Batch_SCLAP

#!/usr/bin/perl
######## Sub Chloroplast Loclaization using ADABOOST predictor (SCLAP)#####################
#        Developed by SARAVANAN VIJAYAKUMAR
#         Centre for Bioinformatics, Pondicherry University
#         brsaran@gmail.com
#         Date: 15-03-2012
#

use List::Util qw[max];
use CGI qw(:standard);

print "Enter Protein File:";
$input = <STDIN>;
open(FIL1,"$input");
@Seq_hold1 = <FIL1>;

foreach(@Seq_hold1){
         if(substr(@Seq_hold1[$j],0,1) eq ">"){
                $i=$i+1;
                @Seq_submit1[$i]= @Seq_hold1[$j]."\n";
                @FASTA_Header[$i]= substr($Seq_hold1[$j],1,11);
                $j++;
             }
             else{
                  @Rawseq1[$i].= @Seq_hold1[$j];
                  $Rawseq1[$i]=~s/\s//g;
                  @Seq_submit1[$i].= @Seq_hold1[$j];
                  $j++;
                  $k++;
             }
}

for($m=1;$m<=@Rawseq1;$m++){
	$x = int(rand(10002)).".fasta";
	open(FL,">$x");
	print FL $Rawseq1[$m];
	close(FL);
	$FileOh = $FASTA_Header[$m];
	$FileOh=~s/\W//g;
	`./SCLAP $x $FileOh`;
	unlink($x);
	print "$FASTA_Header[$m] Completed !\n"
}