Bio::Cluster::UniGene(3)

NAME
Bio::Cluster::UniGene - UniGene object

SYNOPSIS
        use Bio::Cluster::UniGene;
        use Bio::ClusterIO;

        $stream  = Bio::ClusterIO->new('-file' => "Hs.data",
                                       '-format' => "unigene");
        # note: we quote -format to keep older perl's from complaining.

        while ( my $in = $stream->next_cluster() ) {
                print $in->unigene_id() . "\n";
                while ( my $sequence = $in->next_seq() ) {
                        print $sequence->accession_number() . "\n";
                }
       }

DESCRIPTION
This UniGene object implements the Bio::Cluster::UniGeneI interface for the representation if UniGene clusters in Bioperl. It is returned by the Bio::ClusterIO parser for unigene format and contains all the data associated with one UniGene record.

This class implements several interfaces and hence can be used wherever instances of such interfaces are expected. In particular, the interfaces are Bio::ClusterI as the base interface for all cluster representations, and in addition Bio::IdentifiableI and Bio::DescribableI.

The following lists the UniGene specific methods that are available (see below for details). Be aware next_XXX iterators take a snapshot of the array property when they are first called, and this snapshot is not reset until the iterator is exhausted. Hence, once called you need to exhaust the iterator to see any changes that have been made to the property in the meantime. You will usually want to use the non-iterator equivalents and loop over the elements yourself.

new() - standard new call

unigene_id() - set/get unigene_id

title() - set/get title (description)

gene() - set/get gene

cytoband() - set/get cytoband

mgi() - set/get mgi

locuslink() - set/get locuslink

homol() - set/get homologene

gnm_terminus() - set/get gnm_terminus

scount() - set/get scount

express() - set/get express, currently takes/returns a reference to an array of expressed tissues

next_express() - returns the next tissue expression from the expressed tissue array

chromosome() - set/get chromosome, currently takes/returns a reference to an array of chromosome lines

next_chromosome() - returns the next chromosome line from the array of chromosome lines

sts() - set/get sts, currently takes/returns a reference to an array of sts lines

next_sts() - returns the next sts line from the array of sts lines

txmap() - set/get txmap, currently takes/returns a reference to an array of txmap lines

next_txmap() - returns the next txmap line from the array of txmap lines

protsim() - set/get protsim, currently takes/returns a reference to an array of protsim lines

next_protsim() - returns the next protsim line from the array of protsim lines

sequences() - set/get sequence, currently takes/returns a reference to an array of references to seq info

next_seq() - returns a Seq object that currently only contains an accession number

Implemented Interfaces
This class implementes the following interfaces.

Bio::Cluster::UniGeneI
    This includes implementing Bio::ClusterI.

Bio::IdentifiableI
Bio::DescribableI
Bio::AnnotatableI
Bio::Factory::SequenceStreamI

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 one of 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 the web:

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

AUTHOR - Andrew Macgregor
Email andrew at cbbc.murdoch.edu.au

CONTRIBUTORS
Hilmar Lapp, hlapp at gmx.net

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

  new
 Title   : new
 Usage   : used by ClusterIO
 Returns : a new Bio::Cluster::Unigene object

Bio::Cluster::UniGeneI methods

  unigene_id
 Title   : unigene_id
 Usage   : unigene_id();
 Function: Returns the unigene_id associated with the object.
 Example : $id = $unigene->unigene_id or $unigene->unigene_id($id)
 Returns : A string
 Args    : None or an id

  title
 Title   : title
 Usage   : title();
 Function: Returns the title associated with the object.
 Example : $title = $unigene->title or $unigene->title($title)
 Returns : A string
 Args    : None or a title

  gene
 Title   : gene
 Usage   : gene();
 Function: Returns the gene associated with the object.
 Example : $gene = $unigene->gene or $unigene->gene($gene)
 Returns : A string
 Args    : None or a gene

  cytoband
 Title   : cytoband
 Usage   : cytoband();
 Function: Returns the cytoband associated with the object.
 Example : $cytoband = $unigene->cytoband or $unigene->cytoband($cytoband)
 Returns : A string
 Args    : None or a cytoband

  mgi
 Title   : mgi
 Usage   : mgi();
 Function: Returns the mgi associated with the object.
 Example : $mgi = $unigene->mgi or $unigene->mgi($mgi)
 Returns : A string
 Args    : None or a mgi

  locuslink
 Title   : locuslink
 Usage   : locuslink();
 Function: Returns or stores a reference to an array containing locuslink data.
 Returns : An array reference
 Args    : None or an array reference

  homol
 Title   : homol
 Usage   : homol();
 Function: Returns the homol entry associated with the object.
 Example : $homol = $unigene->homol or $unigene->homol($homol)
 Returns : A string
 Args    : None or a homol entry

  restr_expr
 Title   : restr_expr
 Usage   : restr_expr();
 Function: Returns the restr_expr entry associated with the object.
 Example : $restr_expr = $unigene->restr_expr or $unigene->restr_expr($restr_expr)
 Returns : A string
 Args    : None or a restr_expr entry

  gnm_terminus
 Title   : gnm_terminus
 Usage   : gnm_terminus();
 Function: Returns the gnm_terminus associated with the object.
 Example : $gnm_terminus = $unigene->gnm_terminus or
           $unigene->gnm_terminus($gnm_terminus)
 Returns : A string
 Args    : None or a gnm_terminus

  scount
 Title   : scount
 Usage   : scount();
 Function: Returns the scount associated with the object.
 Example : $scount = $unigene->scount or $unigene->scount($scount)
 Returns : A string
 Args    : None or a scount

  express
 Title   : express
 Usage   : express();
 Function: Returns or stores a reference to an array containing
           tissue expression data
 Returns : An array reference
 Args    : None or an array reference

  chromosome
 Title   : chromosome
 Usage   : chromosome();
 Function: Returns or stores a reference to an array containing
           chromosome lines
 Returns : An array reference
 Args    : None or an array reference

  sts
 Title   : sts
 Usage   : sts();
 Function: Returns or stores a reference to an array containing sts lines

 Returns : An array reference
 Args    : None or an array reference

  txmap
 Title   : txmap
 Usage   : txmap();
 Function: Returns or stores a reference to an array containing txmap lines

 Returns : An array reference
 Args    : None or an array reference

  protsim
 Title   : protsim
 Usage   : protsim();
 Function: Returns or stores a reference to an array containing protsim lines
           This should really only be used by ClusterIO, not directly
 Returns : An array reference
 Args    : None or an array reference

  sequences
 Title   : sequences
 Usage   : sequences();
 Function: Returns or stores a reference to an array containing
           sequence data.

           This is mostly reserved for ClusterIO parsers. You should
           use get_members() for get and add_member()/remove_members()
           for set.

 Returns : An array reference, or undef
 Args    : None or an array reference or undef

  species
 Title   : species
 Usage   : $obj->species($newval)
 Function: Get/set the species object for this Unigene cluster.
 Example :
 Returns : value of species (a L<Bio::Species> object)
 Args    : on set, new value (a L<Bio::Species> object or
           the binomial name, or undef, optional)

Bio::ClusterI methods

  display_id
 Title   : display_id
 Usage   :
 Function: Get/set the display name or identifier for the cluster

           This is aliased to unigene_id().

 Returns : a string
 Args    : optional, on set the display ID ( a string)

  description
 Title   : description
 Usage   : Bio::ClusterI->description("POLYUBIQUITIN")
 Function: get/set for the consensus description of the cluster

           This is aliased to title().

 Returns : the description string
 Args    : Optional the description string

  size
 Title   : size
 Usage   : Bio::ClusterI->size();
 Function: get for the size of the family,
           calculated from the number of members

           This is aliased to scount().

 Returns : the size of the cluster
 Args    :

  cluster_score
 Title   : cluster_score
 Usage   : $cluster ->cluster_score(100);
 Function: get/set for cluster_score which
           represent the score in which the clustering
           algorithm assigns to this cluster.

           For UniGene clusters, there really is no cluster score that
           would come with the data. However, we provide an
           implementation here so that you can score UniGene clusters
           if you want to.

 Returns : a number
 Args    : optionally, on set a number

  get_members
 Title   : get_members
 Usage   : Bio::ClusterI->get_members(($seq1, $seq2));
 Function: retrieve the members of the family by some criteria

           Will return all members if no criteria are provided.

           At this time this implementation does not support
           specifying criteria and will always return all members.

 Returns : the array of members
 Args    :

Annotatable view at the object properties

  annotation
 Title   : annotation
 Usage   : $obj->annotation($newval)
 Function: Get/set the L<Bio::AnnotationCollectionI> object for
           this UniGene cluster.

           Many attributes of this class are actually stored within
           the annotation collection object as L<Bio::AnnotationI>
           compliant objects, so you can conveniently access them
           through the same interface as you would e.g. access
           L<Bio::SeqI> annotation properties.

           If you call this method in set mode and replace the
           annotation collection with another one you should know
           exactly what you are doing.

 Example :
 Returns : a L<Bio::AnnotationCollectionI> compliant object
 Args    : on set, new value (a L<Bio::AnnotationCollectionI>
           compliant object or undef, optional)

Implementation specific methods
 These are mostly for adding/removing to array properties, and for
 methods with special functionality.

  add_member
 Title   : add_member
 Usage   :
 Function: Adds a member object to the list of members.
 Example :
 Returns : TRUE if the new member was successfuly added, and FALSE
           otherwise.
 Args    : The member to add.

  remove_members
 Title   : remove_members
 Usage   :
 Function: Remove the list of members for this cluster such that the
           member list is undefined afterwards (as opposed to zero members).
 Example :
 Returns : the previous list of members
 Args    : none

  next_locuslink
 Title   : next_locuslink
 Usage   : next_locuslink();
 Function: Returns the next locuslink from an array referred
           to using $obj->{'locuslink'}

           If you call this iterator again after it returned undef, it
           will re-cycle through the list of elements. Changes in the
           underlying array property while you loop over this iterator
           will not be reflected until you exhaust the iterator.

 Example :      while ( my $locuslink = $in->next_locuslink() ) {
                                print "$locuslink\n";
                        }
 Returns : String
 Args    : None

  next_express
 Title   : next_express
 Usage   : next_express();
 Function: Returns the next tissue from an array referred
           to using $obj->{'express'}

           If you call this iterator again after it returned undef, it
           will re-cycle through the list of elements. Changes in the
           underlying array property while you loop over this iterator
           will not be reflected until you exhaust the iterator.

 Example :      while ( my $express = $in->next_express() ) {
                                print "$express\n";
                        }
 Returns : String
 Args    : None

  next_chromosome
 Title   : next_chromosome
 Usage   : next_chromosome();
 Function: Returns the next chromosome line from an array referred
           to using $obj->{'chromosome'}

           If you call this iterator again after it returned undef, it
           will re-cycle through the list of elements. Changes in the
           underlying array property while you loop over this iterator
           will not be reflected until you exhaust the iterator.

 Example :      while ( my $chromosome = $in->next_chromosome() ) {
                                print "$chromosome\n";
                        }
 Returns : String
 Args    : None

  next_protsim
 Title   : next_protsim
 Usage   : next_protsim();
 Function: Returns the next protsim line from an array referred
           to using $obj->{'protsim'}

           If you call this iterator again after it returned undef, it
           will re-cycle through the list of elements. Changes in the
           underlying array property while you loop over this iterator
           will not be reflected until you exhaust the iterator.

 Example :      while ( my $protsim = $in->next_protsim() ) {
                                print "$protsim\n";
                        }
 Returns : String
 Args    : None

  next_sts
 Title   : next_sts
 Usage   : next_sts();
 Function: Returns the next sts line from an array referred
           to using $obj->{'sts'}

           If you call this iterator again after it returned undef, it
           will re-cycle through the list of elements. Changes in the
           underlying array property while you loop over this iterator
           will not be reflected until you exhaust the iterator.

 Example :      while ( my $sts = $in->next_sts() ) {
                                print "$sts\n";
                        }
 Returns : String
 Args    : None

  next_txmap
 Title   : next_txmap
 Usage   : next_txmap();
 Function: Returns the next txmap line from an array
           referred to using $obj->{'txmap'}

           If you call this iterator again after it returned undef, it
           will re-cycle through the list of elements. Changes in the
           underlying array property while you loop over this iterator
           will not be reflected until you exhaust the iterator.

 Example :      while ( my $tsmap = $in->next_txmap() ) {
                                print "$txmap\n";
                        }
 Returns : String
 Args    : None

Bio::IdentifiableI methods

  object_id
 Title   : object_id
 Usage   : $string    = $obj->object_id()
 Function: a string which represents the stable primary identifier
           in this namespace of this object. For DNA sequences this
           is its accession_number, similarly for protein sequences

           This is aliased to unigene_id().

 Returns : A scalar

  version
 Title   : version
 Usage   : $version    = $obj->version()
 Function: a number which differentiates between versions of
           the same object. Higher numbers are considered to be
           later and more relevant, but a single object described
           the same identifier should represent the same concept

           Unigene clusters usually won't have a version, so this
           will be mostly undefined.

 Returns : A number
 Args    : on set, new value (a scalar or undef, optional)

  authority
 Title   : authority
 Usage   : $authority    = $obj->authority()
 Function: a string which represents the organisation which
           granted the namespace, written as the DNS name for
           organisation (eg, wormbase.org)

 Returns : A scalar
 Args    : on set, new value (a scalar or undef, optional)

  namespace
 Title   : namespace
 Usage   : $string    = $obj->namespace()
 Function: A string representing the name space this identifier
           is valid in, often the database name or the name
           describing the collection

 Returns : A scalar
 Args    : on set, new value (a scalar or undef, optional)

Bio::DescribableI methods

  display_name
 Title   : display_name
 Usage   : $string    = $obj->display_name()
 Function: A string which is what should be displayed to the user
           the string should have no spaces (ideally, though a cautious
           user of this interface would not assumme this) and should be
           less than thirty characters (though again, double checking
           this is a good idea)

           This is aliased to unigene_id().

 Returns : A scalar
 Status  : Virtual

  description()
 Title   : description
 Usage   : $string    = $obj->description()
 Function: A text string suitable for displaying to the user a
           description. This string is likely to have spaces, but
           should not have any newlines or formatting - just plain
           text. The string should not be greater than 255 characters
           and clients can feel justified at truncating strings at 255
           characters for the purposes of display

           This is already demanded by Bio::ClusterI and hence is
           present anyway.

 Returns : A scalar

Bio::Factory::SequenceStreamI methods

  next_seq
 Title   : next_seq
 Usage   : next_seq();
 Function: Returns the next seq as a Seq object as defined by
           $seq->sequence_factory(),
           at present an empty Bio::Seq::RichSeq object with
           just the accession_number() and pid() set

           This iterator will not exhaust the array of member
           sequences. If you call next_seq() again after it returned
           undef, it will re-cycle through the list of member
           sequences.

 Example :  while ( my $sequence = $in->next_seq() ) {
             print $sequence->accession_number() . "\n";
            }
 Returns : Bio::PrimarySeqI object
 Args    : None

  sequence_factory
 Title   : sequence_factory
 Usage   : $seqio->sequence_factory($seqfactory)
 Function: Get/Set the Bio::Factory::SequenceFactoryI
 Returns : Bio::Factory::SequenceFactoryI
 Args    : [optional] Bio::Factory::SequenceFactoryI

Private methods

  _annotation_value
 Title   : _annotation_value
 Usage   :
 Function: Private method.
 Example :
 Returns : the value (a string)
 Args    : annotation key (a string)
           on set, annotation value (a string)

  _annotation_value_ary
 Title   : _annotation_value_ary
 Usage   :
 Function: Private method.
 Example :
 Returns : reference to the array of values
 Args    : annotation key (a string)
           on set, reference to an array holding the values

  _annotation_dblink
 Title   : _annotation_dblink
 Usage   :
 Function: Private method.
 Example :
 Returns : array of accessions for the given database (namespace)
 Args    : annotation key (a string)
           dbname (a string) (optional on get, mandatory on set)
           on set, accession or ID (a string), and version

  _remove_dblink
 Title   : _remove_dblink
 Usage   :
 Function: Private method.
 Example :
 Returns : array of accessions for the given database (namespace)
 Args    : annotation key (a string)
           dbname (a string) (optional)