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Christopher Fields > BioPerl > Bio::Assembly::IO::sam



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Module Version: 1.007002   Source  


Bio::Assembly::IO::sam - An IO module for assemblies in Sam format *BETA*


 $aio = Bio::Assembly::IO( -file => "mysam.bam",
                           -refdb => "myrefseqs.fas");
 $assy = $aio->next_assembly;


This is a (currently) read-only IO module designed to convert Sequence/Alignment Map (SAM; formatted alignments to Bio::Assembly::Scaffold representations, containing .Bio::Assembly::Contig and Bio::Assembly::Singlet objects. It uses lstein's Bio::DB::Sam to parse binary formatted SAM (.bam) files guided by a reference sequence fasta database.

NB: Bio::DB::Sam is not a BioPerl module; it can be obtained via CPAN. It in turn requires the libbam library; source can be downloaded at




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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.

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Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

AUTHOR - Mark A. Jensen ^

Email maj -at- fortinbras -dot- us


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

Bio::Assembly::IO compliance ^


    Title   : next_assembly
    Usage   : my $scaffold = $asmio->next_assembly();
    Function: return the next assembly in the sam-formatted stream
    Returns : Bio::Assembly::Scaffold object
    Args    : none


    Title   : next_contig
    Usage   : my $contig = $asmio->next_contig();
    Function: return the next contig or singlet from the sam stream
    Returns : Bio::Assembly::Contig or Bio::Assembly::Singlet
    Args    : none


 Title   : write_assembly
 Usage   : 
 Function: not implemented (module currrently read-only)
 Returns : 
 Args    : 

Internal ^


    Title   : _store_contig
    Usage   : my $contigobj = $self->_store_contig(\%contiginfo);
    Function: create and load a contig object
    Returns : Bio::Assembly::Contig object
    Args    : Bio::DB::Sam::Segment object


    Title   : _store_read
    Usage   : my $readobj = $self->_store_read($readobj, $contigobj);
    Function: store information of a read belonging to a contig in a contig object
    Returns : Bio::LocatableSeq
    Args    : Bio::DB::Bam::AlignWrapper, Bio::Assembly::Contig


    Title   : _store_singlet
    Usage   : my $singletobj = $self->_store_singlet($contigobj);
    Function: convert a contig object containing a single read into
              a singlet object
    Returns : Bio::Assembly::Singlet
    Args    : Bio::Assembly::Contig (previously loaded with only one seq)

REALLY Internal ^


 Title   : _init_sam
 Usage   : $self->_init_sam($fasfile)
 Function: obtain a Bio::DB::Sam parsing of the associated sam file
 Returns : true on success
 Args    : [optional] name of the fasta reference db (scalar string)
 Note    : The associated file can be plain text (.sam) or binary (.bam);
           If the fasta file is not specified, and no file is contained in 
           the refdb() attribute, a .fas file with the same
           basename as the sam file will be searched for.


 Title   : _get_contig_segs_from_coverage
 Usage   : 
 Function: calculates separate contigs using coverage info 
           in the segment
 Returns : array of Bio::DB::Sam::Segment objects, representing
           each contig
 Args    : Bio::DB::Sam::Segment object


 Title   : _calc_consensus_quality
 Usage   : @qual = $aio->_calc_consensus_quality( $contig_seg );
 Function: calculate an average or other data-reduced quality
           over all sites represented by the features contained
           in a Bio::DB::Sam::Segment
 Returns : 
 Args    : a Bio::DB::Sam::Segment object


 Title   : _calc_consensus
 Usage   : @qual = $aio->_calc_consensus( $contig_seg );
 Function: calculate a simple quality-weighted consensus sequence
           for the segment
 Returns : a SeqWithQuality object
 Args    : a Bio::DB::Sam::Segment object


 Title   : refdb
 Usage   : $obj->refdb($newval)
 Function: the name of the reference db fasta file
 Example : 
 Returns : value of refdb (a scalar)
 Args    : on set, new value (a scalar or undef, optional)


 Title   : _segset
 Usage   : $segset_hashref = $self->_segset()
 Function: hash container for the Bio::DB::Sam::Segment objects that
           represent each set of contigs for each seq_id
           { $seq_id => [@contig_segments], ... }
 Example : 
 Returns : value of _segset (a hashref) if no arg, 
           or the arrayref of contig segments, if arg == a seq id
 Args    : [optional] seq id (scalar string)
 Note    : readonly; hash elt set in _init_sam()


 Title   : _current_refseq_id
 Usage   : $obj->_current_refseq_id($newval)
 Function: the "current" reference sequence id
 Example : 
 Returns : value of _current_refseq (a scalar)
 Args    : on set, new value (a scalar or undef, optional)


 Title   : current_contig_seg_idx
 Usage   : $obj->current_contig_seg_idx($newval)
 Function: the "current" segment index in the "current" refseq
 Example : 
 Returns : value of current_contig_seg_idx (a scalar)
 Args    : on set, new value (a scalar or undef, optional)


 Title   : sam
 Usage   : $obj->sam($newval)
 Function: store the associated Bio::DB::Sam object
 Example : 
 Returns : value of sam (a Bio::DB::Sam object)
 Args    : on set, new value (a scalar or undef, optional)
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