Bio::Tools::Run::Maq(3pm)				User Contributed Perl Documentation				 Bio::Tools::Run::Maq(3pm)

NAME

       Bio::Tools::Run::Maq - Run wrapper for the Maq short-read assembler *BETA*

SYNOPSIS

	# create an assembly
	$maq_fac = Bio::Tools::Run::Maq->new();
	$maq_assy = $maq_fac->run( 'reads.fastq', 'refseq.fas' );
	# if IO::Uncompress::Gunzip is available...
	$maq_assy = $maq_fac->run( 'reads.fastq.gz', 'refseq.gz');
	# paired-end
	$maq_assy = $maq_fac->run( 'reads.fastq', 'refseq.fas', 'paired-reads.fastq');
	# be more strict
	$maq_fac->set_parameters( -c2q_min_map_quality => 60 );
	$maq_assy = $maq_fac->run( 'reads.fastq', 'refseq.fas', 'paired-reads.fastq');

	# run maq commands separately
	$maq_fac = Bio::Tools::Run::Maq->new(
	   -command => 'pileup',
	   -single_end_quality => 1 );
	$maq_fac->run_maq( -bfa => 'refseq.bfa',
			   -map => 'maq_assy.map',
			   -txt => 'maq_assy.pup.txt' );

DESCRIPTION

       This module provides a wrapper interface for Heng Li's reference-directed short read assembly suite "maq" (see
       http://maq.sourceforge.net/maq-man.shtml <http://maq.sourceforge.net/maq-man.shtml> for manuals and downloads).

       There are two modes of action.

       o   EasyMaq

	   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.

       o   BigMaq

	   The second mode is direct access to "maq" commands. To run a "maq" 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"):

	    $maqfac->Bio::Tools::Run::Maq->new( -command => 'fasta2bfa' );

	   To execute, use the "run_maq" methods. Input and output files are specified in the arguments of "run_maq" (see "FILES"):

	    $maqfac->run_maq( -fas => "myref.fas", -bfa => "myref.bfa" );

OPTIONS

       "maq" 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:

	$maqfac = Bio::Tools::Run::Maq->new( -command => 'assemble' );
	# all maq commands
	@all_commands = $maqfac->available_parameters('commands');
	@all_commands = $maqfac->available_commands; # alias
	# just for assemble
	@assemble_params = $maqfac->available_parameters('params');
	@assemble_switches = $maqfac->available_parameters('switches');
	@assemble_all_options = $maqfac->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://maq.sourceforge.net/maq-manpage.shtml <http://maq.sourceforge.net/maq-manpage.shtml> for the gory details.

FILES

       When a command requires filenames, these are provided to the "run_maq" method, not the constructor ("new()"). To see the set of files
       required by a command, use "available_parameters('filespec')" or the alias "filespec()":

	 $maqfac = Bio::Tools::Run::Maq->new( -command => 'map' );
	 @filespec = $maqfac->filespec;

       This example returns the following array:

	map
	bfa
	bfq1
	#bfq2
	2>#log

       This indicates that map ("maq" binary mapfile), bfa ("maq" binary fasta), and bfq ("maq" binary fastq) files MUST be specified, another bfq
       file MAY be specified, and a log file receiving STDERR also MAY be specified. Use these in the "run_maq" call like so:

	$maqfac->run_maq( -map => 'my.map', -bfa => 'myrefseq.bfa',
			  -bfq1 => 'reads1.bfq', -bfq2 => 'reads2.bfq' );

       Here, the "log" parameter was unspecified. Therefore, the object will store the programs STDERR output for you in the "stderr()" attribute:

	handle_map_warning($maqfac) if ($maqfac->stderr =~ /warning/);

       STDOUT for a run is also saved, in "stdout()", unless a file is specified to slurp it according to the filespec. "maq" STDOUT usually
       contains useful information on the run.

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::Maq();
	Function: Builds a new Bio::Tools::Run::Maq object
	Returns : an instance of Bio::Tools::Run::Maq
	Args	:

   run
	Title	: run
	Usage	: $assembly = $maq_assembler->run($read1_fastq_file,
						  $refseq_fasta_file,
						  $read2_fastq_file);
	Function: Run the maq 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
	Note	: gzipped inputs are allowed if IO::Uncompress::Gunzip
		  is available

   run_maq()
	Title	: run_maq
	Usage	: $obj->run_maq( @file_args )
	Function: Run a maq 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 maq assembly pipeline
	Returns :   depends on call (An assembly file)
	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 maq 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

perl v5.12.3							    2011-06-18						 Bio::Tools::Run::Maq(3pm)