFlNm<\n";
        while ($in2 = <IN2>){
            chomp($in2);
            @subFlds = split(/,/, $in2);
            if($subFlds[1] eq ''){
                #print ">@subFlds\n";
                $subFlds[1] =~ s/^\s+//; $subFlds[1] =~ s/\s+$//;
                if("$mainFlds[3]" eq "$subFlds[2]" && "$mainFlds[4]" e
+q "$subFlds[3]"  && "$subFlds[4]" ne ''){
                    if($in1 =~ /,,$/ || $mainFlds[7] ne '' || $mainFld
+s[8] ne ''){
                        print OUT "$in1,$subFlds[5]\n";
                    }
                    elsif ($mainFlds[6] ne ''){
                        print OUT "$in1,,$subFlds[5]\n";
                    }
                    else {
                        print OUT "$in1,,,$subFlds[5]\n";
                    }
                }
            }
        }
        close IN2;
    }
    else{
        if($in1 =~ /Date/){
            @date = split(/_/, $inFlNm);
            $date[1] =~ s/\-\d\d\-\d\d\-\d\d\.csv//;
            print OUT "$in1,$date[1]\n";
        }
        else{
            print OUT "$in1\n";
        }
    }
    next;
}
[download]

I am big fan of SQLite. If I were you I'd load each of your CVS files into SQLite relation database and deal with the data via SQL.

You seem to be loading your first csv file into a hash called %subRcd, but then you are never using that hash anywhere else in the code (it's "write-only").

Maybe you should read your second file into that same hash (assuming that the contents of both files are structured the same way, or at least that it's easy to tell them apart in terms of their contents).

When the second file has a key field that matches something in the first file, you'll need to update the hash value for that key, in order to combine the info from the two files into the one record. Apart from that, keys that occur only in the "master" will remain unmodified in the hash, and keys that occur only in the second file will be loaded and kept as-is in the hash.

Then just print out all the hash elements to get the complete union of contents from the two files.

(But I really like Plankton's idea of using SQLite -- definitely worthwhile. Also, you really should start with use strict; and use warnings; -- it will make you a better programmer, and you'll grow to appreciate it.)