Bio::Assembly::IO::maq(3)

NAME
Bio::Assembly::IO::maq - Driver to read assembly files in maq format *BETA*

SYNOPSIS
    # 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   => 'all.maq',
                                        -format => 'maq' );
    my $scaffold = $asmio->next_assembly;

DESCRIPTION
This package loads and writes map information in/from "maq" map files converted by the "maq mapview" utility. This module is a driver module for Bio::Assembly::IO input/output.

Parsing is based on Heng Li's description of "maq mapview" output, found at the "maq" manpage: <http://maq.sourceforge.net/maq-manpage.shtml>.

The basic "maq" workflow is: map reads to a reference sequence (with "maq map"), then create a consensus from the map (with "maq assemble"). To read a complete assembly with this module, the following files need to be available:

 [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

"maq" produces only one "contig"; all reads map to the reference sequence, which covers everything. This module breaks the reads into contigs by dividing the "maq" consensus into pieces for which there are contiguous non-zero quality values.

The module "Bio::Tools::Run::Maq" will help in this process (eventually).

This module has no write capability.

  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 "map" files; the division of the map into contigs is calculated in this module.

Additional assembly information is stored as features. Contig objects have SeqFeature information associated with the primary_tag:

    _main_contig_feature:$contig_id -> misc contig information

Read objects have sub_seqFeature information associated with the primary_tag:

    _main_read_feature:$read_id     -> misc read information

Singlets are contigs of a single sequence, as calculated within this module. They are cataloged separately, as specified in Bio::Assembly::Scaffold.

TODO

•   Add pod descriptions of maq descriptive data (currently SeqFeatures added to each contig component)

•   Add features describing the aggregate status of reads and contigs based on the maq "paired flag"

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 lists 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 the bugs and their resolution. Bug reports can be submitted via email or the web:

  bioperl-bugs@bio.perl.org
  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Mark A. Jensen
Email maj -at- fortinbras -dot- us

CONTRIBUTORS
Further improvements by Florent Angly (florent dot angly at gmail dot com)

ACKNOWLEDGEMENT
Code and some POD text ripped liberally from Florent Angly's Bio::Assembly::IO::tigr.

APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a "_".

  next_assembly
 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

  next_contig
 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

  _init_contig()
    Title   : _init_contig
    Usage   : my $contigobj; $contigobj = $self->_init_contig(
              \%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

  _store_contig()
    Title   : _store_contig
    Usage   : my $contigobj; $contigobj = $self->_store_contig(
              \%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

  _parse_cns_file()
 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

  _cons()
 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

  _next_cons()

  _store_read()
    Title   : _store_read
    Usage   : my $readobj = $self->_store_read(\%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

  _store_singlet()
    Title   : _store_singlet
    Usage   : my $singletobj = $self->_store_read(\%readinfo, \%contiginfo);
    Function: store information of a singlet belonging to a scaffold in a singlet object
    Returns : Bio::Assembly::Singlet
    Args    : hash, hash

  write_assembly()
    Title   : write_assembly
    Usage   :
    Function: not currently available for maq assemblies
    Returns : throw
    Args    :

  _basename()
 Title   : _basename
 Usage   : $self->_basename
 Function: return the basename of the associate IO file
 Returns : scalar string
 Args    : none