Venerable monks

I have some objects called $slice which basically represent a very long character string (e.g. millions of characters long). A code library i am using takes a $slice object and breaks it down into a set of subslices of a particular length. It returns an array of slice objects where each slice now represents a bit of the original string. For example it can take a slice of 100 characters and break it down into 10 * 10 character strings. These are returned in an array of $slice objects. For example slice 1 will now represent characters 1 to 10, slice 2 represents characers 11-20 etc. (actually the function works out the length of the slice to use based on user input

I thought the code would return slices/substrings in order when i looked at it. e.g. 1-10, 11-20, 21-30, but when using it the subslices are not in order. I am a perl beginner and can't modify the code to get it to do what i want. I was hoping you might be able to help. I thought they would be in order because the push function is putting each successive slice onto the end of the array.

Arg [1]    : ref to list of slices  
Arg [2]    : int maxlength of sub slices  
Arg [3]    : int overlap length (optional)  Example    : my $sub_slice
+s = split_Slices($slices,$maxlen,$overlap)  Description: splits a sli
+ce into smaller slices   Returntype : ref to list of slices  
Exceptions : maxlen <1 or overlap < 0

sub split_Slices {
  my ($slice_big,$max_length,$overlap)=@_;

  if(!defined($max_length) or $max_length < 1){
    throw("maxlength needs to be set and > 0");
  }

  if(!defined($overlap)){
    $overlap = 0;
  }
  elsif($overlap < 0){
    throw("negative overlaps not allowed");
  }

  my @out=();

  foreach my $slice (@$slice_big){

    my $start = $slice->start;
    my $end;
    my $multiple;
    my $number;
    my $length = $slice->length;

    if($max_length && ($length > $overlap)) {
      #No seq region may be longer than max_length but we want to make
+      
#them all similar size so that the last one isn't much shorter.      
#Divide the seq_region into the largest equal pieces that are shorter 
+     
#than max_length
      #calculate number of slices to create      
$number = ($length-$overlap) / ($max_length-$overlap);      
$number = ceil($number); 
#round up to int
      #calculate length of created slices      
$multiple = $length / $number;      
$multiple   = floor($multiple); #round down to int    } else {
      #just one slice of the whole seq_region      
$number = 1;
      $multiple = $length;
    }

    my $i;
    for(my $i=0; $i < $number; $i++) {
      $end = $start + $multiple + $overlap;

      #any remainder gets added to the last slice of the seq_region   
+   $end = $slice->end if($i == $number-1);
      push @out, Bio::EnsEMBL::Slice->new
        (-START             => $start,
         -END               => $end,
         -STRAND            => 1,
         -SEQ_REGION_NAME   => $slice->seq_region_name,
         -SEQ_REGION_LENGTH => $slice->seq_region_length,
         -COORD_SYSTEM      => $slice->coord_system,
         -ADAPTOR           => $slice->adaptor);
      $start += $multiple + 1;
    }
  }

  return\@ out;
}



1;
}

[download]
thanks very much

In reply to sorting problem by Anonymous Monk

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