I would like to place each of these in a hash and increment a count
Your code could be simplified and fit your needs :
#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;
my ( %h, $count );
while (<DATA>) {
next unless /^>(\d+)/;
$count++;
defined $1 and $h{$1} = $count;
}
print Dumper \%h;
__DATA__
>34513
-------------------------------MVAIIFDMDGVLYRG
-----N-RAIPGVRELIEF-------LKE-R--------G------
>22476
------------------------------ALKAVLVDLNGTLHI-
--------AVPGAQEALKR---------------------------
>56832
------MARCERLRGA-----ALRDVLG--RAQGVLFDCDGVLWNG-
----E-RAVPGAPELLER-------LAR-------------------
>12543
---------------------------E--QFDILLLDLDGVVYVG-
----D-RLLPGARRALRR----------------------------G
>29078
---------------------------------AVLFDIDGVLVLS-
----W-RAIPGAAETVRQ-------LTH-R--------G--------
hth, PooLpi
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