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 listsSupport
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/issuesAUTHOR - 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 objectBio::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 idtitle
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 titlegene
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 genecytoband
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 cytobandmgi
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 mgilocuslink
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 referencehomol
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 entryrestr_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 entrygnm_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_terminusscount
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 scountexpress
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 referencechromosome
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 referencests
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 referencetxmap
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 referenceprotsim
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 referencesequences
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 undefspecies
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 stringsize
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 : $cluster ->cluster_score(100);
Function: get/set for cluster_score which
represent the score in which the clustering
algorithm assigns to this cluster.
For UniGene clusters, there really is no cluster score that
would come with the data. However, we provide an
implementation here so that you can score UniGene clusters
if you want to.
Returns : a number
Args : optionally, on set a numberget_members
Title : get_members
Usage : Bio::ClusterI->get_members(($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 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 : nonenext_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 : Nonenext_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 : Nonenext_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 : Nonenext_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 : Nonenext_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 : Nonenext_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 : NoneBio::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 scalarversion
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 : Virtualdescription()
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 scalarBio::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 : Nonesequence_factory
Title : sequence_factory
Usage : $seqio->sequence_factory($seqfactory)
Function: Get/Set the Bio::Factory::SequenceFactoryI
Returns : Bio::Factory::SequenceFactoryI
Args : [optional] Bio::Factory::SequenceFactoryIPrivate 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)