#!/usr/bin/perl -w
use strict;
use Data::Dumper;

# this is a way to specify short files within a Perl
# program.

my $uniprot = 
"Q6GZX4 ORFNames=FV3-001R ;PF04947
Q6GZX3 ORFNames=FV3-002L ;PF03003
Q197F8 ORFNames=IIV3-002R 
Q197F7 ORFNames=IIV3-003L 
Q6GZX2 ORFNames=FV3-003R 
Q6GZX1 ORFNames=FV3-004R 
Q197F5 ORFNames=IIV3-005L 
";

my $Activator = 
"Q6GZX4 | PF04947.9
Q96355 | PF01486.12 PF00319.13
Q96356 | PF01486.12 PF00319.13
Q39371 | PF01486.12 PF00319.13
";

my $anti_oxidant =
"0EYG3 | PF10262.4
E7QVU5 | PF10417.4 PF00578.16
D1JAS4 | PF10417.4 PF00578.16
";

my $toxin = 
"C7T183 | PF02950.12
C7T1P5 | PF02950.12
E2E4E4 | PF00918.12
A2PU44 | PF01375.12
";

# Open the input "files"
# A Perl scalar can be opened for reading
# and this how to do it...

open (my $UNIPROT_IN,   '<',  \$uniprot)
   or die ("cannot open uniprot for reading ",      "$!\n");    
open (my $ACTIVATOR_IN, '<',  \$Activator) 
   or die ("cannot open activator for reading ",    "$!\n");
open (my $ANTIOX_IN,    '<',  \$anti_oxidant)  
   or die ("cannot open anti_oxidant for reading ", "$!\n");
open (my $TOXIN_IN,     '<',  \$toxin)
   or die ("cannot open toxin for reading ",        "$!\n");

# some local output "files"..
# use "real files" in the actual application

my $activator_out;
my $antiox_out;
my $toxin_out;

# Open the output "files"
#
# A Perl scalar can be opened for file system write
# and this is how to do that...

open (my $ACTIVATOR_OUT, '>', \$activator_out)
   or die ("cannot open activator_out for write! ", "$!\n");
open (my $ANTIOX_OUT,    '>',  \$antiox_out)
   or die ("cannot open antiox_out for write! ",    "$!\n");
open (my $TOXIN_OUT,    '>',   \$toxin_out)
   or die ("cannot open toxin_out for write! ",     "$!\n");
    
# I personally prefer all caps for file handles
# If you don't, then I'm fine with that.

# This part seems odd, because you only get the first 
# PF value...I just guessing that these other PF values do
# mean something?

my %activ =  map { /(.+)\s+\|\s+(PF.{5})/; $1 => $2 } <$ACTIVATOR_IN>;
my %antiox = map { /(.+)\s+\|\s+(PF.{5})/; $1 => $2 } <$ANTIOX_IN>;
my %toxin =  map { /(.+)\s+\|\s+(PF.{5})/; $1 => $2 } <$TOXIN_IN>;
#
# This a way to print the contents of a Perl data stucture..
# Data::Dumper is a standard part of Perl.
#
print "dumping the active hash...\n";
print Dumper \%activ;
print "dumping the anitox hash...\n";
print Dumper \%antiox;
print "dumping the toxin hash...\n";
print Dumper \%toxin;
print "###########\n";

#perhaps you meant something like this???:

print "\nAnother Possible Data Structure...\n";

seek ($ACTIVATOR_IN, 0, 0); # needed to "rewind the file"
seek ($ANTIOX_IN, 0,0);     # needed to "rewind the file"
seek ($TOXIN_IN,0, 0);      # needed to "rewind the file"

# There are many ways to do the regex or use split...
# but it seems to me that somehow you need all of the
# PF values, not just the first one???

my %activ_2 =  map {my ($key, @pfvalues) = /([\w\.]+)/g;
                    $key, [@pfvalues];} <$ACTIVATOR_IN>;
my %antiox_2 = map {my ($key, @pfvalues) = /([\w\.]+)/g;
                    $key, [@pfvalues];}  <$ANTIOX_IN>;
my %toxin_2 =  map {my ($key, @pfvalues) = /([\w\.]+)/g;
                    $key, [@pfvalues];} <$TOXIN_IN>;

print Dumper \%activ_2;
print Dumper \%antiox_2;
print Dumper \%toxin_2;

# this part here: 
# /.{6})\s+.+=([^\s]+)/ 
# just completely lost me, sorry about that

__END__
Prints:
dumping the active hash...
$VAR1 = {
          'Q96355' => 'PF01486',
          'Q96356' => 'PF01486',
          'Q6GZX4' => 'PF04947',
          'Q39371' => 'PF01486'
        };
dumping the anitox hash...
$VAR1 = {
          'E7QVU5' => 'PF10417',
          'D1JAS4' => 'PF10417',
          '0EYG3' => 'PF10262'
        };
dumping the toxin hash...
$VAR1 = {
          'E2E4E4' => 'PF00918',
          'A2PU44' => 'PF01375',
          'C7T183' => 'PF02950',
          'C7T1P5' => 'PF02950'
        };
###########

Another Possible Data Structure...
$VAR1 = {
          'Q96355' => [
                        'PF01486.12',
                        'PF00319.13'
                      ],
          'Q96356' => [
                        'PF01486.12',
                        'PF00319.13'
                      ],
          'Q6GZX4' => [
                        'PF04947.9'
                      ],
          'Q39371' => [
                        'PF01486.12',
                        'PF00319.13'
                      ]
        };
$VAR1 = {
          'E7QVU5' => [
                        'PF10417.4',
                        'PF00578.16'
                      ],
          'D1JAS4' => [
                        'PF10417.4',
                        'PF00578.16'
                      ],
          '0EYG3' => [
                       'PF10262.4'
                     ]
        };
$VAR1 = {
          'E2E4E4' => [
                        'PF00918.12'
                      ],
          'A2PU44' => [
                        'PF01375.12'
                      ],
          'C7T183' => [
                        'PF02950.12'
                      ],
          'C7T1P5' => [
                        'PF02950.12'
                      ]
        };