#the file name
$filename= hwk2.seq;

use strict;
use warnings;
use lib '/class/bi617a/share/textbook';
use BeginPerlBioinfo;

#Declare initialize the variables
my @file_data=();
my %seqs= '';
my $query= '';
my $dna= '';

#Read the contents of the file hwk3.seq
@file_data=get_file_data("hwk2.seq");


print "Please enter the clone ID:\n";
$query=<STDIN>;
chomp $query;

my $seqs= &get_fasta(@file_data);
if (exists $seqs{$query}) { print " This is the sequence: $seqs{$query
+},
\n";
}
else{ print "Not an ID\n\n;";}
exit;

sub get_fasta{
my $header;
my $first = 0;

for my $file_data(@file_data){
if ($file_data =~ /^>/) {
        $query = $file_data;
        $query=~ s/^>//;
        $query=~ s/\s,*//;
        if ($first == 0) {
        $first =1;
        }
        next;
}
if ($first == 0) {die("Not a standard FASTA file.\n"); }
        $seqs{$query} = $file_data;
return \%seqs;
}
}
return \%seqs;
}
}
[download]

I'm not sure where line 17 is but my %seqs= ''; is wrong because a hash is not a string. I think you meant to say my %seqs = (); Also, there's no reason to assign empty values to newly declared variables so you can simply say my %seqs; instead. Actually, I'd just pull all those forward declarations together in one line like so...

my (@file_data, %seqs, $query, $dna);
[download]

Of course, this is Perl, so you can declare variables when you use them, but I don't want to overwhelm you so I'll leave it here for now.

When you get errors like that, look at the line the error message says and try to see what's wrong. When you show code, please mark which line is 17 (well, the line with the error) because many of us can spot errors without downloading and running the code.