--- name: "Bio::Tools::Run::BWA" section: "3pm" platform: "linux" package: "libbio-perl-run-perl" version: "1.7.2-4" release: "Debian 10 (Buster)" platforms: ["linux"] url: "https://new.carta.tech/Bio::Tools::Run::BWA" --- # Bio::Tools::Run::BWA(3pm) Run wrapper for the BWA short-read assembler \*BETA\* ## NAME Bio::Tools::Run::BWA - Run wrapper for the BWA short-read assembler \*BETA\* ## SYNOPSIS ``` # create an assembly # run BWA commands separately ``` ## DESCRIPTION This module provides a wrapper interface for Heng Li's reference-directed short read assembly suite `"bwa"` (see \ for manuals and downloads). Manipulating the alignments requires `"samtools"` (\) and Lincoln Stein's package `"Bio-SamTools"` (\). 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" ); ``` ## OPTIONS `"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 \ for the gory details. ## FILES 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()*\>. ## 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 the Bioperl mailing list. 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 of the bugs and their resolution. Bug reports can be submitted via the web: ``` http://redmine.open-bio.org/projects/bioperl/ ``` ## AUTHOR - Mark A. Jensen ``` Email maj -at- fortinbras -dot- us ``` ## APPENDIX 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) ``` ## Bio::Tools::Run::AssemblerBase overrides ### *\_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 ```