#!/usr/bin/perl -w

package runnetcglyc;

use base 'Exporter';
our @EXPORT = qw/netcglyc_extract_results/;

use strict;
use IO::File;

use formatAlleleSeq;

# extract results after running netcglyc applied to 1 result file

sub netcglyc_extract_results($$$$){
	
	my ($delta, $netcglyc_result_file, $name_encoding_file, $output_file) = @_;
	
	print "runnetcglyc::netcglyc_extract_results: Searching C-mannosilation loss or gain between 2 alleles:\n";
	print "Name\tgain/loss/diff\tscore_allele1\tscore_allele2...\n";
	
	my $prog = "netcglyc";
	
	my %netcglyc_res = ();
	
	my ($i,$fh_in,$name,$line,$pos,$score,$tag,$allele,$basis_name,$diff_score,$fh_out);
	
	my %score_allele1 = ();
	my %score_allele2 = ();
	my %tag_allele1 = ();
	my %tag_allele2 = ();
			
	# get the encoding names
	my ($h_encodingName,$h_encodingID,$h_name_allele,$h_name_position) = getEncoding($name_encoding_file);
		
	$fh_out	= new IO::File ">$output_file" || die "Can not open $output_file : $! \n";
	
	my $outpath = $output_file;
	$outpath =~ s/\/([^\/]+)$//;
	
	my $fh_title = new IO::File ">$outpath/$prog\_title.txt" || die "Can not open $outpath/$prog\_title.txt : $! \n";
	print $fh_title ("Sequence Name\tCase\tscore allele1\tscore allele2\n");	
	$fh_title->close();
	
		
	# get the C mannolisation predictions	
	# extract name, position and score of C manosylation.
	print "FILE::*$netcglyc_result_file*\n";
	$fh_in = new IO::File $netcglyc_result_file || die "Can not open file $netcglyc_result_file : $! \n";
	$/="\n";
	while($line=<$fh_in>){
		
		if(not $line =~ /^\#/){
			
			($name,$pos,$score,$tag) = $line=~/([^\s]+)\s*[^\s]+\s*[^\s]+\s*([^\s]+)\s*[^\s]+\s*([^\s]+)\s*[^\s]+\s*([^\n]+)\n/;
			print "BASE_NAME: $name, POSITION: $pos, SCORE: $score, TAG_W: $tag\n";
			($basis_name,$allele) = $h_encodingID->{$name} =~ /(.*)_(allele\d)$/;
									
			print "NAME_POS: $h_name_position->{$name}, BASIS_NAME: *$basis_name*, ALLELE_NUM: $allele, ENCODING: $h_encodingID->{$name}\n";
			
			if(defined $h_encodingID->{$name}){
												
				if(defined $h_encodingID->{$name} && ($h_name_position->{$name} eq $pos) && ($allele eq "allele1")){
				
					$score_allele1{$basis_name} = $score;			
					$tag_allele1{$basis_name} = $tag;		
				}
				elsif(defined $h_encodingID->{$name} && ($h_name_position->{$name} eq $pos) && ($allele eq "allele2")){
					
					$score_allele2{$basis_name} = $score;			
					$tag_allele2{$basis_name} = $tag;			
				}		
			}
			else{
			
				print "runnetcglyc::netcglyc_extract_results unkown name: $name\n";
				exit(11);
			}
		}
	}
	$fh_in->close();
	
	# to analyse the difference between the 2 alleles
	foreach $name (keys %score_allele1){
						
		if((not defined $score_allele2{$name}) && ($tag_allele1{$name} eq 'W')){
			
			print $fh_out ("$name\tloss\t$score_allele1{$name}\t\n");
			print (">>HEHO: $name\tloss\t$score_allele1{$name}\t\n");
			
		}
		elsif(defined $score_allele2{$name}){
		
			print "SCORES: $score_allele1{$basis_name} - $score_allele2{$basis_name}\n";
			$diff_score = $score_allele1{$basis_name} - $score_allele2{$basis_name};
			$diff_score =~ s/-//;
			
			print "DIIF_SCORE: $diff_score\n";
			
			if(($diff_score >= $delta) && ($score_allele1{$basis_name} > $score_allele2{$basis_name})){
				
				print $fh_out ("$name\tloss?\t$score_allele1{$name}\t$score_allele2{$name}\n");
			}
			elsif(($diff_score >= $delta) && ($score_allele1{$basis_name} < $score_allele2{$basis_name})){
				
				print $fh_out ("$name\tgain?\t$score_allele1{$name}\t$score_allele2{$name}\n");
			}
			
			delete $score_allele2{$name};
		}		
	}
	
	foreach $name (keys %score_allele2){
		
		
		if((not defined $score_allele1{$name}) && ($tag_allele2{$name} eq 'W')){
			
			print ">>HEHA: $score_allele1{$name} | $tag_allele2{$name} | $score_allele2{$name} | $tag_allele1{$name}\n";
			print $fh_out ("$name\tgain\t\t$score_allele2{$name}\n");
			
		}
		elsif(defined $score_allele1{$name}){
		
			$diff_score = $score_allele1{$basis_name} - $score_allele2{$basis_name};
			$diff_score =~ s/-//;
			
			if(($diff_score >= $delta) && ($score_allele1{$basis_name} > $score_allele2{$basis_name})){
				
				print $fh_out ("$name\tloss?\t$score_allele1{$name}\t$score_allele2{$name}\n");
			}
			elsif(($diff_score >= $delta) && ($score_allele1{$basis_name} < $score_allele2{$basis_name})){
				
				print $fh_out ("$name\tgain?\t$score_allele1{$name}\t$score_allele2{$name}\n");
			}
		}		
	}
	$fh_out->close;
}
	
	
	#~ #Find variations
	#~ $tmp = new IO::File "$path/fic/temp-netcglyc_$date" || die "Can not open netcglyc temp file : $! \n";
	#~ my $netcglyc = new IO::File ">output_file" || die "Can not create file output_file: $! \n";
	#~ my %a1;
	#~ my %a2;
	#~ my %check;
	#~ my $allele = "";
	#~ my $name = "";
	#~ my $c = 2;
	#~ for($i=0;$i<=$#$netcglyc_res;$i++);{
	#~ while(<$tmp>){
		#~ my $line = $netcglyc_res[$i];
		#~ if($line =~ s/^(\d*)/$id{$1}/){#Substitute the ID by his coresponding name
			#~ if($line =~ m/^(\S*)_allele(\d)\s*(\d*)\s(\S*)\s(\S*)/){
				#~ if($2 eq $allele){
					#~ if($c == 0){#Same allele1
						#~ $allele = $2;
						#~ if($5 eq "W"){
							#~ my $position = $3;
							#~ my $score = $4;
							#~ $a1{$position}.=$score;
							#~ $check{$position}.="1";
						#~ }
					#~ }
					#~ elsif($c == 1){#Same allele2
						#~ $allele = $2;
						#~ if($5 eq "W"){
							#~ my $position = $3;
							#~ my $score = $4;
							#~ $a2{$position}.= $score;
							#~ $check{$position}.="2";
						#~ }
					#~ }
				#~ }
				#~ else{
					#~ if($c == 0){#Other allele
						#~ $c++;
						#~ $allele = $2;
						#~ if($5 eq "W"){
							#~ my $position = $3;
							#~ my $score = $4;
							#~ $a2{$position}.=$score;
							#~ $check{$position}.="2";
						#~ }
					#~ }
					#~ elsif($c == 1){#Other transcript
						#~ compare($netcglyc,$delta,\%a1,\%a2,\%check,$name);
						#~ %a1=();
						#~ %a2=();
						#~ %check=();
						#~ $allele = $2;
						#~ $name = $1;
						#~ if($5 eq "W"){
							#~ my $position = $3;
							#~ my $score = $4;
							#~ $a1{$position}.=$score;
							#~ $check{$position}.="1";
						#~ }
						#~ $c = 0;
					#~ }
					#~ elsif($c == 2){#Initialisation
						#~ $name = $1;
						#~ $allele = $2;
						#~ if($5 eq "W"){
							#~ my $position = $3;
							#~ my $score = $4;
							#~ $a1{$position}.=$score;
							#~ $check{$position}.="1";
						#~ }
						#~ $c = 0;
					#~ }
				#~ }
			#~ }
		#~ }
	#~ }
	#~ compare($netcglyc,$delta,\%a1,\%a2,\%check,$name);#For the last transcript
	#~ $tmp->close();
	#~ $netcglyc->close();
#~ }
#~ 
#~ sub compare($$$$){
#~ 
	#~ my ($netcglyc,$delta,$ref1,$ref2,$ref3,$name) = @_;
	#~ my %a1=%$ref1;
	#~ my %a2=%$ref2;
	#~ my %check=%$ref3;
	#~ foreach my $k (keys(%check)){
		#~ my $v = $check{$k};
		#~ if($v eq "12"){
			#~ my $diffscore = $a1{$k}-$a2{$k};
			#~ if($diffscore >= $delta){
				#~ print $netcglyc "$name : Signal lost at position $k. Score allele 1 = $a1{$k} - Score allele 2 = $a2{$k}\n";
			#~ }
			#~ elsif($diffscore <= -$delta){
				#~ print $netcglyc "$name : Signal gain at position $k. Score allele 1 = $a1{$k} - Score allele 2 = $a2{$k}\n";
			#~ }
		#~ }
		#~ elsif($v eq "1"){
			#~ print $netcglyc "$name : Signal lost at position $k . Score : $a1{$k}\n";
		#~ }
		#~ elsif($v eq "2"){
			#~ print $netcglyc "$name : Signal gain at position $k. Score : $a2{$k}\n";
		#~ }
	#~ }
#~ }

1;