Is the solution as simple as using chomp on the lines of your array?

no ok it can't be. Ok let me see if I can explain it a different way and tell you what the program needs to do. First ask me to enter the clone ID. After i enter the ID using something like $id=<STDIN>; search thru my FASTA file and give me as an answer the sequence from the ID I put in, do you get me? by the way I can't thank you enough for helping me

This is the code I have until now, it is telling me Odd number of elements in hahs assigment at line 17, any ideas

#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]