sub parseFile {
    my ($fIn) = @_; # a filehandle
    my $fastaData;

    ... #yada yada yada

    while (<$fIn>) { # $/ has not been undefined, $fIn is read line by line
        $fastaData = $_;
        $fastaData =~ s/\n//gms; #/gms are all useless because:
                                 #g - each time $fastaData will have exactly one \n (at the end)
                                 #m - regex doesn't use ^ or $, and it's always a single line anyways
                                 #s - regex doesn't use . and it's always a single line anyways
            # effectively performs the same function as
        # chomp($fastaData);
            # or even
        # chomp($fastaData = $_);

        ...
    }
    ...
}