#!/usr/bin/perl -w

=pod

=head1  NAME

runnetoglyc Module


=head1  SYNOPSIS

use runnetoglyc;

=head1  OPTIONS



=head1 DESCRIPTION


=head1 VERSION

Version 1


=head1 DATE

20 janvier 2012

=head1 AUTHORS

Sabrina Rodriguez (sabrina.rodriguez@jouy.inra.fr)
Johann Beghain 

=cut

package runnetoglyc;

use strict;
use IO::File;

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

use formatAlleleSeq;


sub netoglyc_extract_results($$$$$){
	
	my ($delta, $netoglyc_result_file, $name_encoding_file, $output_file, $BASE_SEQ_NAME) = @_;

	my ($fh_in,$fh_out,$fh_tmp,$allele,$name,$line,$seq_name,$pos,$Gscore,$Iscore,$signal);
	my ($nameA1,$nameA2,$score_diff,$score,$basis_name);
	my ($start,$end,$ref,$alt,$info,$end_alt,$i);

	
	my %score_allele1 = (); # key : initial complete name => score value (for the alléle 1 position)
	my %score_allele2 = (); # key : initial complete name => signal value (for the alléle 1 position : ++)
	my %signal_allele1 = (); # key : initial complete name => score value (for the alléle 2 position)
	my %signal_allele2 = (); # key : initial complete name => signal value (for the alléle 2 position : ++)
	my %ref_pos = ();
	my %alt_pos = ();
	
	my ($h_encodingName,$h_encodingID,$h_name_allele,$h_name_position,$h_name_var_type) = getEncoding($name_encoding_file);
	
	my $prog = "netoglyc";
	
	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\tsignal allele1\tsignal allele2\n");	
	$fh_title->close();
	
	#Find variations	
	$fh_in = new IO::File "$netoglyc_result_file" || die "Can not opennetoglyc_result_file $netoglyc_result_file : $! \n";
	$fh_out = new IO::File ">$output_file" || die "Can not create final results of netoglyc $output_file: $! \n";

	print "$netoglyc_result_file\n";
	
	while($line = <$fh_in>){

		#~ print "$line\n";
		
		if($line =~ m/^$BASE_SEQ_NAME\d+\s*\S*\s*(\d*)\s*(\S*)\s*(\S*)\s*(\S*)/){
			
			($seq_name,$pos,$Gscore,$Iscore,$signal) = $line =~ /^($BASE_SEQ_NAME\d+)\s*\S*\s*(\d*)\s*(\S*)\s*(\S*)\s*(\S*)/;
			
			#~ print "$seq_name,$pos,$Gscore,$Iscore,$signal\n";
					
			($basis_name) = $h_encodingID->{$seq_name} =~ /(.*)_allele\d$/;	
			
			if($line =~ s/^($BASE_SEQ_NAME\d+)/$h_encodingID->{$seq_name}/){#Substitute the ID by his coresponding name
			
				#~ my $a = $h_name_position->{$seq_name};
				#~ my $b = $h_name_allele->{$seq_name} ;
				#~ print "hash_pos:$a\nhash_allele:$b\n";
								
				if(($signal eq "S") or ($signal eq "T")){
					
					#~ print ">>seq_name:*$seq_name*, pred_pos : $pos, pred_score : $Gscore , $signal\n\n";
					
					
					if($h_name_var_type->{$seq_name} eq "snp"){ ###
					
						if($pos eq $h_name_position->{$seq_name}){
							
							if($h_name_allele->{$seq_name} eq "allele1"){
								
								$signal_allele1{$basis_name} = $signal;
								$score_allele1{$basis_name} = $Gscore;
								
								#~ print "===> $seq_name : $signal || $Gscore \n";
								
							}
							elsif($h_name_allele->{$seq_name} eq "allele2"){
								
								$signal_allele2{$basis_name} = $signal;
								$score_allele2{$basis_name} = $Gscore;
								
								#~ print "=======> $seq_name : $signal || $Gscore \n";
							}
							else{
							
								print "PB: $seq_name :$h_name_allele->{$seq_name}: $basis_name\n";	
								exit(12);
							}				
						}
					}
					else{	
																	
						#~ print "HERE\n";
						
						# get the [REF/ALT-POS] information
						#~ print "$h_encodingID->{$name}\n";
						($info) = $h_encodingID->{$seq_name} =~  /\[([^\/]+\/.+\-\d*\-*\d+)\]_allele\d*/;
						
						# retrives the amino acids to check on					
						($start,$end,$end_alt) = analyseIndelChange($info);
						
						#~ print "coordinates: $start,$end,$end_alt\nPOSITION: $pos\n";
						
						# get the signals from the reference
						%ref_pos = ();															
						for($i=$start;$i<=$end;$i++){
							
							$ref_pos{$i} = "";						
							#~ print "ref:$i\n";		
						}
						
						# get the signals from the alternative
						%alt_pos = ();															
						for($i=$start;$i<=$end_alt;$i++){
							
							$alt_pos{$i} = "";											
							#~ print "alt:$i\n";
						}
								
						#~ print "--> POS FROM RES: $pos\n";							
						
						if((defined $ref_pos{$pos}) and ($h_name_allele->{$seq_name} eq "allele1")){							
					
							$score_allele1{$basis_name} = "indel";	
							
							if(not defined $signal_allele1{$basis_name}){
								
								$signal_allele1{$basis_name} = 1;
							}
							else{
										
								$signal_allele1{$basis_name} = $signal_allele1{$basis_name} + 1; # number of signals on the reference for the indel
							}
							
							#~ print "REF:$basis_name:$signal_allele1{$basis_name}\n";
						}
						
						if((defined $alt_pos{$pos}) and ($h_name_allele->{$seq_name} eq "allele2")){
							
							$score_allele2{$basis_name} = "indel";			
							
							if(not defined $signal_allele2{$basis_name}){
								
								$signal_allele2{$basis_name} = 1;
							}
							else{
								$signal_allele2{$basis_name} = $signal_allele2{$basis_name} + 1;	# number of signals on the alternative for the indel		
							}
							
							#~ print "ALT:$basis_name:$signal_allele2{$basis_name}\n";
						}																																			
					}	
				}											
			}
			else{
				
				print "PB: NON existing sequence name for id:$1\n";
			}
		}		
		elsif($line =~ /netOglyc: surface prediction failed in entry/){
			
			print "Error: NETOGLYC FAILED:\n$line\n";
			exit(11);
		}
	}
	
	
	foreach $basis_name (keys %signal_allele1){
									
		#~ ($basis_name) = $h_encodingID->{$seq_name} =~ /(.*)_allele\d$/;		
		print "=====>>> $seq_name:$basis_name\n";	
		#~ 
		#~ $nameA1 = $seq_name;
		#~ $name = $h_encodingID->{$seq_name};
		#~ $name =~ s/allele1/allele2/;		
		#~ $nameA2 = $h_encodingName->{$name};				
		
		# indel
		if($score_allele1{$basis_name} eq "indel" ){
			
			print "$basis_name : $signal_allele1{$basis_name} != $signal_allele2{$basis_name}\n";
			
			# the number of signals is different between reference and alternative at the indel part 
			if ($signal_allele1{$basis_name} != $signal_allele2{$basis_name}){
				
				print $fh_out ("$basis_name\tdiff\t\t\t$signal_allele1{$basis_name}\t$signal_allele2{$basis_name}\n"); #####
			}
			delete $signal_allele2{$basis_name};
		}
		# snp
		else{
		
			if((not defined $signal_allele2{$basis_name}) && (($signal_allele1{$basis_name} eq 'S') || ($signal_allele1{$basis_name} eq 'T'))){
			
				print $fh_out ("$basis_name\tloss\t$score_allele1{$basis_name}\t\t$signal_allele1{$basis_name}\t\n");
				print ("$name\tloss\t$score_allele1{$basis_name}\t$signal_allele1{$basis_name}\n");
			}
			elsif(defined $score_allele2{$basis_name}){
				
				$score_allele1{$basis_name} =~ s /\,/\./;
				$score_allele2{$basis_name} =~ s /\,/\./;
				
				$score_diff = $score_allele1{$basis_name} - $score_allele2{$basis_name};
				$score_diff =~ s/-//;
				
				if(($score_diff >= $delta) && ($score_allele1{$basis_name} > $score_allele2{$basis_name})){
									
					print $fh_out ("$basis_name\tloss?\t$score_allele1{$basis_name}\t$score_allele2{$basis_name}\t$signal_allele1{$basis_name}\t$signal_allele2{$basis_name}\n");
				}
				elsif(($score_diff >= $delta) && ($score_allele1{$basis_name} < $score_allele2{$basis_name})){
					
					print $fh_out ("$basis_name\tgain?\t$score_allele1{$basis_name}\t$score_allele2{$basis_name}\t$signal_allele1{$basis_name}\t$signal_allele2{$basis_name}\n");
				}
			}
			
			delete $signal_allele2{$basis_name};
		}
	}
	
	foreach $basis_name (keys %signal_allele2){
		
		#~ ($basis_name) = $h_encodingID->{$seq_name} =~ /(.*)_allele\d$/;	
		
		#~ print "=====>>> $seq_name:$basis_name\n";	
		
		#~ $nameA2 = $seq_name;
		#~ $name = $h_encodingID->{$seq_name};
		#~ $name =~ s/allele2/allele1/;
		#~ $nameA1 = $h_encodingName->{$name};
		#~ 
		# indel
		if($score_allele2{$basis_name} eq "indel" ){
			
			#~ print ">>>$basis_name : $signal_allele1{$basis_name} != $signal_allele2{$basis_name}\n";
			
			# the number of signals is different between reference and alternative at the indel part 
			if ($signal_allele1{$basis_name} != $signal_allele2{$basis_name}){
				
				print $fh_out ("$basis_name\tdiff\t\t\t$signal_allele1{$basis_name}\t$signal_allele2{$basis_name}\n"); #####
			}
		}
		# snp
		else{
						
			if((not defined $signal_allele1{$basis_name}) && (($signal_allele2{$basis_name} eq 'S') || ($signal_allele2{$basis_name} eq 'T'))){
			
				print $fh_out ("$basis_name\tgain\t\t$score_allele2{$basis_name}\t\t$signal_allele2{$basis_name}\n");
			}
			elsif(defined $score_allele1{$basis_name}){
				
				$score_allele1{$basis_name} =~ s /\,/\./;
				$score_allele2{$basis_name} =~ s /\,/\./;
				
				$score_diff = $score_allele1{$basis_name} - $score_allele2{$basis_name};
				$score_diff =~ s/-//;
				
				if(($score_diff >= $delta) && ($score_allele1{$basis_name} > $score_allele2{$basis_name})){
									
					print $fh_out ("$basis_name\tloss?\t$score_allele1{$basis_name}\t$score_allele2{$basis_name}\t$signal_allele1{$basis_name}\t$signal_allele2{$basis_name}\n");
				}
				elsif(($score_diff >= $delta) && ($score_allele1{$basis_name} < $score_allele2{$basis_name})){
					
					print $fh_out ("$basis_name\tgain?\t$score_allele1{$basis_name}\t$score_allele2{$basis_name}\t$signal_allele1{$basis_name}\t$signal_allele2{$basis_name}\n");
				}
			}		
		}
	}
	
	$fh_out->close;
	$fh_in->close;
}

1;