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

my $hash = {};
for (<DATA>) {
  chomp;
  my @fields = split(/\s{4}/, $_);
  my @genes  = split(',', $fields[3]);
  @genes = map { (split('\|'))[1] } @genes;
  push(@{$hash->{$fields[0]}}, \@genes);
}
print Dumper($hash);

__DATA__
malS    1    forward    malS|b3571,
malT    1    forward    malT|b3418,
malXY    2    forward    malX|b1621,malY|b1622,
malZ    1    forward    malZ|b0403,
manA    1    forward    manA|b1613,

__OUTPUT__
$VAR1 = {
          'malZ' => [
                      [
                        'b0403'
                      ]
                    ],
          'malS' => [
                      [
                        'b3571'
                      ]
                    ],
          'manA' => [
                      [
                        'b1613'
                      ]
                    ],
          'malXY' => [
                       [
                         'b1621',
                         'b1622'
                       ]
                     ],
          'malT' => [
                      [
                        'b3418'
                      ]
                    ]
        };