Perhaps the following will be helpful:

use strict;
use warnings;

local $/ = '>';

while (<>) {
    chomp;
    my ( $id, $seq ) = /(.+?\n)(.+)/s or next;
    $seq =~ s/\s+//g;
    print ">$id$seq\n";
}
[download]

Command-line usage: perl script.pl fastaIn [>fastaOut]

The last, optional parameter directs output to a file.