use strict;
use warnings;
use Bio::SeqIO;

print "Please type the file name of the protein sequence data: ";
chomp( my $proteinfilename = <STDIN> );
print "\n";

my $fastaIN = Bio::SeqIO->new( -file => $proteinfilename, -format => 'Fasta' );

while ( my $seq = $fastaIN->next_seq() ) {
	print $seq->seq, "\n";
}