Bio::Assembly::IO::sam(3)

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

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

DESCRIPTION
This is a (currently) read-only IO module designed to convert Sequence/Alignment Map (SAM; <http://samtools.sourceforge.net/>) 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 <http://samtools.sourceforge.net/>.

DETAILS

•   Required files

    A binary SAM (".bam") alignment and a reference sequence database in FASTA format are required. Various required indexes (".fai", ".bai") will be created as necessary (via Bio::DB::Sam).

•   Compressed files

    ...can be specified directly , if IO::Uncompress::Gunzip is installed. Get it from your local CPAN mirror.

•   BAM vs. SAM

    The input alignment should be in (possibly gzipped) binary SAM (".bam") format. If it isn't, you will get a message explaining how to convert it, viz.:

     $ samtools view -Sb mysam.sam > mysam.bam

    The bam file must also be sorted on coordinates: do

     $ samtools sort mysam.unsorted.bam > mysam.bam

•   Contigs

    Contigs are calculated by this module, using the 'coverage' feature of the Bio::DB::Sam object. A contig represents a contiguous portion of a reference sequence having non-zero coverage at each base.

    The bwa assembler (<http://bio-bwa.sourceforge.net/>) can assign read sequences to multiple reference sequence locations. The present implementation currently assigns such reads only to the first contig in which they appear.

•   Consensus sequences

    Consensus sequence and quality objects are calculated by this module, using the "pileup" callback feature of "Bio::DB::Sam". The consensus is (currently) simply the residue at a position that has the maximum sum of quality values. The consensus quality is the integer portion of the simple average of quality values for the consensus residue.

•   SeqFeatures

    Read sequences stored in contigs are accompanied by the following features:

     contig : name of associated contig
     cigar  : CIGAR string for this read

    If the read is paired with a successfully mapped mate, these features will also be available:

     mate_start  : coordinate of to which the mate was aligned
     mate_len    : length of mate read
     mate_strand : strand of mate (-1 or 1)
     insert_size : size of insert spanned by the mate pair

    These features are obtained as follows:

     @ids = $contig->get_seq_ids;
     $an_id = $id[0]; # or whatever
     $seq = $contig->get_seq_by_name($an_id);
     # Bio::LocatableSeq's aren't SeqFeature containers, so...
     $feat = $contig->get_seq_feat_by_tag(
                $seq, "_aligned_coord:".$s->id
             );
     ($cigar) = $feat->get_tag_values('cigar');
     # etc.

TODO

•   Supporting both text SAM (TAM) and binary SAM (BAM)

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 list. 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 of the bugs and their resolution. Bug reports can be submitted via the web:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Mark A. Jensen
Email maj -at- fortinbras -dot- us

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

Bio::Assembly::IO compliance

  next_assembly()
    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

  next_contig()
    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

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

Internal

  _store_contig()
    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

  _store_read()
    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

  _store_singlet()
    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

  _init_sam()
 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.

  _get_contig_segs_from_coverage()
 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

  _calc_consensus_quality()
 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

  _calc_consensus()
 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

  refdb()
 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)

  _segset()
 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()

  _current_refseq_id()
 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)

  _current_contig_seg_idx()
 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)

  sam()
 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)