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.\" ========================================================================
.\"
.IX Title "Bio::Tools::Run::Maq 3pm"
.TH Bio::Tools::Run::Maq 3pm "2013-11-15" "perl v5.18.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::Tools::Run::Maq \- Run wrapper for the Maq short\-read assembler *BETA*
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 10
\& # create an assembly
\& $maq_fac = Bio::Tools::Run::Maq\->new();
\& $maq_assy = $maq_fac\->run( \*(Aqreads.fastq\*(Aq, \*(Aqrefseq.fas\*(Aq );
\& # if IO::Uncompress::Gunzip is available...
\& $maq_assy = $maq_fac\->run( \*(Aqreads.fastq.gz\*(Aq, \*(Aqrefseq.gz\*(Aq);
\& # paired\-end 
\& $maq_assy = $maq_fac\->run( \*(Aqreads.fastq\*(Aq, \*(Aqrefseq.fas\*(Aq, \*(Aqpaired\-reads.fastq\*(Aq);
\& # be more strict
\& $maq_fac\->set_parameters( \-c2q_min_map_quality => 60 );
\& $maq_assy = $maq_fac\->run( \*(Aqreads.fastq\*(Aq, \*(Aqrefseq.fas\*(Aq, \*(Aqpaired\-reads.fastq\*(Aq);
\&
\& # run maq commands separately
\& $maq_fac = Bio::Tools::Run::Maq\->new(
\&    \-command => \*(Aqpileup\*(Aq,
\&    \-single_end_quality => 1 );
\& $maq_fac\->run_maq( \-bfa => \*(Aqrefseq.bfa\*(Aq,
\&                    \-map => \*(Aqmaq_assy.map\*(Aq,
\&                    \-txt => \*(Aqmaq_assy.pup.txt\*(Aq );
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This module provides a wrapper interface for Heng Li's
reference-directed short read assembly suite \f(CW\*(C`maq\*(C'\fR (see
<http://maq.sourceforge.net/maq\-man.shtml> for manuals and
downloads).
.PP
There are two modes of action.
.IP "\(bu" 4
EasyMaq
.Sp
The first is a simple pipeline through the \f(CW\*(C`maq\*(C'\fR 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 \f(CW\*(C`maq.pl easyrun\*(C'\fR:
.Sp
.Vb 4
\& 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)
.Ve
.Sp
Command-line options can be directed to the \f(CW\*(C`map\*(C'\fR, \f(CW\*(C`assemble\*(C'\fR, and
\&\f(CW\*(C`cns2fq\*(C'\fR steps. See \*(L"\s-1OPTIONS\*(R"\s0 below.
.IP "\(bu" 4
BigMaq
.Sp
The second mode is direct access to \f(CW\*(C`maq\*(C'\fR commands. To run a \f(CW\*(C`maq\*(C'\fR
command, construct a run factory, specifying the desired command using
the \f(CW\*(C`\-command\*(C'\fR argument in the factory constructor, along with
options specific to that command (see \*(L"\s-1OPTIONS\*(R"\s0):
.Sp
.Vb 1
\& $maqfac\->Bio::Tools::Run::Maq\->new( \-command => \*(Aqfasta2bfa\*(Aq );
.Ve
.Sp
To execute, use the \f(CW\*(C`run_maq\*(C'\fR methods. Input and output files are
specified in the arguments of \f(CW\*(C`run_maq\*(C'\fR (see \*(L"\s-1FILES\*(R"\s0):
.Sp
.Vb 1
\& $maqfac\->run_maq( \-fas => "myref.fas", \-bfa => "myref.bfa" );
.Ve
.SH "OPTIONS"
.IX Header "OPTIONS"
\&\f(CW\*(C`maq\*(C'\fR 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:
.PP
.Vb 8
\& $maqfac = Bio::Tools::Run::Maq\->new( \-command => \*(Aqassemble\*(Aq );
\& # all maq commands
\& @all_commands = $maqfac\->available_parameters(\*(Aqcommands\*(Aq); 
\& @all_commands = $maqfac\->available_commands; # alias
\& # just for assemble
\& @assemble_params = $maqfac\->available_parameters(\*(Aqparams\*(Aq);
\& @assemble_switches = $maqfac\->available_parameters(\*(Aqswitches\*(Aq);
\& @assemble_all_options = $maqfac\->available_parameters();
.Ve
.PP
Reasonably mnemonic names have been assigned to the single-letter
command line options. These are the names returned by
\&\f(CW\*(C`available_parameters\*(C'\fR, and can be used in the factory constructor
like typical BioPerl named parameters.
.PP
See <http://maq.sourceforge.net/maq\-manpage.shtml> for the gory details.
.SH "FILES"
.IX Header "FILES"
When a command requires filenames, these are provided to the \f(CW\*(C`run_maq\*(C'\fR method, not
the constructor (\f(CW\*(C`new()\*(C'\fR). To see the set of files required by a command, use
\&\f(CW\*(C`available_parameters(\*(Aqfilespec\*(Aq)\*(C'\fR or the alias \f(CW\*(C`filespec()\*(C'\fR:
.PP
.Vb 2
\&  $maqfac = Bio::Tools::Run::Maq\->new( \-command => \*(Aqmap\*(Aq );
\&  @filespec = $maqfac\->filespec;
.Ve
.PP
This example returns the following array:
.PP
.Vb 5
\& map
\& bfa 
\& bfq1 
\& #bfq2 
\& 2>#log
.Ve
.PP
This indicates that map (\f(CW\*(C`maq\*(C'\fR binary mapfile), bfa (\f(CW\*(C`maq\*(C'\fR binary
fasta), and bfq (\f(CW\*(C`maq\*(C'\fR binary fastq) files \s-1MUST\s0 be specified, another
bfq file \s-1MAY\s0 be specified, and a log file receiving \s-1STDERR\s0 also \s-1MAY\s0 be
specified. Use these in the \f(CW\*(C`run_maq\*(C'\fR call like so:
.PP
.Vb 2
\& $maqfac\->run_maq( \-map => \*(Aqmy.map\*(Aq, \-bfa => \*(Aqmyrefseq.bfa\*(Aq,
\&                   \-bfq1 => \*(Aqreads1.bfq\*(Aq, \-bfq2 => \*(Aqreads2.bfq\*(Aq );
.Ve
.PP
Here, the \f(CW\*(C`log\*(C'\fR parameter was unspecified. Therefore, the object will store
the programs \s-1STDERR\s0 output for you in the \f(CW\*(C`stderr()\*(C'\fR attribute:
.PP
.Vb 1
\& handle_map_warning($maqfac) if ($maqfac\->stderr =~ /warning/);
.Ve
.PP
\&\s-1STDOUT\s0 for a run is also saved, in \f(CW\*(C`stdout()\*(C'\fR, unless a file is specified
to slurp it according to the filespec. \f(CW\*(C`maq\*(C'\fR \s-1STDOUT\s0 usually contains useful
information on the run.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
bioperl\-l@bioperl.org
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \- Mark A. Jensen"
.IX Header "AUTHOR - Mark A. Jensen"
.Vb 1
\& Email maj \-at\- fortinbras \-dot\- us
.Ve
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "\fInew()\fP"
.IX Subsection "new()"
.Vb 5
\& 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    :
.Ve
.SS "run"
.IX Subsection "run"
.Vb 11
\& 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
.Ve
.SS "\fIrun_maq()\fP"
.IX Subsection "run_maq()"
.Vb 5
\& 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:
.Ve
.SS "\fIstdout()\fP"
.IX Subsection "stdout()"
.Vb 7
\& 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)
.Ve
.SS "\fIstderr()\fP"
.IX Subsection "stderr()"
.Vb 7
\& 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)
.Ve
.SH "Bio::Tools::Run::AssemblerBase overrides"
.IX Header "Bio::Tools::Run::AssemblerBase overrides"
.SS "\fI_check_sequence_input()\fP"
.IX Subsection "_check_sequence_input()"
.Vb 1
\& No\-op.
.Ve
.SS "\fI_check_optional_quality_input()\fP"
.IX Subsection "_check_optional_quality_input()"
.Vb 1
\& No\-op.
.Ve
.SS "_prepare_input_sequences"
.IX Subsection "_prepare_input_sequences"
.Vb 1
\& Convert input fastq and fasta to maq format.
.Ve
.SS "\fI_collate_subcmd_args()\fP"
.IX Subsection "_collate_subcmd_args()"
.Vb 7
\& 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 \*(Aqrun\*(Aq]
.Ve
.SS "\fI_run()\fP"
.IX Subsection "_run()"
.Vb 7
\& 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
.Ve
.SS "\fIavailable_parameters()\fP"
.IX Subsection "available_parameters()"
.Vb 10
\& Title   : available_parameters
\& Usage   : @cmds = $fac\->available_commands(\*(Aqcommands\*(Aq);
\& Function: Use to browse available commands, params, or switches
\& Returns : array of scalar strings
\& Args    : \*(Aqcommands\*(Aq : all maq commands
\&           \*(Aqparams\*(Aq   : parameters for this object\*(Aqs command
\&           \*(Aqswitches\*(Aq : boolean switches for this object\*(Aqs command
\&           \*(Aqfilespec\*(Aq : the filename spec for this object\*(Aqs command
\& 4Geeks  : Overrides Bio::ParameterBaseI via 
\&           Bio::Tools::Run::AssemblerBase
.Ve