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