--- name: "Bio::Cluster::UniGene" section: "3pm" platform: "linux" package: "libbio-cluster-perl" version: "1.7.3-6" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/Bio::Cluster::UniGene" --- # Bio::Cluster::UniGene(3pm) UniGene object ## 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 object) Args : on set, new value (a L 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 object for this UniGene cluster. Many attributes of this class are actually stored within the annotation collection object as L compliant objects, so you can conveniently access them through the same interface as you would e.g. access L 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 compliant object Args : on set, new value (a L 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 successfully 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 assume 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) ```