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

 # 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' );

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 for manuals and downloads).

There are two modes of action.

* 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.

* 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" );

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 for the gory details.

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.

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

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.

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/

 Email maj -at- fortinbras -dot- us

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

 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    :

 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

 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:

 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)

 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)

 No-op.

 No-op.

 Convert input fastq and fasta to maq format.

 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']

 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

 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