Christopher Fields
and 1 contributors


Bio::Tools::Run::Cap3 - wrapper for CAP3


  use Bio::Tools::Run::Cap3;
  # Run Cap3 using an input FASTA file
  my $factory = Bio::Tools::Run::Cap3->new( -clipping_range => 150 );
  my $asm_obj = $factory->run($fasta_file, $qual_file);
  # An assembly object is returned by default
  for my $contig ($assembly->all_contigs) {
    ... do something ...

  # Read some sequences
  use Bio::SeqIO;
  my $sio = Bio::SeqIO->new(-file => $fasta_file, -format => 'fasta');
  my @seqs;
  while (my $seq = $sio->next_seq()) {
    push @seqs,$seq;

  # Run Cap3 using input sequence objects and returning an assembly file
  my $asm_file = 'results.ace';


  Wrapper module for CAP3 program


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Marc Logghe


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : new
 Usage   : $factory->new(
             -overlap_length_cutoff   => 35,
             -overlap_identity_cutoff => 98 # %
 Function: Create a new Cap3 factory
 Returns : A Bio::Tools::Run::Cap3 object
 Args    : Cap3 options available in this module:
  band_expansion_size        specify band expansion size N > 10 (20)
  differences_quality_cutoff specify base quality cutoff for differences N > 15 (20)
  clipping_quality_cutoff    specify base quality cutoff for clipping N > 5 (12)
  max_qscore_sum             specify max qscore sum at differences N > 20 (200)
  extra_nof_differences      specify clearance between no. of diff N > 10 (30)
  max_gap_length             specify max gap length in any overlap N > 1 (20)
  gap_penalty_factor         specify gap penalty factor N > 0 (6)
  max_overhang_percent       specify max overhang percent length N > 2 (20)
  match_score_factor         specify match score factor N > 0 (2)
  mismatch_score_factor      specify mismatch score factor N < 0 (-5)
  overlap_length_cutoff / minimum_overlap_length
                             specify overlap length cutoff > 20 (40)
  overlap_identity_cutoff / minimum_overlap_similarity
                             specify overlap percent identity cutoff N > 65 (80)
  reverse_orientation_value  specify reverse orientation value N >= 0 (1)
  overlap_score_cutoff       specify overlap similarity score cutoff N > 400 (900)
  max_word_occurrences       specify max number of word matches N > 30 (300)
  min_correction_constraints specify min number of constraints for correction N > 0 (3)
  min_linking_constraints    specify min number of constraints for linking N > 0 (2)
  clipping_info_file         specify file name for clipping information (none)
  output_prefix_string       specify prefix string for output file names (cap)
  clipping_range             specify clipping range N > 5 (250)
  min_clip_good_reads        specify min no. of good reads at clip pos N > 0 (3)


 Title   : out_type
 Usage   : $assembler->out_type('Bio::Assembly::ScaffoldI')
 Function: Get/set the desired type of output
 Returns : The type of results to return
 Args    : Desired type of results to return (optional):
                 'Bio::Assembly::IO' object
                 'Bio::Assembly::ScaffoldI' object (default)
                 The name of a file to save the results in


 Title   :   run
 Usage   :   $asm = $factory->run($fasta_file);
 Function:   Run CAP3
 Returns :   Assembly results (file, IO object or assembly object)
 Args    :   - sequence input (FASTA file or sequence object arrayref)
             - optional quality score input (QUAL file or quality score object


 Title   :   _run
 Usage   :   $factory->_run()
 Function:   Make a system call and run Cap3
 Returns :   An assembly file
 Args    :   - FASTA file
             - optional QUAL file