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.
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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