Here's one option:

use strict;
use warnings;

for my $fastaRec ( extract_query_data('fastaFile.fa') ) {
    print $fastaRec, "\n";
}

sub extract_query_data {
    my ($file) = @_;
    my @arr;
    local $/ = '>';

    open my $fh, '<', $file or die $!;

    while (<$fh>) {
        chomp;
        my ( $id, $seq ) = /(.+?\n)(.+)/s or next;
        $seq =~ s/\s+//g;
        push @arr, ">$id$seq";
    }

    close $fh;

    return @arr;
}
[download]

You'll note that the subroutine returns an array of fasta records.