IIY86TY04J1FRV,IIY86TY04IIJKA,IIY86TY04JGLTI
IIY86TY04JH3LU
IIY86TY04I9BQV,IIY86TY04JEKGS,IIY86TY04JWBSL,IIY86TY04JUIVK
IIY86TY04JUW5G,IIY86TY04JAWV0


##</code><code>##

IIY86TY04J1FRV_HG1
IIY86TY04IIJKA_HG3
IIY86TY04JGLTI_HG4
IIY86TY04JH3LU_HG1
IIY86TY04I9BQV_crop4
IIY86TY04JEKGS_HG1
IIY86TY04JWBSL_HG4
IIY86TY04JUIVK_HG4
IIY86TY04JUW5G_HG2
IIY86TY04JAWV0_HG3


##</code><code>##

IIY86TY04J1FRV_HG1,IIY86TY04IIJKA_HG3,IIY86TY04JGLTI_HG4
IIY86TY04JH3LU_HG1
IIY86TY04I9BQV_crop4,IIY86TY04JEKGS_HG1,IIY86TY04JWBSL_HG4,IIY86TY04JUIVK_HG4
IIY86TY04JUW5G_HG2,IIY86TY04JAWV0_HG3


##</code><code>##

#!/usr/local/bin/perl

	use warnings;
	use strict;

	my $f1 = '1.txt'; # set up files 1 through 3
	my $f2 = '2.txt';
	my $f3 = '3.txt'; 

	my (@strings, $text);

	open (FH, $f1) || die;  # open file 1 in a file handle
	chomp(@strings = <FH>); # take off the line breaks

	open (FH, $f2) || die; # open file 2 in a file handle
	$text = join '', <FH>; # joins files 1 and 2? - I don't think I want to do this...
	$text =~ s/\Q$_\E/$f3/g for @strings; # this is the problem spot, I think...


	open (FH, ">$f3") || die;
	print FH $text;
	close FH;

##</code><code>##

IIY86TY04J1FRV_HG1
IIY86TY04IIJKA_HG3
IIY86TY04JGLTI_HG4
3.txt_HG1
IIY86TY04I9BQV_crop4
IIY86TY04JEKGS_HG1
IIY86TY04JWBSL_HG4
IIY86TY04JUIVK_HG4
IIY86TY04JUW5G_HG2
IIY86TY04JAWV0_HG3


##</code><code>##


  use warnings;
  use strict;

  my $f1 = '1.txt'; # file that needs the treatments added on
  my $f2 = '2.txt'; # file that has all of the treatments and an underscore 
  my $f3 = '3.txt'; # output file

  my %ids;
  my $fh;

  open $fh, '<', $f2 or die;
  while (<$fh>) {
      chomp;
      my ($name, $id) = split /_/;
      $ids{$name} = $id;
  }
  close $fh;

  open my $fho, '>', $f3 or die;
  open $fh, '<', $f1 or die;

  while (<$fh>) {
      chomp;
      my @names = split /,/;
      foreach my $name (@names) {
          $name = $name . '_' . $ids{$name};
      }
      my $line = join(',', @names);
      print $fho $line, "\n";
  }

  close $fh;
  close $fho;