Hi, I submitted this problem a few days ago and din't get much of a response (probably because I didn't explain it properly).... my program below is getting two errors messages and i really can't find anything wrong with it. the lines containing errors are: 
   if( ($counter > $pos_end) && ($orf_counter < @orf_array_pos) ) 
  and

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the error message for above is "uninitailised value in numeric gt (>) <FASTA> and 
   
  if( ($counter >= $pos_start) && ($counter <= $pos_end) )

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in which the error message is "uninitalised vlaue in numeric le (<=) <FASTA> Maybe the problem is something to do with $pos_end. All the variables in these two lines are declared so i can't see the problem.

If it helps the program reads in strings of DNA and prints to an output file the bits that don't overlap. $counter reads along one string, and $orf_counter counts the position in the second file. $pos_start and $pos_end just refer to the start and stop positions of matches. The first command line input file contains three columns of data which are orf no, then start and stop positions of each orf. the second command line input file is a genome sequence. The program reads through the orf file trying to match the orfs to the genome sequence. Please help me monks, i need you!!!!!! 


  #! /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";

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Edit by tye

In reply to uninitalised value in numeric by Anonymous Monk

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