#!/usr/bin/perl -w
# Count charge of polypeptide as in [1]
# (c) 2008 Tobias Abenius, licence: GPL
# 1. Yu Shi, Coreceptor Usage and Sensitivity to Neutralization of HIV-1 & HIV-2
sub charge($) {
	@aa = split //, $_[0];
	$charge = (grep /[rk]/i, @aa)-(grep /[ed]/i, @aa);
	return $charge;
}

if ($#ARGV != 0) {
	print "Syntax: perl $0 <file>\n";
	exit 1;
}

print STDERR "Reading sequences separated by newline from file '$ARGV[0]'\n";
while($seq = <>) {
	$charge = charge($seq);
	print $charge."\n";
}