/ 
BioPerl-1.007000
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Assembly::IO::maq

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