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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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)