Bio::Cluster::UniGene.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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
 
 
  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
 
 
  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
 
 
  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
 
 
  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)