use warnings;
use strict;

my %HoProPos = (1 => 1916);
my %snpHash = (PF14_0747 => [1]);
my @geneArr = qw(PF14_0747);

while (my $line = <DATA>) {
    my $header = 1;
    chomp $line;
    next if $line !~ m/^Gene:\s*(.*)/;

    my $geneName = $1;

    next if ! grep (/^$geneName$/, @geneArr);

    while (substr ($line, 0, 3) ne "---") {
        $line = <DATA>;
        chomp $line;
        next if $line !~ m/(\d+)\s*([A-Z]+)\s*(\d+)-(\d+)/;

        my ($epitope, $epiSeq, $locBeg, $locEnd) = ($1, $2, $3, $4);

        foreach my $snpID (@{$snpHash{$geneName}}) {
            next if $locBeg > $HoProPos{$snpID} || $HoProPos{$snpID} > $locEnd;

            print "Gene: $geneName\n" if $header;
            print "SNP $snpID found in epitope $epitope at protein position $HoProPos{$snpID}\n";
            $header = undef;
        }
    }
}

__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

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

##</code><code>##

open my $inFile, '<', $dataFileName or die "Unable to open $dataFileName: $!\n";