#
# BioPerl module for Bio::Cluster::UniGene.pm
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Andrew Macgregor <andrew at cbbc.murdoch.edu.au>
#
# Copyright Andrew Macgregor, Jo-Ann Stanton, David Green
# Molecular Embryology Group, Anatomy & Structural Biology, University of Otago
# http://meg.otago.ac.nz/
#
# You may distribute this module under the same terms as perl itself
#
# _history
# April 17, 2002 - Initial implementation by Andrew Macgregor
# POD documentation - main docs before the code
=head1 NAME
Bio::Cluster::UniGene - UniGene object
=head1 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";
}
}
=head1 DESCRIPTION
This UniGene object implements the L<Bio::Cluster::UniGeneI> interface
for the representation if UniGene clusters in Bioperl. It is returned
by the L<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 L<Bio::ClusterI> as the base interface for all cluster
representations, and in addition L<Bio::IdentifiableI> and
L<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
=head1 Implemented Interfaces
This class implementes the following interfaces.
=over 4
=item Bio::Cluster::UniGeneI
This includes implementing Bio::ClusterI.
=item Bio::IdentifiableI
=item Bio::DescribableI
=item Bio::AnnotatableI
=item Bio::Factory::SequenceStreamI
=back
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Andrew Macgregor
Email andrew at cbbc.murdoch.edu.au
=head1 CONTRIBUTORS
Hilmar Lapp, hlapp at gmx.net
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a "_".
=cut
# Let the code begin...
package Bio::Cluster::UniGene;
use strict;
use Bio::Annotation::Collection;
use Bio::Annotation::DBLink;
use Bio::Annotation::SimpleValue;
use Bio::Species;
use Bio::Seq::SeqFactory;
use base qw(Bio::Root::Root Bio::Cluster::UniGeneI Bio::IdentifiableI Bio::DescribableI Bio::AnnotatableI Bio::Factory::SequenceStreamI);
my %species_map = (
'Aga' => "Anopheles gambiae",
'Ame' => "Apis mellifera",
'At' => "Arabidopsis thaliana",
'Bmo' => "Bombyx mori",
'Bt' => "Bos taurus",
'Cel' => "Caenorhabditis elegans",
'Cfa' => "Canine familiaris",
'Cin' => "Ciona intestinalis",
'Cre' => "Chlamydomonas reinhardtii",
'Csa' => "Ciona savignyi",
'Csi' => "Citrus sinensis",
'Ddi' => "Dictyostelium discoideum",
'Dr' => "Danio rerio",
'Dm' => "Drosophila melanogaster",
'Gga' => "Gallus gallus",
'Gma' => "Glycine max",
'Han' => "Helianthus annus",
'Hs' => "Homo sapiens",
'Hma' => "Hydra magnipapillata",
'Hv' => "Hordeum vulgare",
'Lco' => "Lotus corniculatus",
'Les' => "Lycopersicon esculentum",
'Lsa' => "Lactuca sativa",
'Mdo' => "Malus x domestica",
'Mgr' => "Magnaporthe grisea",
'Mm' => "Mus musculus",
'Mtr' => "Medicago truncatula",
'Ncr' => "Neurospora crassa",
'Oar' => "Ovis aries",
'Omy' => "Oncorhynchus mykiss",
'Os' => "Oryza sativa",
'Ola' => "Oryzias latipes",
'Ppa' => "Physcomitrella patens",
'Pta' => "Pinus taeda",
'Ptp' => "Populus tremula x Populus tremuloides",
'Rn' => "Rattus norvegicus",
'Sbi' => "Sorghum bicolor",
'Sma' => "Schistosoma mansoni",
'Sof' => "Saccharum officinarum",
'Spu' => "Strongylocentrotus purpuratus",
'Ssa' => "Salmo salar",
'Ssc' => "Sus scrofa",
'Str' => "Xenopus tropicalis",
'Stu' => "Solanum tuberosum",
'Ta' => "Triticum aestivum",
'Tgo' => "Toxoplasma gondii",
'Tru' => "Takifugu rubripes",
'Vvi' => "Vitis vinifera",
'Xl' => "Xenopus laevis",
'Zm' => "Zea mays",
);
=head2 new
Title : new
Usage : used by ClusterIO
Returns : a new Bio::Cluster::Unigene object
=cut
sub new {
# standard new call..
my($caller,@args) = @_;
my $self = $caller->SUPER::new(@args);
my ($ugid,$desc,$mems,$size,$species,$dispid,$id,$ns,$auth,$v,$seqfact) =
$self->_rearrange([qw(UNIGENE_ID
DESCRIPTION
MEMBERS
SIZE
SPECIES
DISPLAY_ID
OBJECT_ID
NAMESPACE
AUTHORITY
VERSION
SEQFACTORY
)], @args);
$self->{'_alphabet'} = 'dna';
$self->unigene_id($ugid) if $ugid;
$self->description($desc) if $desc;
$self->sequences($mems) if $mems;
$self->size($size) if defined($size);
$self->display_id($dispid) if $dispid; # overwrites ugid
$self->object_id($id) if $id; # overwrites dispid
$self->namespace($ns || 'UniGene');
$self->authority($auth || 'NCBI');
$self->version($v) if defined($v);
if( ! defined $seqfact ) {
$seqfact = Bio::Seq::SeqFactory->new
(-verbose => $self->verbose(),
-type => 'Bio::Seq::RichSeq');
}
$self->sequence_factory($seqfact);
if( (! $species) && (defined $self->unigene_id() &&
$self->unigene_id() =~ /^([A-Za-z]+)\.[0-9]/)) {
# try set a default one depending on the ID
$species = $species_map{$1};
}
$self->species($species);
return $self;
}
=head1 L<Bio::Cluster::UniGeneI> methods
=cut
=head2 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
=cut
sub unigene_id {
my ($obj,$value) = @_;
if( defined $value) {
$obj->{'unigene_id'} = $value;
}
return $obj->{'unigene_id'};
}
=head2 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
=cut
sub title {
my ($obj,$value) = @_;
if( defined $value) {
$obj->{'title'} = $value;
}
return $obj->{'title'};
}
=head2 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
=cut
sub gene {
my $self = shift;
return $self->_annotation_value('gene_name', @_);
}
=head2 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
=cut
sub cytoband {
my $self = shift;
return $self->_annotation_value('cyto_band', @_);
}
=head2 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
=cut
sub mgi {
my $self = shift;
my $acc;
if(@_) {
# purge first
$self->_remove_dblink('dblink','MGI');
# then add if a valid value is present
if($acc = shift) {
$self->_annotation_dblink('dblink','MGI',$acc);
}
} else {
($acc) = $self->_annotation_dblink('dblink','MGI');
}
return $acc;
}
=head2 locuslink
Title : locuslink
Usage : locuslink();
Function: Returns or stores a reference to an array containing locuslink data.
Returns : An array reference
Args : None or an array reference
=cut
sub locuslink {
my ($self,$ll) = @_;
if($ll) {
# purge first
$self->_remove_dblink('dblink','LocusLink');
# then add as many accessions as are present
foreach my $acc (@$ll) {
$self->_annotation_dblink('dblink','LocusLink',$acc);
}
} else {
my @accs = $self->_annotation_dblink('dblink','LocusLink');
$ll = [@accs];
}
return $ll;
}
=head2 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
=cut
sub homol {
my $self = shift;
return $self->_annotation_value('homol', @_);
}
=head2 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
=cut
sub restr_expr {
my $self = shift;
return $self->_annotation_value('restr_expr', @_);
}
=head2 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
=cut
sub gnm_terminus {
my $self = shift;
return $self->_annotation_value('gnm_terminus', @_);
}
=head2 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
=cut
sub scount {
my ($obj,$value) = @_;
if( defined $value) {
$obj->{'scount'} = $value;
} elsif((! defined($obj->{'scount'})) && defined($obj->sequences())) {
$obj->{'scount'} = $obj->size();
}
return $obj->{'scount'};
}
=head2 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
=cut
sub express {
my $self = shift;
return $self->_annotation_value_ary('expressed',@_);
}
=head2 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
=cut
sub chromosome {
my $self = shift;
return $self->_annotation_value_ary('chromosome',@_);
}
=head2 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
=cut
sub sts {
my $self = shift;
return $self->_annotation_value_ary('sts',@_);
}
=head2 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
=cut
sub txmap {
my $self = shift;
return $self->_annotation_value_ary('txmap',@_);
}
=head2 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
=cut
sub protsim {
my $self = shift;
return $self->_annotation_value_ary('protsim',@_);
}
=head2 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
=cut
sub sequences {
my $self = shift;
return $self->{'members'} = shift if @_;
return $self->{'members'};
}
=head2 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)
=cut
sub species{
my $self = shift;
if(@_) {
my $species = shift;
if($species && (! ref($species))) {
my @class = reverse(split(' ',$species));
$species = Bio::Species->new(-classification => \@class);
}
return $self->{'species'} = $species;
}
return $self->{'species'};
}
=head1 L<Bio::ClusterI> methods
=cut
=head2 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)
=cut
sub display_id{
return shift->unigene_id(@_);
}
=head2 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
=cut
sub description{
return shift->title(@_);
}
=head2 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 :
=cut
sub size {
my $self = shift;
# hard-wiring the size is allowed if there are no sequences
return $self->scount(@_) unless defined($self->sequences());
# but we can't change the number of members through this method
my $n = scalar(@{$self->sequences()});
if(@_ && ($n != $_[0])) {
$self->throw("Cannot change cluster size using size() from $n to ".
$_[0]);
}
return $n;
}
=head2 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
=cut
sub cluster_score{
my $self = shift;
return $self->{'cluster_score'} = shift if @_;
return $self->{'cluster_score'};
}
=head2 get_members
Title : get_members
Usage : Bio::ClusterI->get_members(($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 :
=cut
sub get_members {
my $self = shift;
my $mems = $self->sequences() || [];
# already objects?
if(@$mems && (ref($mems->[0]) eq "HASH")) {
# nope, we need to build the object list from scratch
my @memlist = ();
while(my $seq = $self->next_seq()) {
push(@memlist, $seq);
}
# we cache this array of objects as the new member list
$mems = \@memlist;
$self->sequences($mems);
}
# done
return @$mems;
}
=head1 Annotatable view at the object properties
=cut
=head2 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)
=cut
sub annotation{
my $self = shift;
if(@_) {
return $self->{'annotation'} = shift;
} elsif(! exists($self->{'annotation'})) {
$self->{'annotation'} = Bio::Annotation::Collection->new();
}
return $self->{'annotation'};
}
=head1 Implementation specific methods
These are mostly for adding/removing to array properties, and for
methods with special functionality.
=cut
=head2 add_member
Title : add_member
Usage :
Function: Adds a member object to the list of members.
Example :
Returns : TRUE if the new member was successfuly added, and FALSE
otherwise.
Args : The member to add.
=cut
sub add_member{
my ($self,@mems) = @_;
my $memlist = $self->{'members'} || [];
# this is an object interface; is the member list already objects?
if(@$memlist && (ref($memlist->[0]) eq "HASH")) {
# nope, convert to objects
$memlist = [$self->get_members()];
}
# add new member(s)
push(@$memlist, @mems);
# store if we created this array ref ourselves
$self->sequences($memlist);
# done
return 1;
}
=head2 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
=cut
sub remove_members{
my $self = shift;
my @mems = $self->get_members();
$self->sequences(undef);
return @mems;
}
=head2 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
=cut
sub next_locuslink {
my ($obj) = @_;
return $obj->_next_element("ll","locuslink");
}
=head2 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
=cut
sub next_express {
my ($obj) = @_;
return $obj->_next_element("express","express");
}
=head2 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
=cut
sub next_chromosome {
my ($obj) = @_;
return $obj->_next_element("chr","chromosome");
}
=head2 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
=cut
sub next_protsim {
my ($obj) = @_;
return $obj->_next_element("protsim","protsim");
}
=head2 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
=cut
sub next_sts {
my ($obj) = @_;
return $obj->_next_element("sts","sts");
}
=head2 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
=cut
sub next_txmap {
my ($obj) = @_;
return $obj->_next_element("txmap","txmap");
}
###############################
# private method
#
# args: prefix name for the queue
# name of the method from which to re-fill
# returns: the next element from that queue, or undef if the queue is empty
###############################
sub _next_element{
my ($self,$queuename,$meth) = @_;
$queuename = "_".$queuename."_queue";
if(! exists($self->{$queuename})) {
# re-initialize from array of sequence data
$self->{$queuename} = [@{$self->$meth() }];
}
my $queue = $self->{$queuename};
# is queue exhausted (equivalent to end of stream)?
if(! @$queue) {
# yes, remove queue and signal to the caller
delete $self->{$queuename};
return;
}
return shift(@$queue);
}
=head1 L<Bio::IdentifiableI> methods
=cut
=head2 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
=cut
sub object_id {
return shift->unigene_id(@_);
}
=head2 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)
=cut
sub version {
my $self = shift;
return $self->{'version'} = shift if @_;
return $self->{'version'};
}
=head2 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)
=cut
sub authority {
my $self = shift;
return $self->{'authority'} = shift if @_;
return $self->{'authority'};
}
=head2 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)
=cut
sub namespace {
my $self = shift;
return $self->{'namespace'} = shift if @_;
return $self->{'namespace'};
}
=head1 L<Bio::DescribableI> methods
=cut
=head2 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
=cut
sub display_name {
return shift->unigene_id(@_);
}
=head2 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
=cut
=head1 L<Bio::Factory::SequenceStreamI> methods
=cut
=head2 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 $sequence->accession_number() . "\n";
}
Returns : Bio::PrimarySeqI object
Args : None
=cut
sub next_seq {
my ($obj) = @_;
if(! exists($obj->{'_seq_queue'})) {
# re-initialize from array of sequence data
$obj->{'_seq_queue'} = [@{$obj->sequences()}];
}
my $queue = $obj->{'_seq_queue'};
# is queue exhausted (equivalent to end of stream)?
if(! @$queue) {
# yes, remove queue and signal to the caller
delete $obj->{'_seq_queue'};
return;
}
# no, still data in the queue: get the next one from the queue
my $seq_h = shift(@$queue);
# if this is not a simple hash ref, it's an object already, and we'll
# return just that
return $seq_h if(ref($seq_h) ne 'HASH');
# nope, we need to assemble this object from scratch
#
# assemble the annotation collection
my $ac = Bio::Annotation::Collection->new();
foreach my $k (keys %$seq_h) {
next if $k =~ /acc|pid|nid|version/;
my $ann = Bio::Annotation::SimpleValue->new(-tagname => $k,
-value => $seq_h->{$k});
$ac->add_Annotation($ann);
}
# assemble the initialization parameters and create object
my $seqobj = $obj->sequence_factory->create(
-accession_number => $seq_h->{acc},
-pid => $seq_h->{pid},
# why does NCBI prepend a 'g' to its own identifiers??
-primary_id => $seq_h->{nid} && $seq_h->{nid} =~ /^g\d+$/ ?
substr($seq_h->{nid},1) : $seq_h->{nid},
-display_id => $seq_h->{acc},
-seq_version => $seq_h->{version},
-alphabet => $obj->{'_alphabet'},
-namespace => $seq_h->{acc} =~ /^NM_/ ? 'RefSeq' : 'GenBank',
-authority => $obj->authority(), # default is NCBI
-species => $obj->species(),
-annotation => $ac
);
return $seqobj;
}
=head2 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
=cut
sub sequence_factory {
my ($self,$obj) = @_;
if( defined $obj ) {
if( ! ref($obj) || ! $obj->isa('Bio::Factory::SequenceFactoryI') ) {
$self->throw("Must provide a valid Bio::Factory::SequenceFactoryI object to ".ref($self)." sequence_factory()");
}
$self->{'_seqfactory'} = $obj;
}
$self->{'_seqfactory'};
}
=head1 Private methods
=cut
=head2 _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)
=cut
sub _annotation_value{
my $self = shift;
my $key = shift;
my ($ann, $val);
if(@_) {
$val = shift;
if(! defined($val)) {
($ann) = $self->annotation->remove_Annotations($key);
return $ann ? $ann->value() : undef;
}
}
($ann) = $self->annotation->get_Annotations($key);
if(defined $ann && (! $val)) {
# get mode and exists
$val = $ann->value();
} elsif($val) {
# set mode
if(!defined $ann) {
$ann = Bio::Annotation::SimpleValue->new(-tagname => $key);
$self->annotation->add_Annotation($ann);
}
$ann->value($val);
}
return $val;
}
=head2 _annotation_value_ary
Title : _annotation_value_ary
Usage :
Function: Private method.
Example :
Returns : reference to the array of values
Args : annotation key (a string)
on set, reference to an array holding the values
=cut
sub _annotation_value_ary{
my ($self,$key,$arr) = @_;
my $ac = $self->annotation;
if($arr) {
# purge first
$ac->remove_Annotations($key);
# then add as many values as are present
foreach my $val (@$arr) {
my $ann = Bio::Annotation::SimpleValue->new(-value => $val,
-tagname => $key
);
$ac->add_Annotation($ann);
}
} else {
my @vals = map { $_->value(); } $ac->get_Annotations($key);
$arr = [@vals];
}
return $arr;
}
=head2 _annotation_dblink
Title : _annotation_dblink
Usage :
Function: Private method.
Example :
Returns : array of accessions for the given database (namespace)
Args : annotation key (a string)
dbname (a string) (optional on get, mandatory on set)
on set, accession or ID (a string), and version
=cut
sub _annotation_dblink{
my ($self,$key,$dbname,$acc,$version) = @_;
if($acc) {
# set mode -- this is adding here
my $ann = Bio::Annotation::DBLink->new(-tagname => $key,
-primary_id => $acc,
-database => $dbname,
-version => $version);
$self->annotation->add_Annotation($ann);
return 1;
} else {
# get mode
my @anns = $self->annotation->get_Annotations($key);
# filter out those that don't match the requested database
if($dbname) {
@anns = grep { $_->database() eq $dbname; } @anns;
}
return map { $_->primary_id(); } @anns;
}
}
=head2 _remove_dblink
Title : _remove_dblink
Usage :
Function: Private method.
Example :
Returns : array of accessions for the given database (namespace)
Args : annotation key (a string)
dbname (a string) (optional)
=cut
sub _remove_dblink{
my ($self,$key,$dbname) = @_;
my $ac = $self->annotation();
my @anns = ();
if($dbname) {
foreach my $ann ($ac->remove_Annotations($key)) {
if($ann->database() eq $dbname) {
push(@anns, $ann);
} else {
$ac->add_Annotation($ann);
}
}
} else {
@anns = $ac->remove_Annotations($key);
}
return map { $_->primary_id(); } @anns;
}
#####################################################################
# aliases for naming consistency or other reasons #
#####################################################################
*sequence = \&sequences;
1;