- AUTHOR - Mark A. Jensen
Bio::Assembly::IO::maq - Driver to read assembly files in maq format *BETA*
# 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;
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.
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.
Bio::Tools::Run::Maq will help in this process (eventually).
This module has no write capability.
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.
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"
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.
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Please direct usage questions or support issues to the mailing list:
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.
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:
Email maj -at- fortinbras -dot- us
Further improvements by Florent Angly (florent dot angly at gmail dot com)
Code and some POD text ripped liberally from Florent Angly's Bio::Assembly::IO::tigr.
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a "_".
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
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
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
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
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
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
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
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
Title : write_assembly Usage : Function: not currently available for maq assemblies Returns : throw Args :
Title : _basename Usage : $self->_basename Function: return the basename of the associate IO file Returns : scalar string Args : none