#! /usr/local/bin/perl -w

  use strict;

  my($num_of_params,$line,$key,$name);
  my @keys;
  my %orf_hash_pos;                              
  $num_of_params = @ARGV;

  if($num_of_params < 3)
  {
    die ("\n Not enough params have been entered!!!!\n");

  }

  open (ORF_POS, $ARGV[0]) or die "unable to open file";
  open (FASTA, $ARGV[1]) or die "unable to open file";


   open (OUTFILE, ">$ARGV[2]");

  foreach $line (<ORF_POS>)
  {
    if(! ($line =~ /(\d+)\s+(\d+)\s+(\d+)/))
    {
      print "CHECK YOR FILE .... continue \n";
      next;
    }

   if($2 <= $3)                               
   {
      $orf_hash_pos{$2} = $3;
    }
    else
    {
      $orf_hash_pos{$3} = $2;
    }

  }

  @keys = sort { $a <=> $b } ( keys %orf_hash_pos );

  #--------------- step 2 ---------------------------

  my $counter=0;
  my $orf_counter=0;
  my $new_pos;
  my $pos_start=0;
  my $pos_end=0;
  my $found_new=0;
  my @lines;
  my @dna;
  my @orf_array_pos;
  my $base;
  my $dna;
  my $orf_names;


  @lines = <FASTA>;

  chomp @lines;       
  $dna = join( '', @lines);

  @dna = split( '', $dna);

  foreach $key (@keys)
  {
    push @orf_array_pos , $key;
    push @orf_array_pos , $orf_hash_pos{$key};
  }                                                 
  $pos_start = $orf_array_pos[$orf_counter];
  $pos_end = $orf_array_pos[$orf_counter+1];
  $found_new=0;

  foreach $base (@dna)
  {

    if( ($counter > $pos_end) && ($orf_counter < @orf_array_pos) )
      {
      $orf_counter += 2;
      $new_pos = $orf_array_pos[$orf_counter];            
   
  if($new_pos < $pos_end)
        {
        $pos_start = $pos_end;
        }
      else
        {
        $pos_start = $new_pos;
        }
      $pos_end = $orf_array_pos[$orf_counter+1];
     }                                  

   if( ($counter >= $pos_start) && ($counter <= $pos_end) )
    {
      $found_new=0;
    }
    else
    {
      if($found_new==0)
        {
        $orf_names = $orf_counter + 1;
        $found_new=1;
        print "\n\n> dORF$orf_names \n";
        print OUTFILE "\n\n> dORF$orf_names \n";

        }
      print $base;
      print OUTFILE $base;

    }
  $counter++;
  }


  print "\n";