NAME

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

SYNOPSIS

         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';
         $factory->out_type($asm_file);
         $factory->run(\@seqs);

DESCRIPTION

         Wrapper module for CAP3 program

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to one of the Bioperl mailing lists.  Your
       participation is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their
       resolution.  Bug reports can be submitted via the web:

         http://redmine.open-bio.org/projects/bioperl/

AUTHORS

       Marc Logghe

APPENDIX

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

   new
        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)

   out_type
        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

   run
        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
                      arrayref)

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