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> 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¶

  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  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 _

 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)

Bio::Tools::Run::AssemblerBase overrides¶

 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