Provided by: libbio-perl-run-perl_1.6.9-2_all
Bio::Tools::Run::BWA - Run wrapper for the BWA short-read assembler *BETA*
# create an assembly # run BWA commands separately
This module provides a wrapper interface for Heng Li's reference-directed short read assembly suite "bwa" (see <http://bio-bwa.sourceforge.net/bwa.shtml> for manuals and downloads). Manipulating the alignments requires "samtools" (<http://sourceforge.net/projects/samtools/>) and Lincoln Stein's package "Bio-SamTools" (<http://search.cpan.org/perldoc?Bio::DB::Sam>). There are two modes of action. · Easy assembly The first is a simple pipeline through the "maq" commands, taking your read data in and squirting out an assembly object of type Bio::Assembly::IO::maq. The pipeline is based on the one performed by "maq.pl easyrun": Action maq commands ------ ------------ data conversion to fasta2bfa, fastq2bfq maq binary formats map sequence reads map to reference seq assemble, creating assemble consensus convert map & cns mapview, cns2fq files to plaintext (for B:A:IO:maq) Command-line options can be directed to the "map", "assemble", and "cns2fq" steps. See "OPTIONS" below. · BWA command mode The second mode is direct access to "bwa" commands. To run a "bwa" command, construct a run factory, specifying the desired command using the "-command" argument in the factory constructor, along with options specific to that command (see "OPTIONS"): $bwafac = Bio::Tools::Run::BWA->new( -command => 'fasta2bfa' ); To execute, use the "run_bwa" methods. Input and output files are specified in the arguments of "run_bwa" (see "FILES"): $bwafac->run_bwa( -fas => "myref.fas", -bfa => "myref.bfa" );
"bwa" is complex, with many subprograms (commands) and command-line options and file specs for each. This module attempts to provide commands and options comprehensively. You can browse the choices like so: $bwafac = Bio::Tools::Run::BWA->new( -command => 'aln' ); # all maq commands @all_commands = $bwafac->available_parameters('commands'); @all_commands = $bwafac->available_commands; # alias # just for aln @aln_params = $bwafac->available_parameters('params'); @aln_switches = $bwafac->available_parameters('switches'); @aln_all_options = $bwafac->available_parameters(); Reasonably mnemonic names have been assigned to the single-letter command line options. These are the names returned by "available_parameters", and can be used in the factory constructor like typical BioPerl named parameters. See <http://bio-bwa.sourceforge.net/bwa.shtml> for the gory details.
When a command requires filenames, these are provided to the "run_bwa" method, not the constructor ("new()"). To see the set of files required by a command, use "available_parameters('filespec')" or the alias "filespec()": $bwafac = Bio::Tools::Run::BWA->new( -command => 'aln' ); @filespec = $bwafac->filespec; This example returns the following array: fas faq >sai This indicates that the FASTA database (faq) and the FASTQ reads (faq) MUST be specified, and the STDOUT of this program (SA coordinates) MAY be slurped into a file specified in the "run_bwa" argument list: $bwafac->run_bwa( -fas => 'my.db.fas', -faq => 'reads.faq', -sai => 'out.sai' ); If files are not specified per the filespec, text sent to STDOUT and STDERR is saved and is accessible with "$bwafac-"stdout()> and "$bwafac-"stderr()>.
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AUTHOR - Mark A. Jensen
Email maj -at- fortinbras -dot- us
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new() Title : new Usage : my $obj = new Bio::Tools::Run::BWA(); Function: Builds a new Bio::Tools::Run::BWA object Returns : an instance of Bio::Tools::Run::BWA Args : run Title : run Usage : $assembly = $bwafac->run( @args ); Function: Run the bwa assembly pipeline. Returns : Assembly results (file, IO object or Assembly object) Args : - fastq file containing single-end reads - fasta file containing the reference sequence - [optional] fastq file containing paired-end reads run_bwa() Title : run_bwa Usage : $obj->run_bwa( @file_args ) Function: Run a bwa command as specified during object contruction Returns : Args : a specification of the files to operate on: stdout() Title : stdout Usage : $fac->stdout() Function: store the output from STDOUT for the run, if no file specified in run_maq() Example : Returns : scalar string Args : on set, new value (a scalar or undef, optional) stderr() Title : stderr Usage : $fac->stderr() Function: store the output from STDERR for the run, if no file is specified in run_maq() Example : Returns : scalar string Args : on set, new value (a scalar or undef, optional)
_check_sequence_input() No-op. _check_optional_quality_input() No-op. _prepare_input_sequences Convert input fastq and fasta to maq format. _collate_subcmd_args() Title : _collate_subcmd_args Usage : $args_hash = $self->_collate_subcmd_args Function: collate parameters and switches into command-specific arg lists for passing to new() Returns : hash of named argument lists Args : [optional] composite cmd prefix (scalar string) [default is 'run'] _run() Title : _run Usage : $factory->_run() Function: Run a bwa assembly pipeline Returns : a text-formatted sam alignment Args : - single end read file in maq bfq format - reference seq file in maq bfa format - [optional] paired end read file in maq bfq format available_parameters() Title : available_parameters Usage : @cmds = $fac->available_commands('commands'); Function: Use to browse available commands, params, or switches Returns : array of scalar strings Args : 'commands' : all bwa commands 'params' : parameters for this object's command 'switches' : boolean switches for this object's command 'filespec' : the filename spec for this object's command 4Geeks : Overrides Bio::ParameterBaseI via Bio::Tools::Run::AssemblerBase