I really didn't understand completely what you are trying to do. like what is $HoProPos{$snpID}?

Anyway 7 levels of "}" is very confusing to say the least and should be a super Red Flag.

Below I just settled for parsing the input and making a data structure. It might give you some hints on how to simplify your code. I didn't understand the basic terminology so the parsing of the line is probably more complex than need be.

A main point is that the depth level below is only 2 vs your 7 levels. The code below looks a bit strange because I don't understand the terminology or what you are trying to accomplish. I was not able to run your code.

Have fun with this...I hope that something is useful for you.

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

my %Gene_DB;  # a hash of hash

while (<DATA>)
{
   my $gene = (/^Gene:\s+(\S+)\s*/)[0] || next;
   add_gene($gene);
}

sub add_gene
{
   my $gene = shift;
   my @tokens;
   my %gene_hash;
   while (<DATA>)
   {
      last if (/^-/);       #End of Record
      next unless (/^\d/);  #the single line we care about!
      @tokens = split;  
   }
   
   #I probably don't understand OP right!
   #but first 3 on line, last 2 on line, then what's left over
   
   my ($Epitope, $Sequence, $Location) = splice(@tokens,  0, 3);
   my ($Strain, $Confidence)           = splice(@tokens, -2);
   my ($Protein) = join (" ",@tokens);
   
   @gene_hash{'Epitope', 'Sequence', 'Location' ,'Strain', 
              'Confidence' ,'Protein'}
            = ($Epitope, $Sequence, $Location,$Strain, 
               $Confidence,$Protein);
   $Gene_DB{$gene}=\%gene_hash;               
}

print Dumper (\%Gene_DB);
#prints:
#$VAR1 = {
#          'PF14_0747' => {
#                           'Protein' => 'Plasmodium falciparum',
#                           'Epitope' => '26850',
#                           'Confidence' => 'Medium',
#                           'Strain' => '3D7',
#                           'Location' => '1914-1917',
#                           'Sequence' => 'IKND'
#                         },
#          'PF14_0711' => {
#                           'Protein' => 'Plasmodium falciparum',
#                           'Epitope' => '26850',
#                           'Confidence' => 'Medium',
#                           'Strain' => '3D7',
#                           'Location' => '9-12',
#                           'Sequence' => 'IKND'
#                         }
#        };
#
__DATA__
Gene: PF14_0747

TABLE: Epitopes from IEDB

Epitope Sequence Location on Protein Strain Confidence

26850 IKND 1914-1917 Plasmodium falciparum 3D7 Medium

------------------------------------------------------------

Gene: PF14_0711

TABLE: Epitopes from IEDB

Epitope Sequence Location on Protein Strain Confidence

26850 IKND 9-12 Plasmodium falciparum 3D7 Medium

------------------------------------------------------------
[download]