#!/usr/bin/perl -w
use strict;
use warnings;

my $file = $ARGV[0];
my @currentProtein;
my %protein;
open (FASTA, "<", $file) || die "Can't open $file\n";
my $fastaLine; 
my $protSequence;
my @fastaTag;
my @tagOrder;

while (<FASTA>) 
  {
    print STDERR "CURRENT: $_";
    chomp;
    if (($_ !~ /^>/) && ($_ =~ /\w/)) 
      {
        push (@currentProtein, $_);
      }
    if ((/^>/) || (eof))
      {
       
        if ((@currentProtein > 0) || (eof))
          {
            $protSequence = join("", @currentProtein);
            $protSequence =~ s/ //g;
            @fastaTag = split(" ", $fastaLine);
            $protein{$fastaTag[0]} = $protSequence; 
            push (@tagOrder, $fastaTag[0]);
            @currentProtein = ();
          }
         $fastaLine = $_ if $_ =~ /\w/; 
      }
   
    }
close FASTA;
for(@tagOrder)
    {
      my $count_of_acidic = 0;
      my $count_of_basic = 0;
      my $count_of_neutral = 0;
      my $aa;
      my $sequence = "$protein{$_}";

      $sequence =~ s/\s//g;
      my @prot=split("",$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 "\nName: $_\n";
      print "Number of acidic amino acids:".$count_of_acidic."\n";
      print "Number of basic amino acids:".$count_of_basic."\n";
      print "Number of neutral amino acids:".$count_of_neutral."\n";
    }