If you want to convert N 44°42', E 013°24' to 44.70,13.40, you can do much of editing and extraction of data with just one regular expression:

my $re = qr/([NS]?)\s*(\d+)(?:\D*)(\d*).*?,\s*([EW]?)\s*(\d+)(?:\D*)(\
+d*)/;
unless ($latlong =~ /$re/) {
  die "unable to parse position\n";
}
my $lat = $2 + $3/60;
my $long = $5 + $6/60;
if ($1 eq 'S') { $lat = -$lat; }
if ($4 eq 'W') { $long = -$long; }
return sprintf("%.2f,%.2f", $lat, $long);
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The regular expression makes heavy use of greedy and non-greedy matches, so it may be a little difficult to verify that it works, but I'm pretty confident that it's accurate.