#!/usr/bin/perl -w

# -----------------------------------------------------------------------
# simpleRepeatStatistics.pl 1.0
#
# This script creates a statistic for simple repeat in a repeat table file. 
#
#  Copyright by Joern Hameister (2006)
# -----------------------------------------------------------------------

sub printHelp {
	
	print "This script creates a statistic for simple repeat in a repeat table file.\n";
	print "\n";
	print "Example: simpleRepeatStatistics.pl INPUTFILE OUTPUT\n";
	print "INPUTFILE: Repeat table\n";
	print "OUTPUT: Output file with statistics.\n";
	
}


if(@ARGV<2) {
	if($ARGV[0] ne '-h') { 
		print "Wrong arguments!\n";
	}
	printHelp();
	exit(-1);
}

	# load input file
	open(INPUT , "<", $ARGV[0]);
	open(OUTPUT, ">", $ARGV[1]);
	
	open(LOG, ">", "log.txt");
	open(LOGREST, ">", "logrest.txt");
	
	my $repClass = "Simple_repeat";
	
	my %patterns;
	my %patternsLength;
	print OUTPUT "start\tend\tlength\trawPattern\tpattern\tpatternlength\n";
	while(defined ($line = <INPUT>)) {
	  chomp($line);
		
	
		# Use tabs as separator	  
	  @fields = split /\t/,$line;
	
		# Ignore first line
	  if($fields[0] ne "#bin") {
	
  			my $set = 0;
		  	
				if($fields[11] eq $repClass) {
					$startPos = $fields[6];
					$endPos = $fields[7];
					$length = $endPos - $startPos;
					$patternRaw = $fields[10];
					
		      $patternRaw =~ /((A|C|G|T)+)/;
		      $pattern = $1;
					$patternLength = length $pattern;
					
					
					my $value = $patterns{$pattern};
					my $valueLength = $patternsLength{$pattern};
					if(defined $value) {
						$value = $value + 1;
						$valueLength = $valueLength + $length;
					}
					else {
						$value = 1;
						$valueLength = $length;
					}
					#print "$value\n";
					$patterns{$pattern} = $value;
					$patternsLength{$pattern} = $valueLength;					
					
		  		# print "$startPos, $endPos, $length, $patternRaw, $pattern, $patternLength \n";			
	
					
					print OUTPUT "$startPos\t$endPos\t$length\t$patternRaw\t$pattern\t$patternLength\n";			
					print LOG "$line\n";	
					$set = 1;
				}
	
		  
				# Rest
				if($set==0) {
					#$startPos = $fields[6]+1;
					#print OUTPUTREST "{$startPos, $fields[7]}\n";					
					print LOGREST "$line\n";	
				}	
				$set=0;  
			}
			
	}
	
	print OUTPUT "---------------------------------------------------------------------------\n";
	print OUTPUT "Number of occurence of a pattern in the Repeat table file:\n\n";
	print OUTPUT "Pattern: The pattern\n";
	print OUTPUT "Occurences: Number of occurrences of the pattern in the repeat table\n";
	print OUTPUT "CompleteLength: Sum of all (endpos-startpos) of the repeate table\n";
	print OUTPUT "tAbsoluteOccurence: CompleteLength divided by pattern length\n\n";
	print OUTPUT "Pattern\tOccurences\tCompleteLength\tAbsoluteOccurence\n";
	@keyList = sort keys %patterns;
	foreach $keyValue (@keyList) {
		my $count = $patterns{$keyValue};
		my $countLength = $patternsLength{$keyValue};
		my $counter = $countLength/(length $keyValue);
		print OUTPUT "($keyValue)n = $count\t$countLength\t$counter\n";
	}