print "\n\n\t\#################### Count the number of acidic/basic/neutral amino acids #################### \n\n";
print "This script will count the number of acidic/basic/neutral amino acids\n\n";
use strict;

#variables
my $count_of_acidic=0;
my $count_of_basic=0;
my $count_of_neutral=0;
my @prot;
my $prot_filename;
my $line;
my $sequence;
my $aa;

print "PLEASE ENTER THE FILENAME OF THE PROTEIN SEQUENCE:=";
chomp($prot_filename=<STDIN>);

open(PROTFILE,$prot_filename) or die "unable to open the file";
@prot=<PROTFILE>;
close PROTFILE;


foreach $line (@prot) {

# discard blank line
if ($line =~ /^\s*$/) {
next;

# discard comment line
} elsif($line =~ /^\s*#/) {
next;

# discard fasta header line
} elsif($line =~ /^>/) {
next;

# keep line, add to sequence string
} else {
$sequence .= $line;
}
}

# remove non-sequence data (in this case, whitespace) from $sequence string
$sequence =~ s/\s//g;
@prot=split("",$sequence); #splits string into an array
#print " \nThe original PROTEIN file is:\n$sequence \n";

while(@prot){
$aa = shift (@prot);
if($aa =~/[DNEQ]/ig){
$count_of_acidic++;
}
if($aa=~/[KRH]/ig){
$count_of_basic++;
}
if($aa=~/[DNEQKRH]/ig){
$count_of_neutral++;
}
}

print "\nNumber of acidic amino acids:".$count_of_acidic."\n";
print "Number of basic amino acids:".$count_of_basic."\n";
print "Number of neutral amino acids:".$count_of_neutral."\n";