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> 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" );
  

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> 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.

  [email protected]                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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