use warnings;
use strict;
use lib '/opt/deepak/bioperl-1.5.1';
use lib 'lib/perl5/site_perl/5.8.5/';

use Bio::SimpleAlign;
use Bio::SearchIO;
use Bio::AlignIO;
use Error qw(:try);

use Config::Simple;


&blastParser;


sub blastParser
{
  my $outFileName = "OutPutFile";
  open (outFILE,">$outFileName") or die "can't Open output file file";
      
  try{   
  print "\nTEST-Inside...";
  
  my $hitCount = 0;
  $hitCount = $ARGV[0]; 
  my $hitAllignCnt = 0;
  my $seqCnt = 0;
  my $arrayCntr = 0;
  
  #This is the file that is transfered by ftp to the current working
  #directory
  my $file = "tempBlastFile";

  my $in = new Bio::SearchIO(-format => 'blast',
	 # comment out the next line to read STDIN
			   -file   => $file );
   
   while ( my $result = $in->next_result ) 
   { 
      print "\nTEST-Inside result..";
           
        my @stats =  $result->available_statistics;
        my @params = $result->available_parameters;
          
        while ( my $hit = $result->next_hit and $hitCount) 
        {     
            $hitCount--;
            $hitAllignCnt++;
            print "\n\nTEST-Recordcount ::\t$hitCount\n\n";   
          	my $id =         $hit->matches('id');
          	my $cons =       $hit->matches('cons');
          	my @accs =       $hit->each_accession_number;
          	my @qidentical = $hit->seq_inds('query','identical');
          	my @qconserved = $hit->seq_inds('query','conserved');
          	my @hidentical = $hit->seq_inds('hit','identical');
          	my @hconserved = $hit->seq_inds('hit','conserved');
     
            $seqCnt=0;
            while(my $hsp = $hit->next_hsp)
            {
            $seqCnt++;
     	      my ($qid,$qcons) = $hsp->matches('hit');
            my ($id,$cons) = $hsp->matches('query');
            @qidentical = $hsp->seq_inds('query','identical');
    	      @qconserved = $hsp->seq_inds('query','conserved');
	          @hidentical = $hsp->seq_inds('hit','identical');
      	    @hconserved = $hsp->seq_inds('hit','conserved');
      	    my @hrange =  $hsp->range('hit');
      	    my @qrange =  $hsp->range('query');
    	      my $aln =     $hsp->get_aln;
      	    my $alnIO =
            Bio::AlignIO->new(-format=>"clustalw",-file=>'>tempHitFile');
            print outFILE "\nHIT-NUMBER=$hitAllignCnt.$seqCnt";
            print outFILE "\nHIT-NAME=".$hit->name;
            print outFILE "\nHIT-ACCESSION=".$hit->accession;
            print outFILE "\nHIT-ROW-SCORE=".$hit->raw_score;
            print outFILE "\nHIT-BITS=".$hit->bits;
            print outFILE "\nHIT-GAPS=".$hit->gaps;            
            print outFILE "\nHIT-EVALUE=".$hsp->evalue;
            print outFILE "\nHIT-PERCENT-IDENTITY=".$hsp->percent_identity;
            
            $alnIO->write_aln($aln);
            open hitFile, "tempHitFile" or die "Can't read file";
            undef $/;
            my $allignMent =  <hitFile>;
            close  hitFile;  
            
            print outFILE "\nALLIGNMENT=START";
            print outFILE "\n$allignMent";
            print outFILE "\nEND";
            undef $hsp;
            undef $allignMent;
            undef $alnIO;
            undef $aln;
            undef @qrange;
            undef @hrange;
            undef @hconserved;
            undef @hidentical;
            undef @qconserved;
            undef @qidentical;
         	}#hsp while ends
          undef $hit;
       }#hit while ends
       undef $result;
    }#result while end
     undef $in;
     print "\nTEST=Returning and Closing the OutPutFile\n";
     close outFILE;
  } 
  catch Error with 
  {
     my $ex = shift;
     #print "\nException...:$ex\n";
     close outFILE;
     my $commandLine = "rm $outFileName";
     system($commandLine);
     
     open (outFILE,">$outFileName") or die "can't Open output file file";
     print outFILE "\nERROR=$ex\n";
     close outFILE;
     return ;  
  }
}