/ 
BioPerl-Run-1.007001
River stage one • 2 direct dependents • 2 total dependents
/ Bio::Tools::Run::BWA

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 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" );

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 http://bio-bwa.sourceforge.net/bwa.shtml 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