### ----------------------------------------------------
### Script for sorting and comparing multi-sample report
### values from Avadis NGS
###
### Written by Niklas Malmqvist 2012
### ----------------------------------------------------

#!/usr/bin/perl
use strict;
use warnings;
use Getopt::Long;

## Declare various variables;
my $sortColumn;
my $sortDescending = 0;
my $INPUT;
my @splitline = ();
my $noTotalHighScores = 0;
my $minScore;
my $offset;
my $noSamples;
my $noSampleHighScores = 0;
my $minSampleCount = 0;

GetOptions(	"col=i" => \$sortColumn,
		"r" => \$sortDescending,
		"s=n" => \$noSamples,	## TODO: Figure out how to automatically read nbr of samples
		"m=n" => \$minScore,
		"c=n" => \$minSampleCount,
		"i=s" =>  \$INPUT);

## Options input check
if ($sortDescending) { $sortDescending = "r"; } else { $sortDescending = ""; }
unless ($sortColumn && $INPUT && $noSamples && $minScore && $minSampleCount)
{ print "$0: Missing mandatory input arguments!\n"; exit 1; }

## Open the input file
open INFILE, "<", $INPUT or die "Can't open the input file!";

## Open the output file
open OUTFILE , ">", $INPUT."-highscores" or die "Can't open the output file!";

## Sort the file and filter out rows with "Sample count" below treshold
system("head -n1 $INPUT > tmpPart1.csv");
system("tail -n+2 $INPUT | sort -k".$sortColumn."n".$sortDescending." > tmpPart2.csv");
system("awk \'\$7 >= $minSampleCount\' tmpPart2.csv > tmpPart3.csv");
system("cat tmpPart1.csv tmpPart3.csv > $INPUT.sorted");
system("rm tmpPart1.csv tmpPart2.csv tmpPart3.csv");

close (INFILE);

## Go through the sorted file line-by-line and check for scores
open INFILE_SORTED, "<", $INPUT.".sorted" or die "Can't open the sorted input file!";
my $lineCount = 1;

while (my $line = <INFILE_SORTED>) {
	# Skip first line (header)
	if ($lineCount == 1) {
		## Print the header to the output
		print OUTFILE $line;
	}
	else {

		# The score for the first sample is stored in column 14, next sample in column 20 and so on
		# This is handled by $offset
		$offset = 14;
		@splitline = split('\t', $line);

		$noSampleHighScores = 0;
		## Check the scores of all the samples in the report
		for (1 .. $noSamples) {

			if ($splitline[$offset-1] && ($splitline[$offset-1] >= $minScore)) {
				## Score threshold OK
				$noSampleHighScores++;
			}
			$offset += 6;
		}

		if ($noSampleHighScores == $noSamples) {
			$noTotalHighScores++;
			print OUTFILE $line;
		}
	}
	$lineCount++;
}

print "Done!\nSamples with score > threshold: $noTotalHighScores\n";

close (INFILE_SORTED);
close (OUTFILE);