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.\" ========================================================================
.\"
.IX Title "Bio::Assembly::IO::maq 3pm"
.TH Bio::Assembly::IO::maq 3pm "2014-07-13" "perl v5.18.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH "NAME"
Bio::Assembly::IO::maq \- Driver to read assembly files in maq format *BETA*
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&    # convert the native maq map format to plain text
\&    $ maq mapview all.map > all.maq
\&
\&    # Building an input stream
\&    use Bio::Assembly::IO;
\&
\&    # Assembly loading methods
\&    my $asmio = Bio::Assembly::IO\->new( \-file   => \*(Aqall.maq\*(Aq,
\&                                        \-format => \*(Aqmaq\*(Aq );
\&    my $scaffold = $asmio\->next_assembly;
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This package loads and writes map information in/from \f(CW\*(C`maq\*(C'\fR map files converted by the \f(CW\*(C`maq mapview\*(C'\fR utility. This module is a driver module for
Bio::Assembly::IO input/output.
.PP
Parsing is based on Heng Li's description of \f(CW\*(C`maq mapview\*(C'\fR output, found 
at the \f(CW\*(C`maq\*(C'\fR manpage: <http://maq.sourceforge.net/maq\-manpage.shtml>.
.PP
The basic \f(CW\*(C`maq\*(C'\fR workflow is: map reads to a reference sequence (with
\&\f(CW\*(C`maq map\*(C'\fR), then create a consensus from the map (with \f(CW\*(C`maq
assemble\*(C'\fR). To read a complete assembly with this module, the
following files need to be available:
.PP
.Vb 4
\& [basename].maq : created by maq mapview [basename].map > [basename].maq
\& [basename].cns.fastq : created as follows
\&    $ maq assemble [basename].cns [refseq].bfa [basename].map
\&    $ maq cns2fq [basename].cns > [basename].cns.fastq
.Ve
.PP
\&\f(CW\*(C`maq\*(C'\fR produces only one \*(L"contig\*(R"; all reads map to the reference
sequence, which covers everything. This module breaks the reads into
contigs by dividing the \f(CW\*(C`maq\*(C'\fR consensus into pieces for which there
are contiguous non-zero quality values.
.PP
The module \f(CW\*(C`Bio::Tools::Run::Maq\*(C'\fR will help in this process (eventually).
.PP
This module has no write capability.
.SS "Implementation"
.IX Subsection "Implementation"
Assemblies are loaded into Bio::Assembly::Scaffold objects composed of
Bio::Assembly::Contig and Bio::Assembly::Singlet objects. Contigs are 
not explicitly specified in \f(CW\*(C`map\*(C'\fR files; the division of the map into 
contigs is calculated in this module.
.PP
Additional assembly information is stored as features. Contig objects have
SeqFeature information associated with the primary_tag:
.PP
.Vb 1
\&    _main_contig_feature:$contig_id \-> misc contig information
.Ve
.PP
Read objects have sub_seqFeature information associated with the
primary_tag:
.PP
.Vb 1
\&    _main_read_feature:$read_id     \-> misc read information
.Ve
.PP
Singlets are contigs of a single sequence, as calculated within this module. 
They are cataloged separately, as specified in Bio::Assembly::Scaffold.
.SH "TODO"
.IX Header "TODO"
.IP "\(bu" 4
Add pod descriptions of maq descriptive data (currently SeqFeatures
added to each contig component)
.IP "\(bu" 4
Add features describing the aggregate status of reads and contigs based
on the maq \*(L"paired flag\*(R"
.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 lists  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
\&\fIbioperl\-l@bioperl.org\fR
.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
the bugs and their resolution. Bug reports can be submitted via email
or the web:
.PP
.Vb 2
\&  bioperl\-bugs@bio.perl.org
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Mark A. Jensen"
.IX Header "AUTHOR - Mark A. Jensen"
Email maj \-at\- fortinbras \-dot\- us
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Further improvements by Florent Angly 
(florent dot angly at gmail dot com)
.SH "ACKNOWLEDGEMENT"
.IX Header "ACKNOWLEDGEMENT"
Code and some \s-1POD\s0 text ripped liberally from Florent Angly's
Bio::Assembly::IO::tigr.
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a \*(L"_\*(R".
.SS "next_assembly"
.IX Subsection "next_assembly"
.Vb 5
\& Title   : next_assembly
\& Usage   : $scaffold = $stream\->next_assembly()
\& Function: return the assembly defined by the map and cns files
\& Returns : Bio::Assembly::Scaffold object
\& Args    : none
.Ve
.SS "next_contig"
.IX Subsection "next_contig"
.Vb 5
\& Title   : next_contig
\& Usage   : $scaffold = $stream\->next_contig()
\& Function: Returns the next contig or singlet in the ACE stream.
\& Returns : a Bio::Assembly::Contig or Bio::Assembly::Single object
\& Args    : none
.Ve
.SS "\fI_init_contig()\fP"
.IX Subsection "_init_contig()"
.Vb 7
\&    Title   : _init_contig
\&    Usage   : my $contigobj; $contigobj = $self\->_init_contig(
\&              \e%contiginfo, $scaffoldobj);
\&    Function: store information of a contig belonging to a scaffold in the
\&              appropriate object
\&    Returns : Bio::Assembly::Contig object
\&    Args    : hash, Bio::Assembly::Scaffold
.Ve
.SS "\fI_store_contig()\fP"
.IX Subsection "_store_contig()"
.Vb 7
\&    Title   : _store_contig
\&    Usage   : my $contigobj; $contigobj = $self\->_store_contig(
\&              \e%contiginfo, $contigobj);
\&    Function: store information of a contig belonging to a scaffold
\&              in the appropriate object
\&    Returns : Bio::Assembly::Contig object
\&    Args    : hash, Bio::Assembly::Contig
.Ve
.SS "\fI_parse_cns_file()\fP"
.IX Subsection "_parse_cns_file()"
.Vb 7
\& Title   : _parse_cns_file
\& Usage   : $self\->_parse_cns_file
\& Function: parse the .cns.fastq (consensus) file
\&           associated with the present map;
\&           set the objects cns attribute
\& Returns : true on success; nil if file dne
\& Args    : none
.Ve
.SS "\fI_cons()\fP"
.IX Subsection "_cons()"
.Vb 5
\& Title   : _cons
\& Usage   : @cons = $self\->_cons
\& Function: get the array of consensus fastq Bio::Seq::Quality objects
\& Returns : array of Bio::Seq::Quality objects
\& Args    : none
.Ve
.SS "\fI_next_cons()\fP"
.IX Subsection "_next_cons()"
.SS "\fI_store_read()\fP"
.IX Subsection "_store_read()"
.Vb 6
\&    Title   : _store_read
\&    Usage   : my $readobj = $self\->_store_read(\e%readinfo, $contigobj);
\&    Function: store information of a read belonging to a contig 
\&              in the appropriate object
\&    Returns : a Bio::LocatableSeq object
\&    Args    : hash, Bio::Assembly::Contig
.Ve
.SS "\fI_store_singlet()\fP"
.IX Subsection "_store_singlet()"
.Vb 5
\&    Title   : _store_singlet
\&    Usage   : my $singletobj = $self\->_store_read(\e%readinfo, \e%contiginfo);
\&    Function: store information of a singlet belonging to a scaffold in a singlet object
\&    Returns : Bio::Assembly::Singlet
\&    Args    : hash, hash
.Ve
.SS "\fIwrite_assembly()\fP"
.IX Subsection "write_assembly()"
.Vb 5
\&    Title   : write_assembly
\&    Usage   : 
\&    Function: not currently available for maq assemblies
\&    Returns : throw
\&    Args    :
.Ve
.SS "\fI_basename()\fP"
.IX Subsection "_basename()"
.Vb 5
\& Title   : _basename
\& Usage   : $self\->_basename
\& Function: return the basename of the associate IO file
\& Returns : scalar string
\& Args    : none
.Ve