bionic (3) Bio::Tools::Run::Maq.3pm.gz
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
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