#!/gpsr/local/bin/perl
use Getopt::Std;
getopts('i:o:');
$infile=$opt_i;
$outfile=$opt_o;

if($infile eq "" or $outfile eq "")
{
        print "\t./algpred.pl -i input_file -o output_file\n\n";
        print "\t-i:\tinput file in fasta format\n";
        print "\t-o:\toutput file\n";
        print "\n\tExample: ./algpred.pl -i /gpsr/examples/example.fasta -o out.algpred\n";
        exit;
}
$ptnnum = `grep -c "^>" $infile`; chomp($ptnnum);
if($ptnnum > 1)
{
        print "\tDon't Enter multiple sequences... Enter single sequence fasta file\n";
        exit;
}
@array=(10001..99999);
$rand =int(rand scalar(@array));
$jobnumber = $rand;
$homedir = "/gpsr/standalone/algpred/progs";
$modeldir = "/gpsr/models/algpred";
$blastdatadir = "/gpsr/data/blastdata/algpred";
$tmpdir = "/gpsr/temp/algpred$jobnumber";
`mkdir $tmpdir`;
`chmod 777 $tmpdir`;

open(OUTMAIN, ">$outfile");
open(OUTHTML, ">$tmpdir/delout.html");

$seqname = "sequence";
$seq = `grep -v "^>" $infile`; chomp($seq);
$seq =~ s/\n//g; $seq =~ s/\s+//g;
$file = "";
$format = "nformat";
@approach = qw(1 2 3 4 5 6);


#-----------------------------------------------
#INPUT FROM WEB PAGE
#-----------------------------------------------
#$seqname=$cgi->param('SEQNAME');
#$seq=$cgi->param('SEQ');
#$file=$cgi->param('seqfile');
#$format=$cgi->param('format');
##@method=$cgi->param('method');
#@approach=$cgi->param('approach');


$datevar = time();
$lt1 = localtime($datevar);

chomp($seqname);
chomp($seq);
#chomp($file);
chomp($format);
chomp($approach);



$file=~m/^.*(\\|\/)(.*)/; # strip the remote path and keep the filename
while(<$file>) {
    $seqfi .= $_;
}

$tmpdir1="$tmpdir";

#opendir(DIR,"$tmpdir1");
#while($direc=readdir(DIR)){
#    if(-M "$tmpdir1/$direc" > 2){
#	system "rm -rf $tmpdir1/$direc";
#    }
#}
#closedir DIR;
#--------------------Sequence Detection------------------------------
#---------------------------------------------------------------------
if(($seq eq "") && ($seqfi eq "")){
    open(FS,"start");
    while($sl=<FS>){
	#print "$sl";
    }
    close FS;
    
    
    #print "<center><BR><BR><h3><Blink><FONT COLOR=\"red\">Warning:<\/BLINK> No input sequence is detected!!<\/H3></FONT></center>";
    
    open(FE,"end");
    while($el=<FE>){
	#print "$el";
    }
    close FE;
    exit;
    
    
} 
if(($seq ne "") && ($seqfi ne "")){
    open(FS,"start");
    while($sl=<FS>){
	#print "$sl";
    }
    close FS;
    
#    print "<center><BR><BR><h3><Blink><FONT COLOR=red>Warning:<\/BLINK>Sequence input from both sources is detected!!</FONT><\/H3></center>";
    
    
    open(FE,"end");
    while($el=<FE>){
#	print "$el";
    }
    close FE;
    exit;
    
}
#if(($seqfi ne "") && ($seq eq "")){
   # $file=~m/^.*(\\|\/)(.*)/; # strip the remote path and keep the filename
   # while(<$file>) {
	#$seqfi .= $_;
#	chomp($seqfi);
#	if($seqfi=~/^>/){
	#    $seqfi="";
#	}
  #  }
    if($seqfi ne ""){
	$seq = $seqfi;
	
    }
#}

#------------------------------------------------------------------
###-------------------format part started--------------------------
#----------------------------------------------------------------

if ($format eq "nformat"){
    $seq=~tr/[a-z]/[A-Z]/;
    $seq=~s/[^ACDEFGHIKLMNPQRSTVWXY]//g;
    $seq=~s/[\s]/b/g;
    $len=length($seq);
}



elsif ($format eq "sformat"){
    
    open (FP1, ">$tmpdir/seqfor");
    print FP1"$seq";
    close FP1;
    open(FP1, "/gpsr/local/bin/readseq -a $tmpdir/seqfor -f8 |");
    $fw1 = <FP1>;
    $seq = ""; 
    while ($seaq = <FP1>){
	$seq .= $seaq;
    }
    $seq =~ tr/[a-z]/[A-Z]/;
    $seq =~ s/[\s]/b/g;
    $seq =~ s/[^ACDEFGHIKLMNPQRSTVWXY]//g;
    
    $len=length($seq);
    
}

####------------warning part for less than 10 amino acids--------------


if($seqname eq ""){
    $seqname="Protein";
}
if($len < 11){
    
    open(FS,"start");
    while($sl=<FS>){
#	print "$sl";
    }
    close FS;
    
    print OUTHTML "<BR><BR><center><b><FONT COLOR=red><BLINK>WARNING:<\/BLINK>Sequence length too small to be analysed! The Resuts may be artifact. Please enter longer sequence.</FONT><center><\/b>";
    print OUTMAIN "Sequence length too small to be analysed! The Resuts may be artifact. Please enter longer sequence.\n";
    
    open(FE,"end");
    while($el=<FE>){
	#print "$el";
    }
    close FE;
    exit;
    
}

##---------------------------ASSESSING VALUES TO METHOD FOR OUTPUT-------

if($approach==1){
    $method1="IgE epitope and its PID";
}
if($approach==2){
    $method1="MEME/MAST motif";
}

if($approach==3){
    $method1="Support vector machine (SVM)based on amino acid composition";
}

if($approach==4){
    $method1="Support vector machine (SVM) based on dipeptide composition";
}
if($approach==5){
    $method1="Blast search on allergen representative peptides(ARP)";
}


####-----------------------------------------
####--------------printing the output of web page (start part)-----------------
open(FS,"starts");
    while($sl=<FS>){
	#print "$sl";
    }
    close FS;

print OUTHTML "<hr>";

print OUTHTML "<td colspan=2><tr><table width=100% bgcolor=\"#1ECDE7\"><tr><td width=20%><span class=\"blacktitle2\"> Name of sequence </span></td><td width=80%><span class=\"blacktitle2\">$seqname</span></td></tr>";
print OUTMAIN "Name of sequence:\t\t$seqname\n";

@yp=split(//,$seq);
$kuk=@yp;


$lenseque = length($seq);
print OUTHTML "</span></p></td></tr> <tr><td width=35%> <span class=\"blacktitle2\">Length of Sequence </span></td><td width=65%><span class=\"bmtext\">$kuk</span></td></tr><tr><tr><td width=35%><span class=\"blacktitle2\">Preicted On</span></td><td width=65%><span class=\"bmtext\">$lt1</span></td></tr></table>";
print OUTMAIN "Length of Sequence:\t\t$lenseque\nPreicted On:\t\t$lt1\n";

# print "<hr>";

#-------------------------------------------------------------------
#                 ANALYZE
#-------------------------------------------------------------------

$length=length($seq);

#$check=0;
#$filenum=0; $finalnum=0;
#until($check>0){
#    $filenum++;
#    if(!(-e "$tmpdir/algpred$filenum.dir/")){
#	
#	$check=1;
#	$finalnum=$filenum;
#    }
#}
$finalnum = $jobnumber;

$mydir="$tmpdir";

$infile="$mydir/input.txt";
$blastfile="$mydir/blast_input.txt";
$finalfile="$mydir/map_out";
open(FO,">$infile");
print FO "$seq\n"; #----------input file specified-----
#print "++++++++$seq\n";
close FO;

open(FB,">$blastfile");
print FB "> Protein\n";
print FB "$seq";
close FB;





$seq="";
open(FG,"$infile");
while($lg=<FG>){
    chomp($lg);
    $lg=~tr/[a-z]/[A-Z]/;
    $seq.=$lg;
}
close FG;

$length=length($seq);
 
##----------------------choosing approach/Pattern generation and output ------
#*********************************************************************

#-----------approach 1--------------------------------------
 for($m5=0;$m5<7;$m5++){ #for loop

if($approach[$m5]==1){ #loop for approach1  
    system "$homedir/map_IgE.pl $finalnum";
    open(FO,"$tmpdir/pid.txt");
    $ik=<FO>;
    
    
    if($ik>0){
print OUTHTML "<table><td><font color=\"red\">Predicted protein by mapping of IgE epitope and PID&nbsp;&nbsp;</center></font><h2><center><font color=\"red\">";
print OUTMAIN "Predicted protein by mapping of IgE epitope and PID\n";
	print OUTHTML "&nbsp;&nbsp;&nbsp;&nbsp;  ALLERGEN and contains IgE epitope";
	print OUTMAIN "ALLERGEN and contains IgE epitope\n";

       
	    print OUTMAIN "Mapping of IgE Epitopes\n";
	    print OUTMAIN "$seq\n";

	open(FP,"$finalfile");
	while($line=<FP>){
	    chomp($line);
	    
	    @pep=split(/\s+/,$line);
	    $actualmotif[$m]=$pep[0];
	    $seq_motif[$m]=$pep[1]; 
	    $pos4[$m]=$pep[5];
	    $mlen[$m]=$pep[3];
	    $pid[$m]=$pep[4];
	    $m++;
	}
	
	close FP;
	
	
	for($i=0;$i<$m;$i++){
	    
	    $limit=$length-$mlen[$i];
	    $pos[$i]=$pos4[$i];

	    $pos8[$i]=$pos[$i]+1;
	    $space=$pos[$i];
	    $dx1="";		
	    for($u=0;$u<$space;$u++){
		$dx1.="-";
	    }
	    $z=$mlen[$i];
	    $space1=$length-($pos[$i]+$z);
		       
		       $dx2="";
		       for($u=0;$u<$space1;$u++){
			   $dx2.="-";
		       }
		       print OUTMAIN sprintf "$dx1%-$mlen[$i]s$dx2",$actualmotif[$i];
		       
		   }
	    
	    print OUTMAIN "\n\n";
	    print OUTMAIN "Full information\n";
	    
	    print OUTHTML sprintf ("<font color=\"blue\">%-22s</font> %-22s %-12s %-8s <br>\n","IgE epitope","Sequence matched","position","PID");
	    print OUTMAIN sprintf ("%-22s %-22s %-12s %-8s \n","IgE epitope","Sequence matched","position","PID");

	    for($i=0;$i<$m;$i++){
		print OUTHTML sprintf ("<font color=\"blue\">%-22s</font> %-22s %-12s %-8s <br>\n","$actualmotif[$i]","$seq_motif[$i]","$pos8[$i]","$pid[$i]");
		print OUTMAIN sprintf ("%-22s %-22s %-12s %-8s \n","$actualmotif[$i]","$seq_motif[$i]","$pos8[$i]","$pid[$i]");

	 
	}	
    } #close loop for $ik>0
    
    else {
	print OUTHTML "<table><td colspan=2>&nbsp;</td></tr><tr><td colspan=2 align=\"center\"><left><table width=\"100%\" align=\"center\"><tr><td bgcolor=\"#F73A07\"><h4><center><font color=\"white\">Prediction by mapping of IgE epitope&nbsp;&nbsp;</center></h4></font><center><h3><font color=\"yellow\">";
	print OUTMAIN "Prediction by mapping of IgE epitope\n";

	print OUTHTML "The protein sequence does not contain experimentally proven IgE epitope";
	print OUTMAIN "The protein sequence does not contain experimentally proven IgE epitope\n";
    } 
    close FO;
} #end loop for approach 1

#-----------approach 2-------------------------------------
if($approach[$m5]==2){ #loop for approach 2

system "/gpsr/local/bin/mast $modeldir/meme_out_set1 $tmpdir/blast_input.txt  -ev 1 -o $tmpdir/mast.out >/dev/null 2>1";

open(MAUM,"$tmpdir/mast.out/mast.txt");

 while($lineM=<MAUM>){
	chomp($lineM);
	@AA=split(/  +/,$line);
	if(("$AA[0]" eq "SEQUENCE NAME") && ("$AA[1]" eq "DESCRIPTION")){ 
	    $mline=<FO>;
	    $kline="--";
	    until($kline =~ m/^$/){
		
		$kline=<FO>;
		$y++;
		
		
	    }
	}
    }


print OUTHTML "<table><td colspan=2>&nbsp;</td></tr><tr><td colspan=2 align=\"center\"><left><table width=\"100%\" align=\"center\"><tr><td bgcolor=\"#F73A07\"><h4><center><font color=\"white\">MAST RESULT &nbsp;&nbsp;</center></h4></font><center><h3><font color=\"yellow\">";
print OUTMAIN "MAST RESULT\n";
	    if($y==0){
	print OUTMAIN "MAST Results : No Hits found\tNON ALLERGEN\n";
		
	    }

else{
  print  OUTMAIN "MAST Results : Hits found\tALLERGEN";
}



close MAUM;
} #end loop for approach 2

#------------approach 3-----------------------------


if($approach[$m5]==3){ #loop for approach 3


 system "$homedir/comp.pl $finalnum $tmpdir";

system "/gpsr/local/bin/svm5_classify $tmpdir/binary1.txt $modeldir/model_comp $tmpdir/output1 >$tmpdir/out1.algpred";


 open(FO1,"$tmpdir/output1");
 $line1=<FO1>;
 $ppv1=0;$npv1=0;
 if($line1> -2.5){
     $alg1=$line1;
 }
 close FO1;
 #---------calculation of  predictive value-----------

 if($alg1>0.8){
     $ppv1=85.64; $npv1=67.96;
 }
elsif(($alg1>0.6) && ($alg1<=0.8)){
     $ppv1=87.05; $npv1=71.53;
 }
elsif(($alg1>0.4) && ($alg1<=0.6)){
     $ppv1=81.83; $npv1=74.03;
 }

elsif(($alg1>0.2) && ($alg1<=0.4)){
     $ppv1=74.81; $npv1=76.94;
 }


elsif(($alg1>0.0) && ($alg1<=0.2)){
     $ppv1=70.05; $npv1=80.74;
 }

elsif(($alg1>-0.2) && ($alg1<=0.0)){
     $ppv1=64.55; $npv1=86.61;
 }

elsif(($alg1>-0.4) && ($alg1<=-0.2)){
     $ppv1=47.13; $npv1=89.71;
 }

elsif(($alg1>-0.6) && ($alg1<=-0.4)){
     $ppv1=18.21; $npv1=71.24;
 }

elsif(($alg1>-0.8) && ($alg1<-0.6)){
     $ppv1=22.82; $npv1=92.94;
 }
elsif($alg1<-1){
     $ppv1=15.19; $npv1=94.18;
 }

 
#------------------
      
print OUTHTML "<table><td colspan=2>&nbsp;</td></tr><tr><td colspan=2 align=\"center\"><left><table width=\"100%\" align=\"center\"><tr><td bgcolor=\"#F73A07\"><h4><center><font color=\"white\">Prediction by SVM method based on amino acid composition&nbsp;&nbsp;</center></h4></font><center><h3><font color=\"yellow\">";
print OUTMAIN "Prediction by SVM method based on amino acid composition\n";
    
   if($alg1 >=0.4){
print OUTHTML "&nbsp;&nbsp;&nbsp;&nbsp; Potential ALLERGEN &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br><br>&nbsp;&nbsp;Score= $alg1 &nbsp;&nbsp;&nbsp;&nbsp;[Threshold= -0.4]<br><br>&nbsp;&nbsp;Positive Predictive Value= $ppv1\%&nbsp;&nbsp;&nbsp;&nbsp;Negative Predictive Value= $npv1\%";
print OUTMAIN "Potential ALLERGEN\tScore= $alg1\t[Threshold= -0.4]\tPositive Predictive Value= $ppv1\tNegative Predictive Value= $npv1\n";
}

elsif($alg1 >=-.4){
print OUTHTML "&nbsp;&nbsp;&nbsp;&nbsp;  ALLERGEN &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br><br>&nbsp;&nbsp;Score= $alg1 &nbsp;&nbsp;&nbsp;&nbsp;[Threshold= -0.4]<br><br>&nbsp;&nbsp;Positive Predictive Value= $ppv1\%&nbsp;&nbsp;&nbsp;&nbsp;Negative Predictive Value= $npv1\%";
print OUTMAIN "ALLERGEN\tScore= $alg1\t[Threshold= -0.4]\tPositive Predictive Value= $ppv1\tNegative Predictive Value= $npv1\n";
}
else{
    print OUTHTML "&nbsp;&nbsp;&nbsp;&nbsp;  NON ALLERGEN &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br><br>&nbsp;&nbsp;Score=$line1 &nbsp;&nbsp;&nbsp;&nbsp;[Threshold=-0.4]<br><br>&nbsp;&nbsp;Positive Predictive Value=$ppv1\% &nbsp;&nbsp;&nbsp;&nbsp;Negative Predictive Value=$npv1\%";
chomp($line1);
    print OUTMAIN "NON ALLERGEN\tScore=$line1\t[Threshold=-0.4]\tPositive Predictive Value=$ppv1\tNegative Predictive Value=$npv1\n";
}
   

	} #end loop for approach 3


#-----------approach 4-----------------------

if($approach[$m5]==4){ #loop for approach 4


 system "$homedir/dipep.pl $finalnum $tmpdir";

system "/gpsr/local/bin/svm5_classify $tmpdir/binary.txt $modeldir/model_dipep $tmpdir/output2 >$tmpdir/out2.algpred";


open(FOU,"$tmpdir/output2");
	$line=<FOU>;
	
	
 $ppv=0;$npv=0;
		
	if($line> -5){
	    $alg=$line;
	}
	close FOU;
#---------calculation of  predictive value-----------

 if($alg>0.8){
     $ppv=100.00; $npv=59.74;
 }
if(($alg>0.6) && ($alg<=0.8)){
     $ppv=82.97; $npv=62.40;
 }
if(($alg>0.4) && ($alg<=0.6)){
     $ppv=86.55; $npv=66.47;
 }

if(($alg>0.2) && ($alg<=0.4)){
     $ppv=85.88; $npv=72.01;
 }


if(($alg>0.0) && ($alg<=0.2)){
     $ppv=74.14; $npv=79.04;
 }

if(($alg>-0.2) && ($alg<=0.0)){
     $ppv=63.10; $npv=85.56;
 }

if(($alg>-0.4) && ($alg<=-0.2)){
     $ppv=39.40; $npv=89.34;
 }

if(($alg>-0.6) && ($alg<=-0.4)){
     $ppv=27.66; $npv=92.40;
 }

if(($alg>-0.8) && ($alg<-0.6)){
     $ppv=13.26; $npv=74.19;
 }
if($alg<-1){
     $ppv=8.69; $npv=75.22;
 }


#------------------
print OUTHTML "<table><td colspan=2>&nbsp;</td></tr><tr><td colspan=2 align=\"center\"><left><table width=\"100%\" align=\"center\"><tr><td bgcolor=\"#F73A07\"><h4><center><font color=\"white\">Prediction based on SVM method based on dipeptide composition &nbsp;&nbsp;</center></h4></font><center><h3><font color=\"yellow\">";
print OUTMAIN "Prediction based on SVM method based on dipeptide composition\n";
    
    
if($alg>=0.2){

    print OUTHTML "&nbsp;&nbsp;&nbsp;&nbsp; Potential ALLERGEN &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br><br>&nbsp;&nbsp;Score= $line &nbsp;&nbsp;&nbsp;&nbsp;[Threshold= -0.2]<br><br>&nbsp;&nbsp;Positive Predictive Value=$ppv\% &nbsp;&nbsp;&nbsp;&nbsp;Negative Predictive Value=$npv\%";
    print OUTMAIN "Potential ALLERGEN\tScore= $line\t[Threshold= -0.2]\tPositive Predictive Value=$ppv\tNegative Predictive Value=$npv\n";
}

elsif($alg>=-0.2){
    print OUTHTML "&nbsp;&nbsp;&nbsp;&nbsp;  ALLERGEN &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br><br>&nbsp;&nbsp;Score= $line &nbsp;&nbsp;&nbsp;&nbsp;[Threshold= -0.2]<br><br>&nbsp;&nbsp;Positive Predictive Value=$ppv\% &nbsp;&nbsp;&nbsp;&nbsp;Negative Predictive Value=$npv\%";
    print OUTMAIN "ALLERGEN\tScore= $line]\t[Threshold= -0.2]\tPositive Predictive Value=$ppv\tNegative Predictive Value=$npv\n";
}

else{
    print OUTHTML "&nbsp;&nbsp;&nbsp;&nbsp;  NON ALLERGEN &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br><br>&nbsp;&nbsp;Score= $line &nbsp;&nbsp;&nbsp;&nbsp;[Threshold= -0.2]<br><br>&nbsp;&nbsp;Positive Predictive Value=$ppv\% &nbsp;&nbsp;&nbsp;&nbsp;Negative Predictive Value=$npv\%";
    print OUTMAIN "NON ALLERGEN\tScore= $line\t[Threshold= -0.2]\tPositive Predictive Value=$ppv\tNegative Predictive Value=$npv\n";
}

	} #end loop for approach 4



#-----------approach 5-----------------------

if($approach[$m5]==5){ #loop for approach 5

#------- handling Blast part*******************************

 system "/gpsr/software/blastpr/blastpgp -e 0.001 -j 1 -d $blastdatadir/ARP_database -i $tmpdir/blast_input.txt -o $tmpdir/blast.out";
	    open(MAB,"$tmpdir/blast.out");
	    while($lin=<MAB>){
		chomp($lin);
		if(($lin=~ /significant/) && ($lin=~ /alignments:/)){
		    $lin=<MAU>;
		    $lin=<MAU>;
		    if($y>0){
			$lin=<MAU>;
		    }
		    $y++;
		chomp($lin);
		    @ff=split(/  +/,$lin);
		}
		
		if($lin=~ /Sbjct: /){
		    $predline=$lin;
		    @pp=split(/ +/,$predline);
		    
		}	
		
	    }
 close MAB;
	    
	    print OUTHTML "<table><td colspan=2>&nbsp;</td></tr><tr><td colspan=2 align=\"center\"><left><table width=\"100%\" align=\"center\"><tr><td bgcolor=\"#F73A07\"><h4><center><font color=\"white\">Blast RESULT &nbsp;&nbsp;</center></h4></font><center><h3><font color=\"yellow\">";
	   print OUTMAIN "BLAST RESULT\n";
	    
	    
 if($y==0){
     print OUTHTML "BLAST Results of ARPS : No Hits found <br><br><br>&nbsp;&nbsp;&nbsp;&nbsp;  NON ALLERGEN &nbsp;&nbsp;&nbsp;";
     print OUTMAIN "BLAST Results of ARPS : No Hits found\tNON ALLERGEN\n";
 }
 
 #if($ff[0]=~ /ARP/)
      else {
     print OUTHTML "Hits found with ARPs database: $pp[2]<br><br><br>&nbsp;&nbsp;&nbsp;&nbsp;  ALLERGEN &nbsp;&nbsp;&nbsp;";
     print OUTMAIN "Hits found with ARPs database: $pp[2]\tALLERGEN\n";
 }


}#end loop for approach 5


#-----------approach 6 Hybrid approach-----------------------

if($approach[$m5]==6){ #loop for approach 6


print OUTHTML "<table><td colspan=2>&nbsp;</td></tr><tr><td colspan=2 align=\"center\"><left><table width=\"100%\" align=\"center\"><tr><td bgcolor=\"#F73A07\"><h4><center><font color=\"white\">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Prediction by Hybrid Approach&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</center></h4></font><center><h3><font color=\"yellow\">";
print OUTMAIN "Prediction by Hybrid Approach\n";

#-------IgE method--------------

system "$homedir/map_IgE_hyb.pl $finalnum";
    open(FOHY,"$tmpdir/pid_hyb.txt");
  $ikH=<FOHY>;
    
    
    if($ikH>0){

	print OUTHTML "&nbsp;&nbsp;&nbsp;&nbsp;  ALLERGEN (By IgE method) &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<br><br>";
	print OUTMAIN "ALLERGEN (By IgE method)]\n";
}

close FOHY;

#------------ARP BLAST---------
 system "/gpsr/software/blastpr/blastpgp -e 0.001 -j 1 -d $blastdatadir/ARP_database -i $tmpdir/blast_input.txt -o $tmpdir/blast_hyb.out";
	    open(MABH,"$tmpdir/blast_hyb.out");
	    while($linH=<MABH>){
		chomp($linH);
		if(($linH=~ /significant/) && ($linH=~ /alignments:/)){
		    $linH=<MAUH>;
		    $linH=<MAUH>;
		   if($yh>0){
			$linH=<MAUH>;
		    }
		    $yh++;
		chomp($linH);
	    @ff=split(/  +/,$linH);
		}
		
		if($linH=~ /Sbjct: /){
		    $predline=$linH;
		    @pp=split(/ +/,$predline);
		    
		}	
		
	  }
 close MABH;
	    	    
	    
if($yh>0){
     
     print OUTHTML " ALLERGEN (By ARPs BLAST method)&nbsp;&nbsp;&nbsp;<br><br>";
     print OUTMAIN "ALLERGEN (By ARPs BLAST method)\n";
 }
 


#---------svmcomp-------------

 system "$homedir/comp_hyb.pl $finalnum $tmpdir";

system "/gpsr/local/bin/svm5_classify $tmpdir/binary1_hyb.txt $modeldir/model_comp $tmpdir/output1_hyb >$tmpdir/out1_hyb.algpred";


 open(FO1H,"$tmpdir/output1_hyb");
 $line1H=<FO1H>;
chomp($line1H);
 if($line1H> -5){
     $alg1H=$line1H;
 }
 close FO1H;
 

if($alg1H >=-0.4){
    print OUTHTML "&nbsp;&nbsp;&nbsp;&nbsp; ALLERGEN &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br><br>&nbsp;";
    print OUTMAIN "ALLERGEN\n";
}
else{
    print OUTHTML "&nbsp;&nbsp;&nbsp;&nbsp; NON ALLERGEN &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;"; 
    print OUTMAIN "NON ALLERGEN\n"; 
}



}#end loop for approach 6



} #end for loop m5  
#----------------------print of end section---------------------------

open(FE,"end1");
    while($el=<FE>){
	#print "$el";
    }
    close FE;


if(-e "/gpsr/standalone/algpred/1") { `rm /gpsr/standalone/algpred/1`; }