Bio::Tools::Run::Cap3(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::Cap3(3pm) |
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'; $factory->out_type($asm_file); $factory->run(\@seqs);
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 arrayref)
Title : _run Usage : $factory->_run() Function: Make a system call and run Cap3 Returns : An assembly file Args : - FASTA file - optional QUAL file
2018-09-14 | perl v5.26.2 |