#!/usr/bin/perl -w -s
##########INPUT Sequence, concatenated into a single string##########
#skip annotation lines in case of fasta. if multiple annotation lines, concatenate these too. 
#
unless(@ARGV==1) {die "please provide name of the file in the command line!!\n";}
my $filename=$ARGV[0]; #takes filenname from input line
open(IN, "< $filename") or die "cannot open $filename:$!"; #assigns filehandle IN to filename or dies

my $seq=''; #assigns empty string
my $line='';
my $name='';
my @bases=(); #assigns empty list

while(defined($line=<IN>)){

	chomp($line);
	if ($line=~/^>/) {  #look for beginning of line starting with > (^ is an anchor for the beginning of the line)
		$name .= $line;
		}
	else {
		$seq .= $line ;
		}
}

#################### move sequence to array
#  check for all CAPS, report non ATGCs, remove white spaces
#
$seq =~ tr/atgc/ATGC/; #translates all ATGC to upper case
$seq =~ s/\s//g;# substitutes all white spaces \s with nothing globally in $seq
@bases=split(//,$seq);  #splits string into separate elements (bases)

my$num_bases=@bases; #length of array

###################calculate GC content 

my$num_GC=0;

for ($i=0; $i<($num_bases); $i++)  #counts Gs and Cs in @bases Note the number of bases is one larger than the array
 	{  
 	if(($bases[$i]=~"G") || ($bases[$i]=~"C")) #if it matches G or C increase counter
		{$num_GC++;
		}
	if (!(($bases[$i]=~"G") || ($bases[$i]=~"A") || ($bases[$i]=~"T") || ($bases[$i]=~"C")))
		{print "Warning there is a strange base $bases[$i] before position $i\n";
		my$errors++;}
	}

if (defined ($errors)){$num_bases=$num_bases-$errors};
$GC_content=($num_GC/$num_bases)*100;
print "\nThe GC content of the sequence in the file ".'"'."$filename".'"'. " is $GC_content\%.\n\n";
if (!($name eq '')) {print "Annotation line(s) in $filename was/were $name\n";}
# print "The sequence analyzed was:\n"; 
# print @bases;

########determine the number of di nucleotide  repeats
for (my $j=0; $j<($num_bases-1); $j++)
	{
	my $di=($bases[$j].$bases[$j+1]);
	
	push(@di_nucleotides, $di);
	}
my %di=(); 
	foreach my $i (@di_nucleotides)
	{

			if(!(exists $di{$i}))
			{
	 			$di{$i}=1;
			}
			else {$di{$i} += 1
			}
	}

	
#foreach $keys (sort keys %di) {
#	print "$keys => $di{$keys}\t";
#	}

########determine the number of tri nucleotide  repeats
for (my $j=0; $j<($num_bases-2); $j++)
	{
	my $tri=($bases[$j].$bases[$j+1].$bases[$j+2]);
	
	push(@tri_nucleotides, $tri);
	}
my %tri=();
	
foreach my $i (@tri_nucleotides)
	{

		if(!(exists $tri{$i}))
		{
 			$tri{$i}=1;
		}
		else 
		{
		$tri{$i} += 1
		}
	}

#foreach $keys (sort keys %tri) {
#	print "$keys => $tri{$keys}\t";
#	}	
########determine the number of di nucleotide  repeats
for (my $j=0; $j<($num_bases-3); $j++) 
	{
	my $quad=($bases[$j].$bases[$j+1].$bases[$j+2].$bases[$j+3]);
	
	push(@quad_nucleotides, $quad);
	}
my %quad=(); 
foreach my $i (@quad_nucleotides)
	{

	if(!(exists $quad{$i}))
	{
	$quad{$i}=1; # you coul dmake the program faster by skipping the (if !(exist ...) statement and just increase the hash for each encounter.   
	}
	else 
	{
	$quad{$i} += 1
	}
		
	}
#you could sort the keys of hash by their their values:
@sorted_array = sort {$quad{$b} <=> $quad{$a} or $a cmp $b } (keys(%quad));

open (OUT, "> out.txt") or die "cannot open $filename:$!";
	
foreach (@sorted_array) {
	print OUT "$_\t$quad{$_}\n";
	print "$_ => $quad{$_}\n";
	
	}
print "\n";
close (OUT);