Bio::EnsEMBL
Translation
Toolbar
Summary
Bio::EnsEMBL::Translation - A class representing the translation of a
transcript
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
my $translation = Bio::EnsEMBL::Translation->new(
-START_EXON => $exon1,
-END_EXON => $exon2,
-SEQ_START => 98,
-SEQ_END => 39
);
# stable ID setter
$translation->stable_id('ENSP00053458');
# get start and end position in start/end exons
my $start = $translation->start;
my $end = $translation->end;
Description
A Translation object defines the CDS and UTR regions of a Transcript
through the use of start_Exon/end_Exon, and start/end attributes.
Methods
Methods description
Arg [1..N] : Bio::EnsEMBL::Attribute $attribute
Attributes to add.
Example : $translation->add_Attributes($selenocysteine_attribute);
Description: Adds an Attribute to the Translation. Usefull to
do _selenocysteine.
If you add an attribute before you retrieve any from database,
lazy load will be disabled.
Returntype : none
Exceptions : throw on incorrect arguments
Caller : general
Status : Stable |
Arg [1] : Bio::EnsEMBL::DBEntry $dbe
The dbEntry to be added
Example : $translation->add_DBEntry($xref);
Description: Associates a DBEntry with this translation. Note that adding
DBEntries will prevent future lazy-loading of DBEntries for this
translation (see get_all_DBEntries).
Returntype : none
Exceptions : thrown on incorrect argument type
Caller : general
Status : Stable |
Arg [1] : Bio::EnsEMBL::ProteinFeature $pf
The ProteinFeature to be added
Example : $translation->add_ProteinFeature($pf);
Description: Associates a ProteinFeature with this translation. Note that
adding ProteinFeatures will prevent future lazy-loading of
ProteinFeatures for this translation (see
get_all_ProteinFeatures).
Returntype : none
Exceptions : thrown on incorrect argument type
Caller : general
Status : Stable |
Arg [1] : (optional) Bio::EnsEMBL::Transcript $transcript
The transcript which this is a translation of.
Example : $translation_cdna_end = $translation->cdna_end();
Description : Returns the end position of the translation in cDNA
coordinates.
If no transcript is given, the method will use
TranscriptAdaptor->fetch_by_translation_id() to locate
the correct transcript.
Return type : Integer
Exceptions : Throws if the given (optional) argument is not a
transcript.
Caller : General
Status : At Risk (Under Development) |
Arg [1] : (optional) Bio::EnsEMBL::Transcript $transcript
The transcript which this is a translation of.
Example : $translation_cdna_start = $translation->cdna_start();
Description : Returns the start position of the translation in cDNA
coordinates.
If no transcript is given, the method will use
TranscriptAdaptor->fetch_by_translation_id() to locate
the correct transcript.
Return type : Integer
Exceptions : Throws if the given (optional) argument is not a
transcript.
Caller : General
Status : At Risk (Under Development) |
Arg [1] : (optional) string $created_date - created date to set
Example : $translation->created_date('2007-01-10 20:52:00');
Description: Getter/setter for attribute created date
Returntype : string
Exceptions : none
Caller : general
Status : Stable |
Example : print $translation->display_id();
Description: This method returns a string that is considered to be
the 'display' identifier. For translations this is (depending on
availability and in this order) the stable Id, the dbID or an
empty string.
Returntype : string
Exceptions : none
Caller : web drawing code
Status : Stable |
Arg [1] : (optional) int $end - end position to set
Example : $translation->end(8);
Description: Getter/setter for the value of end, which is a position within
the exon given by end_Exon.
If you need genomic coordinates, use the genomic_end()
method.
Returntype : int
Exceptions : none
Caller : general
Status : Stable |
Arg [1] : (optional) Bio::EnsEMBL::Exon - start exon to assign
Example : $translation->start_Exon($exon1);
Description: Getter/setter for the value of end_Exon, which denotes the
exon at which translation ends (and within this exon, at the
position indicated by end, see above).
Returntype : Bio::EnsEMBL::Exon
Exceptions : thrown on wrong argument type
Caller : general
Status : Stable |
Args : None
Example : $translation_genomic_end = $translation->genomic_end();
Description : Returns the end position of the translation in genomic
coordinates on the forward strand.
Return type : Integer
Exceptions : None
Caller : General
Status : At Risk (Under Development) |
Args : None
Example : $translation_genomic_start =
$translation->genomic_start();
Description : Returns the start position of the translation in
genomic coordinates on the forward strand.
Return type : Integer
Exceptions : None
Caller : General
Status : At Risk (Under Development) |
Arg [1] : optional string $attrib_code
The code of the attribute type to retrieve values for.
Example : ($sc_attr) = @{$tl->get_all_Attributes('_selenocysteine')};
@tl_attributes = @{$translation->get_all_Attributes()};
Description: Gets a list of Attributes of this translation.
Optionally just get Attrubutes for given code.
Recognized attribute "_selenocysteine"
Returntype : listref Bio::EnsEMBL::Attribute
Exceptions : warning if translation does not have attached adaptor and
attempts lazy load.
Caller : general, modify_translation
Status : Stable |
Function : Retrieves a listref of registered DAS objects
Returntype: DAS objects
Exceptions: none
Caller : webcode
Example : $dasref = $prot->get_all_DASFactories;
Status : Stable |
Example : $features = $prot->get_all_DAS_Features;
Description: Retreives a hash reference to a hash of DAS feature
sets, keyed by the DNS, NOTE the values of this hash
are an anonymous array containing:
(1) a pointer to an array of features;
(2) a pointer to the DAS stylesheet
Returntype : hashref of Bio::SeqFeatures
Exceptions : none
Caller : webcode
Status : Stable |
Arg [1] : (optional) $ex_db_exp - external db name
Example : @dbentries = @{$translation->get_all_DBEntries()};
Description: Retrieves DBEntries (xrefs) for this translation.
This method will attempt to lazy-load DBEntries from a
database if an adaptor is available and no DBEntries are present
on the translation (i.e. they have not already been added or
loaded).
Returntype : list reference to Bio::EnsEMBL::DBEntry objects
Exceptions : none
Caller : get_all_DBLinks, TranslationAdaptor::store
Status : Stable |
Arg [1] : see get_all_DBEntries
Example : see get_all_DBEntries
Description: This is here for consistancy with the Transcript and Gene
classes. It is a synonym for the get_all_DBEntries method.
Returntype : see get_all_DBEntries
Exceptions : none
Caller : general
Status : Stable |
Example : @domain_feats = @{$translation->get_all_DomainFeatures};
Description: A convenience method which retrieves all protein features
that are considered to be 'Domain' features. Features which
are 'domain' features are those with analysis logic names:
'pfscan', 'scanprosite', 'superfamily', 'pfam', 'prints',
'smart', 'pirsf', 'tigrfam'.
Returntype : listref of Bio::EnsEMBL::ProteinFeatures
Exceptions : none
Caller : webcode (protview)
Status : Stable |
Arg [1] : (optional) string $logic_name
The analysis logic_name of the features to retrieve. If not
specified, all features are retrieved instead.
Example : $features = $self->get_all_ProteinFeatures('PFam');
Description: Retrieves all ProteinFeatures associated with this
Translation. If a logic_name is specified, only features with
that logic_name are returned. If no logic_name is provided all
associated protein_features are returned.
ProteinFeatures are lazy-loaded from the database unless they
added manually to the Translation or had already been loaded.
Returntype : Bio::EnsEMBL::ProteinFeature
Exceptions : none
Caller : general
Status : Stable |
Example : my @seqeds = @{$transcript->get_all_SeqEdits()};
Description: Retrieves all post transcriptional sequence modifications for
this transcript.
Returntype : Bio::EnsEMBL::SeqEdit
Exceptions : none
Caller : spliced_seq()
Status : Stable |
Example : print "Peptide length =", $translation->length();
Description: Retrieves the length of the peptide sequence (i.e. number of
amino acids) represented by this Translation object.
Returntype : int
Exceptions : none
Caller : webcode (protview etc.)
Status : Stable |
Arg [1] : (optional) string $modified_date - modification date to set
Example : $translation->modified_date('2007-01-10 20:52:00');
Description: Getter/setter for attribute modified date
Returntype : string
Exceptions : none
Caller : general
Status : Stable |
Arg [1] : Bio::Seq $peptide
Example : my $seq = Bio::Seq->new(-SEQ => $dna)->translate();
$translation->modify_translation($seq);
Description: Applies sequence edits such as selenocysteines to the Bio::Seq
peptide thats passed in
Returntype : Bio::Seq
Exceptions : none
Caller : Bio::EnsEMBL::Transcript->translate
Status : Stable |
Arg [-START_EXON] : The Exon object in which the translation (CDS) starts
Arg [-END_EXON] : The Exon object in which the translation (CDS) ends
Arg [-SEQ_START] : The offset in the start_Exon indicating the start
position of the CDS.
Arg [-SEQ_END] : The offset in the end_Exon indicating the end
position of the CDS.
Arg [-STABLE_ID] : The stable identifier for this Translation
Arg [-VERSION] : The version of the stable identifier
Arg [-DBID] : The internal identifier of this Translation
Arg [-ADAPTOR] : The TranslationAdaptor for this Translation
Arg [-SEQ] : Manually sets the peptide sequence of this translation.
May be useful if this translation is not stored in
a database.
Arg [-CREATED_DATE]: the date the translation was created
Arg [-MODIFIED_DATE]: the date the translation was modified
Example : my $tl = Bio::EnsEMBL::Translation->new
(-START_EXON => $ex1,
-END_EXON => $ex2,
-SEQ_START => 98,
-SEQ_END => 39);
Description: Constructor. Creates a new Translation object
Returntype : Bio::EnsEMBL::Translation
Exceptions : none
Caller : general
Status : Stable |
Arg [1] : hashref to be blessed
Description: Construct a new Bio::EnsEMBL::Translation using the hashref.
Exceptions : none
Returntype : Bio::EnsEMBL::Translation
Caller : general, subclass constructors
Status : Stable |
Example : print $translation->seq();
Description: Retrieves a string representation of the peptide sequence
of this Translation. This retrieves the transcript from the
database and gets its sequence, or retrieves the sequence which
was set via the constructor.
Returntype : string
Exceptions : warning if the sequence is not set and cannot be retrieved from
the database.
Caller : webcode (protview etc.)
Status : Stable |
Arg [1] : (optional) string $stable_id - stable ID to set
Example : $translation->stable_id('ENSP0059890');
Description: Getter/setter for attribute stable_id
Returntype : string
Exceptions : none
Caller : general
Status : Stable |
Arg [1] : (optional) int $start - start position to set
Example : $translation->start(17);
Description: Getter/setter for the value of start, which is a position within
the exon given by start_Exon.
If you need genomic coordinates, use the genomic_start()
method.
Returntype : int
Exceptions : none
Caller : general
Status : Stable |
Arg [1] : (optional) Bio::EnsEMBL::Exon - start exon to assign
Example : $translation->start_Exon($exon1);
Description: Getter/setter for the value of start_Exon, which denotes the
exon at which translation starts (and within this exon, at the
position indicated by start, see above).
Returntype : Bio::EnsEMBL::Exon
Exceptions : thrown on wrong argument type
Caller : general
Status : Stable |
Description: DEPRECATED This method should not be needed. Use dbID,
stable_id or something else. |
Arg [1] : hashref $old_new_exon_map
a hash that maps old to new exons for a whole gene
Description: maps start end end exon according to mapping table.
If an exon is not mapped, just keep the old one.
Returntype: none
Exceptions : none
Caller : Transcript->transform()
Status : Stable |
Arg [1] : (optional) string $version - version to set
Example : $translation->version(2);
Description: Getter/setter for attribute version
Returntype : string
Exceptions : none
Caller : general
Status : Stable |
Methods code
sub add_Attributes
{ my $self = shift;
my @attribs = @_;
if( ! exists $self->{'attributes'} ) {
$self->{'attributes'} = [];
}
for my $attrib ( @attribs ) {
if( ! $attrib->isa( "Bio::EnsEMBL::Attribute" )) {
throw( "Argument to add_Attribute must be a Bio::EnsEMBL::Attribute" );
}
push( @{$self->{'attributes'}}, $attrib );
$self->{seq}=undef;
}} | sub add_DBEntry
{ my $self = shift;
my $dbe = shift;
unless($dbe && ref($dbe) && $dbe->isa('Bio::EnsEMBL::DBEntry')) {
throw('Expected DBEntry argument');
}
$self->{'dbentries'} ||= [];
push @{$self->{'dbentries'}}, $dbe;} | sub add_ProteinFeature
{ my $self = shift;
my $pf = shift;
unless ($pf && ref($pf) && $pf->isa('Bio::EnsEMBL::ProteinFeature')) {
throw('Expected ProteinFeature argument');
}
my $analysis = $pf->analysis;
throw("ProteinFeature has no attached Analysis.") unless $analysis;
push @{ $self->{'protein_features'}->{$analysis->logic_name} }, $pf;} | sub cdna_end
{ my $self = shift;
my ($transcript) = @_;
if ( defined $transcript
&& ( !ref $transcript
|| !$transcript->isa('Bio::EnsEMBL::Transcript') ) )
{
throw("Argument is not a transcript");
}
if ( !exists $self->{'cdna_end'} ) {
if ( !defined $transcript ) {
my $transcript_adaptor =
$self->adaptor()->db()->get_TranscriptAdaptor();
$transcript =
$transcript_adaptor->fetch_by_translation_id(
$self->dbID() );
}
$self->{'cdna_end'} =
$self->end_Exon()->cdna_coding_end($transcript);
}
return $self->{'cdna_end'};
}
} | sub cdna_start
{ my $self = shift;
my ($transcript) = @_;
if ( defined $transcript
&& ( !ref $transcript
|| !$transcript->isa('Bio::EnsEMBL::Transcript') ) )
{
throw("Argument is not a transcript");
}
if ( !exists $self->{'cdna_start'} ) {
if ( !defined $transcript ) {
my $transcript_adaptor =
$self->adaptor()->db()->get_TranscriptAdaptor();
$transcript =
$transcript_adaptor->fetch_by_translation_id(
$self->dbID() );
}
$self->{'cdna_start'} =
$self->start_Exon()->cdna_coding_start($transcript);
}
return $self->{'cdna_start'};
}
} | sub created_date
{ my $self = shift;
$self->{'created_date'} = shift if ( @_ );
return $self->{'created_date'};} | sub display_id
{ my $self = shift;
return $self->{'stable_id'} || $self->dbID || '';} | sub end
{ my $self = shift;
if( @_ ) {
my $value = shift;
$self->{'end'} = $value;
}
return $self->{'end'};} | sub end_Exon
{ my $self = shift;
if( @_ ) {
my $value = shift;
if( !ref $value || !$value->isa('Bio::EnsEMBL::Exon') ) {
throw("Got to have an Exon object, not a $value");
}
$self->{'end_exon'} = $value;
}
return $self->{'end_exon'};} | sub genomic_end
{ my $self = shift;
if ( !exists $self->{'genomic_end'} ) {
if ( $self->end_Exon()->strand() >= 0 ) {
$self->{'genomic_end'} =
$self->end_Exon()->start() + ( $self->end() - 1 );
} else {
$self->{'genomic_end'} =
$self->start_Exon()->end() - ( $self->start() - 1 );
}
}
return $self->{'genomic_end'};} | sub genomic_start
{ my $self = shift;
if ( !exists $self->{'genomic_start'} ) {
if ( $self->start_Exon()->strand() >= 0 ) {
$self->{'genomic_start'} =
$self->start_Exon()->start() + ( $self->start() - 1 );
} else {
$self->{'genomic_start'} =
$self->end_Exon()->end() - ( $self->end() - 1 );
}
}
return $self->{'genomic_start'};} | sub get_all_Attributes
{ my $self = shift;
my $attrib_code = shift;
if( ! exists $self->{'attributes' } ) {
if(!$self->adaptor() ) {
return [];
}
my $aa = $self->adaptor->db->get_AttributeAdaptor();
$self->{'attributes'} = $aa->fetch_all_by_Translation( $self );
}
if( defined $attrib_code ) {
my @results = grep { uc($_->code()) eq uc($attrib_code) }
@{$self->{'attributes'}};
return\@ results;
} else {
return $self->{'attributes'};
}} | sub get_all_DASFactories
{ my $self = shift;
return [ $self->adaptor()->db()->_each_DASFeatureFactory ]; } | sub get_all_DAS_Features
{ my $self = shift;
my $db = $self->adaptor->db;
my $GeneAdaptor = $db->get_GeneAdaptor;
my $Gene = $GeneAdaptor->fetch_by_translation_stable_id($self->stable_id) || return;
my $slice = $Gene->feature_Slice;
return $self->SUPER::get_all_DAS_Features($slice);
}
1; } | sub get_all_DBEntries
{ my $self = shift;
my $ex_db_exp = shift;
my $ex_db_type = shift;
my $cache_name = "dbentries";
if(defined($ex_db_exp)){
$cache_name .= $ex_db_exp;
}
if(defined($ex_db_type)){
$cache_name .= $ex_db_type;
}
if(!defined $self->{$cache_name}) {
my $adaptor = $self->adaptor();
my $dbID = $self->dbID();
return [] if(!$adaptor || !$dbID);
$self->{$cache_name} =
$self->adaptor->db->get_DBEntryAdaptor->fetch_all_by_Translation($self, $ex_db_exp, $ex_db_type);
}
$self->{$cache_name} ||= [];
return $self->{$cache_name};} | sub get_all_DBLinks
{ my $self = shift;
return $self->get_all_DBEntries(@_); } | sub get_all_DomainFeatures
{ my ($self) = @_;
my @features;
my @types = ('pfscan',
'scanprosite',
'superfamily',
'pfam',
'smart',
'tigrfam',
'pirsf',
'prints');
foreach my $type (@types) {
push @features, @{$self->get_all_ProteinFeatures($type)};
}
return\@ features;} | sub get_all_ProteinFeatures
{ my $self = shift;
my $logic_name = shift;
if(!$self->{'protein_features'}) {
my $adaptor = $self->adaptor();
my $dbID = $self->dbID();
return [] if (!$adaptor || !$dbID);
my %hash;
$self->{'protein_features'} =\% hash;
my $pfa = $adaptor->db()->get_ProteinFeatureAdaptor();
my $name;
foreach my $f (@{$pfa->fetch_all_by_translation_id($dbID)}) {
my $analysis = $f->analysis();
if($analysis) {
$name = lc($f->analysis->logic_name());
} else {
warning("ProteinFeature has no attached analysis\n");
$name = '';
}
$hash{$name} ||= [];
push @{$hash{$name}}, $f;
}
}
if(defined($logic_name)) {
$logic_name = lc($logic_name);
return $self->{'protein_features'}->{$logic_name} || [];
}
my @features = ();
foreach my $type (keys %{$self->{'protein_features'}}) {
push @features, @{$self->{'protein_features'}->{$type}};
}
return\@ features;} | sub get_all_SeqEdits
{ my $self = shift;
my @seqeds;
my $attribs;
my @edits = ('initial_met', '_selenocysteine', 'amino_acid_sub');
foreach my $edit(@edits){
$attribs = $self->get_all_Attributes($edit);
foreach my $a (@$attribs) {
push @seqeds, Bio::EnsEMBL::SeqEdit->new(-ATTRIB => $a);
}
}
return\@ seqeds;} | sub length
{ my $self = shift;
my $seq = $self->seq();
return ($seq) ? CORE::length($seq) : 0; } | sub modified_date
{ my $self = shift;
$self->{'modified_date'} = shift if ( @_ );
return $self->{'modified_date'};} | sub modify_translation
{ my ($self, $seq) = @_;
my @seqeds = @{$self->get_all_SeqEdits()};
@seqeds = sort {$b <=> $a} @seqeds;
my $peptide = $seq->seq();
foreach my $se (@seqeds) {
$se->apply_edit(\$peptide);
}
$seq->seq($peptide);
return $seq;} | sub new
{ my $caller = shift;
my $class = ref($caller) || $caller;
my ( $start_exon, $end_exon, $seq_start, $seq_end,
$stable_id, $version, $dbID, $adaptor, $seq,
$created_date, $modified_date ) =
rearrange( [ "START_EXON", "END_EXON", "SEQ_START", "SEQ_END",
"STABLE_ID", "VERSION", "DBID", "ADAPTOR",
"SEQ", "CREATED_DATE", "MODIFIED_DATE" ], @_ );
my $self = bless {
'start_exon' => $start_exon,
'end_exon' => $end_exon,
'adaptor' => $adaptor,
'dbID' => $dbID,
'start' => $seq_start,
'end' => $seq_end,
'stable_id' => $stable_id,
'version' => $version,
'created_date' => $created_date,
'modified_date' => $modified_date,
'seq' => $seq
}, $class;
return $self;} | sub new_fast
{ my $class = shift;
my $hashref = shift;
return bless $hashref, $class; } | sub seq
{ my $self = shift;
if(@_) {
$self->{'seq'} = shift;
return $self->{'seq'};
}
return $self->{'seq'} if($self->{'seq'});
my $adaptor = $self->{'adaptor'};
if(!$adaptor) {
warning("Cannot retrieve sequence from Translation - adaptor is not set.");
}
my $dbID = $self->{'dbID'};
if(!$dbID) {
warning("Cannot retrieve sequence from Translation - dbID is not set.");
}
my $tr_adaptor = $self->{'adaptor'}->db()->get_TranscriptAdaptor;
my $seq = $tr_adaptor->fetch_by_translation_id($dbID)->translate();
if($seq){
$self->{'seq'} = $seq->seq();
return $self->{'seq'};
}
else{
return '';
}} | sub stable_id
{ my $self = shift;
$self->{'stable_id'} = shift if( @_ );
return $self->{'stable_id'};} | sub start
{ my $obj = shift;
if( @_ ) {
my $value = shift;
$obj->{'start'} = $value;
}
return $obj->{'start'};} | sub start_Exon
{ my $self = shift;
if( @_ ) {
my $value = shift;
if( !ref $value || !$value->isa('Bio::EnsEMBL::Exon') ) {
throw("Got to have an Exon object, not a $value");
}
$self->{'start_exon'} = $value;
}
return $self->{'start_exon'};} | sub temporary_id
{ my $self = shift;
deprecate( "I cant see what a temporary_id is good for, please use " .
"dbID or stableID or\n try without an id." );
$self->{'temporary_id'} = shift if( @_ );
return $self->{'temporary_id'};} | sub transform
{ my $self = shift;
my $href_exons = shift;
my $start_exon = $self->start_Exon();
my $end_exon = $self->end_Exon();
if ( exists $href_exons->{$start_exon} ) {
$self->start_Exon($href_exons->{$start_exon});
} else {
}
if ( exists $href_exons->{$end_exon} ) {
$self->end_Exon($href_exons->{$end_exon});
} else {
}} | sub version
{ my $self = shift;
$self->{'version'} = shift if( @_ );
return $self->{'version'};} | General documentation
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html