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:
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):
To execute, use the run_maq methods. Input and output files are specified in the arguments of run_maq (see FILES):
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 = $maqfac->filespec;
This example returns the following array:
map bfa bfq1 #bfq2 2>#log
This indicates that map (maq binary mapfile), bfa (maq binary fasta), and bfq (maq binary fastq) files MUST be specified, another bfq file MAY be specified, and a log file receiving STDERR also MAY be specified. Use these in the run_maq call like so:
Here, the log parameter was unspecified. Therefore, the object will store the programs STDERR output for you in the stderr() attribute:
handle_map_warning($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.
Please direct usage questions or support issues to the mailing list:
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:
Email maj -at- fortinbras -dot- us
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 :
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)
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 objects command switches : boolean switches for this objects command filespec : the filename spec for this objects command 4Geeks : Overrides Bio::ParameterBaseI via Bio::Tools::Run::AssemblerBase
|perl v5.20.3||BIO::TOOLS::RUN::MAQ (3)||2016-04-05|