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.\"
.IX Title "Bio::Tools::Run::Cap3 3pm"
.TH Bio::Tools::Run::Cap3 3pm "2017-01-13" "perl v5.24.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.nh
.SH "NAME"
Bio::Tools::Run::Cap3 \- wrapper for CAP3
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 8
\&  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 => \*(Aqfasta\*(Aq);
\&  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 = \*(Aqresults.ace\*(Aq;
\&  $factory\->out_type($asm_file);
\&  $factory\->run(\e@seqs);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
.Vb 1
\&  Wrapper module for CAP3 program
.Ve
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHORS"
.IX Header "AUTHORS"
Marc Logghe
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 10
\& 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)
.Ve
.SS "out_type"
.IX Subsection "out_type"
.Vb 8
\& Title   : out_type
\& Usage   : $assembler\->out_type(\*(AqBio::Assembly::ScaffoldI\*(Aq)
\& Function: Get/set the desired type of output
\& Returns : The type of results to return
\& Args    : Desired type of results to return (optional):
\&                 \*(AqBio::Assembly::IO\*(Aq object
\&                 \*(AqBio::Assembly::ScaffoldI\*(Aq object (default)
\&                 The name of a file to save the results in
.Ve
.SS "run"
.IX Subsection "run"
.Vb 7
\& 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)
.Ve
.SS "_run"
.IX Subsection "_run"
.Vb 6
\& Title   :   _run
\& Usage   :   $factory\->_run()
\& Function:   Make a system call and run Cap3
\& Returns :   An assembly file
\& Args    :   \- FASTA file
\&             \- optional QUAL file
.Ve