use warnings;
use strict;

my $counter = 0;
my %hash;
while (<DATA>) {
    my @splits = split;
    my $snp = $splits[0];
    $hash{$snp} ||= ++$counter;
    print "$hash{$snp} $snp\n";
}

__DATA__
foo     abc
foo     cde
bar     xyz
foo     hij

##</code><code>##

1 foo
1 foo
2 bar
1 foo

##</code><code>##

1 foo
1 foo
2 bar
2 foo