Bio::Tools::Run::Cap3(3pm) User Contributed Perl Documentation Bio::Tools::Run::Cap3(3pm)
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
perl v5.12.3 2011-06-18 Bio::Tools::Run::Cap3(3pm)