Raw content of Bio::EnsEMBL::Compara::Member
<![CDATA[package Bio::EnsEMBL::Compara::Member;
use strict;
use Bio::Seq;
use Bio::EnsEMBL::Utils::Argument;
use Bio::EnsEMBL::Utils::Exception;
use Bio::EnsEMBL::Gene;
use Bio::EnsEMBL::Compara::GenomeDB;
use Bio::EnsEMBL::Compara::NestedSet;
our @ISA = qw(Bio::EnsEMBL::Compara::NestedSet);
=head2 new (CONSTRUCTOR)
Arg [-DBID] : (opt)
: int $dbID (the database internal ID for this object)
Arg [-ADAPTOR]
: Bio::EnsEMBL::Compara::DBSQL::Member $adaptor
(the adaptor for connecting to the database)
Arg [-DESCRIPTION] (opt)
: string $description
Arg [-SOURCE_NAME] (opt)
: string $source_name
(e.g., "ENSEMBLGENE", "ENSEMBLPEP", "Uniprot/SWISSPROT", "Uniprot/SPTREMBL")
Arg [-TAXON_ID] (opt)
: int $taxon_id
(NCBI taxonomy id for the member)
Arg [-GENOME_DB_ID] (opt)
: int $genome_db_id
(the $genome_db->dbID for a species in the database)
Arg [-SEQUENCE_ID] (opt)
: int $sequence_id
(the $sequence_id for the sequence table in the database)
Example :
my $member = new Bio::EnsEMBL::Compara::Member;
Description: Creates a new Member object
Returntype : Bio::EnsEMBL::Compara::Member
Exceptions : none
Caller : general
Status : Stable
=cut
sub new {
my ($class, @args) = @_;
my $self = bless {}, $class;
if (scalar @args) {
#do this explicitly.
my ($dbid, $stable_id, $description, $source_name, $adaptor, $taxon_id, $genome_db_id, $sequence_id) = rearrange([qw(DBID STABLE_ID DESCRIPTION SOURCE_NAME ADAPTOR TAXON_ID GENOME_DB_ID SEQUENCE_ID)], @args);
$dbid && $self->dbID($dbid);
$stable_id && $self->stable_id($stable_id);
$description && $self->description($description);
$source_name && $self->source_name($source_name);
$adaptor && $self->adaptor($adaptor);
$taxon_id && $self->taxon_id($taxon_id);
$genome_db_id && $self->genome_db_id($genome_db_id);
$sequence_id && $self->sequence_id($sequence_id);
}
return $self;
}
=head2 new_fast
Arg [1] : hash reference $hashref
Example : none
Description: This is an ultra fast constructor which requires knowledge of
the objects internals to be used.
Returntype :
Exceptions : none
Caller :
=cut
sub new_fast {
my ($class, $hashref) = @_;
return bless $hashref, $class;
}
=head2 new_from_gene
Args : Requires both an Bio::Ensembl:Gene object and a
: Bio::Ensembl:Compara:GenomeDB object
Example : $member = Bio::EnsEMBL::Compara::Member->new_from_gene(
-gene => $gene,
-genome_db => $genome_db);
Description: contructor method which takes an Ensembl::Gene object
and Compara:GenomeDB object and creates a new Member object
translating from the Gene object
Returntype : Bio::Ensembl::Compara::Member
Exceptions :
Caller :
=cut
sub new_from_gene {
my ($class, @args) = @_;
my $self = $class->new(@args);
if (scalar @args) {
my ($gene, $genome_db) = rearrange([qw(GENE GENOME_DB)], @args);
unless(defined($gene) and $gene->isa('Bio::EnsEMBL::Gene')) {
throw(
"gene arg must be a [Bio::EnsEMBL::Gene] ".
"not a [$gene]");
}
unless(defined($genome_db) and $genome_db->isa('Bio::EnsEMBL::Compara::GenomeDB')) {
throw(
"genome_db arg must be a [Bio::EnsEMBL::Compara::GenomeDB] ".
"not a [$genome_db]");
}
unless (defined $gene->stable_id) {
throw("COREDB error: does not contain gene_stable_id for gene_id ". $gene->dbID."\n");
}
$self->stable_id($gene->stable_id);
$self->taxon_id($genome_db->taxon_id);
$self->description($gene->description);
$self->genome_db_id($genome_db->dbID);
$self->chr_name($gene->seq_region_name);
$self->chr_start($gene->seq_region_start);
$self->chr_end($gene->seq_region_end);
$self->chr_strand($gene->seq_region_strand);
$self->source_name("ENSEMBLGENE");
$self->version($gene->version);
}
return $self;
}
=head2 new_from_transcript
Arg[1] : Bio::Ensembl:Transcript object
Arg[2] : Bio::Ensembl:Compara:GenomeDB object
Arg[3] : string where value='translate' causes transcript object to translate
to a peptide
Example : $member = Bio::EnsEMBL::Compara::Member->new_from_transcript(
$transcript, $genome_db,
-translate);
Description: contructor method which takes an Ensembl::Gene object
and Compara:GenomeDB object and creates a new Member object
translating from the Gene object
Returntype : Bio::Ensembl::Compara::Member
Exceptions :
Caller :
=cut
sub new_from_transcript {
my ($class, @args) = @_;
my $self = $class->new(@args);
my $peptideBioSeq;
my $seq_string;
my ($transcript, $genome_db, $translate, $description) = rearrange([qw(TRANSCRIPT GENOME_DB TRANSLATE DESCRIPTION)], @args);
#my ($transcript, $genome_db, $translate) = @args;
unless(defined($transcript) and $transcript->isa('Bio::EnsEMBL::Transcript')) {
throw(
"transcript arg must be a [Bio::EnsEMBL::Transcript]".
"not a [$transcript]");
}
unless(defined($genome_db) and $genome_db->isa('Bio::EnsEMBL::Compara::GenomeDB')) {
throw(
"genome_db arg must be a [Bio::EnsEMBL::Compara::GenomeDB] ".
"not a [$genome_db]");
}
$self->taxon_id($genome_db->taxon_id);
if(defined($description)) { $self->description($description); }
else { $self->description("NULL"); }
$self->genome_db_id($genome_db->dbID);
$self->chr_name($transcript->seq_region_name);
$self->chr_start($transcript->coding_region_start);
$self->chr_end($transcript->coding_region_end);
$self->chr_strand($transcript->seq_region_strand);
$self->version($transcript->translation->version);
if(($translate eq 'translate') or ($translate eq 'yes')) {
if(not defined($transcript->translation)) {
throw("request to translate a transcript without a defined translation",
$transcript->stable_id);
}
unless (defined $transcript->translation->stable_id) {
throw("COREDB error: does not contain translation stable id for translation_id ".$transcript->translation->dbID."\n");
}
$self->stable_id($transcript->translation->stable_id);
$self->source_name("ENSEMBLPEP");
unless ($peptideBioSeq = $transcript->translate) {
throw("COREDB error: unable to get a BioSeq translation from ". $transcript->stable_id);
}
eval {
$seq_string = $peptideBioSeq->seq;
};
throw "COREDB error: can't get seq from peptideBioSeq" if $@;
# OR
#$seq_string = $transcript->translation->seq;
if ($seq_string =~ /^X+$/) {
warn("X+ in sequence from translation " . $transcript->translation->stable_id."\n");
}
elsif (length($seq_string) == 0) {
warn("zero length sequence from translation " . $transcript->translation->stable_id."\n");
}
else {
#$seq_string =~ s/(.{72})/$1\n/g;
$self->sequence($seq_string);
}
}
else {
unless (defined $transcript->stable_id) {
throw("COREDB error: does not contain transcript stable id for transcript_id ".$transcript->dbID."\n");
}
$self->stable_id($transcript->stable_id);
$self->source_name("ENSEMBLTRANS");
#$self->sequence($transcript->seq);
}
#print("Member->new_from_transcript\n");
#print(" source_name = '" . $self->source_name . "'\n");
#print(" stable_id = '" . $self->stable_id . "'\n");
#print(" taxon_id = '" . $self->taxon_id . "'\n");
#print(" chr_name = '" . $self->chr_name . "'\n");
return $self;
}
=head2 copy
Arg [1] : int $member_id (optional)
Example :
Description: returns copy of object, calling superclass copy method
Returntype :
Exceptions :
Caller :
=cut
sub copy {
my $self = shift;
my $mycopy = $self->SUPER::copy;
bless $mycopy, "Bio::EnsEMBL::Compara::Member";
$mycopy->dbID($self->dbID);
$mycopy->stable_id($self->stable_id);
$mycopy->version($self->version);
$mycopy->description($self->description);
$mycopy->source_name($self->source_name);
#$mycopy->adaptor($self->adaptor);
$mycopy->chr_name($self->chr_name);
$mycopy->chr_start($self->chr_start);
$mycopy->chr_end($self->chr_end);
$mycopy->chr_strand($self->chr_strand);
$mycopy->taxon_id($self->taxon_id);
$mycopy->genome_db_id($self->genome_db_id);
$mycopy->sequence_id($self->sequence_id);
$mycopy->gene_member_id($self->gene_member_id);
$mycopy->display_label($self->display_label);
return $mycopy;
}
=head2 member_id
Arg [1] : int $member_id (optional)
Example :
Description:
Returntype :
Exceptions :
Caller :
=cut
sub member_id {
my $self = shift;
return $self->dbID(@_);
}
=head2 dbID
Arg [1] : int $dbID (optional)
Example :
Description:
Returntype :
Exceptions :
Caller :
=cut
sub dbID {
my $self = shift;
$self->{'_dbID'} = shift if(@_);
return $self->{'_dbID'};
}
=head2 stable_id
Arg [1] : string $stable_id (optional)
Example :
Description:
Returntype :
Exceptions :
Caller :
=cut
sub stable_id {
my $self = shift;
$self->{'_stable_id'} = shift if(@_);
return $self->{'_stable_id'};
}
=head2 display_label
Arg [1] : string $display_label (optional)
Example :
Description:
Returntype :
Exceptions :
Caller :
=cut
sub display_label {
my $self = shift;
$self->{'_display_label'} = shift if(@_);
return $self->{'_display_label'};
}
=head2 version
Arg [1] :
Example :
Description:
Returntype :
Exceptions :
Caller :
=cut
sub version {
my $self = shift;
$self->{'_version'} = shift if(@_);
$self->{'_version'} = 0 unless(defined($self->{'_version'}));
return $self->{'_version'};
}
=head2 description
Arg [1] : string $description (optional)
Example :
Description:
Returntype : string
Exceptions :
Caller :
=cut
sub description {
my $self = shift;
$self->{'_description'} = shift if(@_);
return $self->{'_description'};
}
=head2 source_name
=cut
sub source_name {
my $self = shift;
$self->{'_source_name'} = shift if (@_);
return $self->{'_source_name'};
}
=head2 adaptor
Arg [1] : string $adaptor (optional)
corresponding to a perl module
Example :
Description:
Returntype :
Exceptions :
Caller :
=cut
sub adaptor {
my $self = shift;
$self->{'_adaptor'} = shift if(@_);
return $self->{'_adaptor'};
}
=head2 chr_name
=cut
sub chr_name {
my $self = shift;
$self->{'_chr_name'} = shift if (@_);
return $self->{'_chr_name'};
}
=head2 chr_start
=cut
sub chr_start {
my $self = shift;
$self->{'_chr_start'} = shift if (@_);
return $self->{'_chr_start'};
}
=head2 chr_end
=cut
sub chr_end {
my $self = shift;
$self->{'_chr_end'} = shift if (@_);
return $self->{'_chr_end'};
}
=head2 chr_strand
Arg [1] : integer
Description: Returns the strand of the member. Defined strands are 1 or -1.
0 is undefined strand.
Returntype : 1,0,-1
Exceptions : none
Caller : general
=cut
sub chr_strand {
my $self = shift;
$self->{'_chr_strand'} = shift if (@_);
$self->{'_chr_strand'}='0' unless(defined($self->{'_chr_strand'}));
return $self->{'_chr_strand'};
}
=head taxon_id
=cut
sub taxon_id {
my $self = shift;
$self->{'_taxon_id'} = shift if (@_);
return $self->{'_taxon_id'};
}
=head2 taxon
=cut
sub taxon {
my $self = shift;
if (@_) {
my $taxon = shift;
unless ($taxon->isa('Bio::EnsEMBL::Compara::NCBITaxon')) {
throw(
"taxon arg must be a [Bio::EnsEMBL::Compara::NCBITaxon".
"not a [$taxon]");
}
$self->{'_taxon'} = $taxon;
$self->taxon_id($taxon->ncbi_taxid);
} else {
unless (defined $self->{'_taxon'}) {
unless (defined $self->taxon_id) {
throw("can't fetch Taxon without a taxon_id");
}
my $NCBITaxonAdaptor = $self->adaptor->db->get_NCBITaxonAdaptor;
$self->{'_taxon'} = $NCBITaxonAdaptor->fetch_node_by_taxon_id($self->taxon_id);
}
}
return $self->{'_taxon'};
}
=head genome_db_id
=cut
sub genome_db_id {
my $self = shift;
$self->{'_genome_db_id'} = shift if (@_);
return $self->{'_genome_db_id'};
}
=head2 genome_db
=cut
sub genome_db {
my $self = shift;
if (@_) {
my $genome_db = shift;
unless ($genome_db->isa('Bio::EnsEMBL::Compara::GenomeDB')) {
throw(
"arg must be a [Bio::EnsEMBL::Compara::GenomeDB".
"not a [$genome_db]");
}
$self->{'_genome_db'} = $genome_db;
$self->genome_db_id($genome_db->dbID);
} else {
unless (defined $self->{'_genome_db'}) {
unless (defined $self->genome_db_id and defined $self->adaptor) {
throw("can't fetch GenomeDB without an adaptor and genome_db_id");
}
my $GenomeDBAdaptor = $self->adaptor->db->get_GenomeDBAdaptor;
$self->{'_genome_db'} = $GenomeDBAdaptor->fetch_by_dbID($self->genome_db_id);
}
}
return $self->{'_genome_db'};
}
=head2 sequence
Arg [1] : string $sequence
Example : my $seq = $member->sequence;
Description: Get/set the sequence string of this member
Will lazy load by sequence_id if needed and able
Returntype : string
Exceptions : none
Caller : general
=cut
sub sequence {
my $self = shift;
if(@_) {
$self->{'_seq_length'} = undef;
$self->{'_sequence'} = shift;
$self->{'_seq_length'} = length($self->{'_sequence'}) if(defined($self->{'_sequence'}));
return $self->{'_sequence'};
}
if(!defined($self->{'_sequence'}) and
defined($self->sequence_id()) and
defined($self->adaptor))
{
$self->{'_sequence'} = $self->adaptor->_fetch_sequence_by_id($self->sequence_id);
$self->{'_seq_length'} = length($self->{'_sequence'}) if(defined($self->{'_sequence'}));
}
return $self->{'_sequence'};
}
=head2 sequence_exon_cased
Args : none
Example : my $sequence_exon_cased = $member->sequence_exon_cased;
Description: Get/set the sequence string of this peptide member with
alternating upper and lower case corresponding to the translateable exons.
Returntype : string
Exceptions : none
Caller : general
=cut
sub sequence_exon_cased {
my $self = shift;
my $sequence = $self->sequence;
my $trans = $self->transcript;
my @exons = @{$trans->get_all_translateable_Exons};
return $sequence if (1 == scalar @exons);
my %splice_site;
my $pep_len = 0;
my $overlap_len = 0;
for my $exon (@exons) {
my $exon_len = $exon->length;
my $pep_seq = $exon->peptide($trans)->length;
# remove the first char of seq if overlap ($exon->peptide()) return full overlapping exon seq
$pep_seq -= 1 if ($overlap_len);
$pep_len += $pep_seq;
if ($overlap_len = (($exon_len + $overlap_len ) %3)){ # if there is an overlap
$splice_site{$pep_len-1}{'overlap'} = $pep_len -1; # stores overlapping aa-exon boundary
} else {
$overlap_len = 0;
}
$splice_site{$pep_len}{'phase'} = $overlap_len; # positions of exon boundary
}
my $seqsplice = '';
my $splice = 0;
foreach my $pep_len (sort {$b<=>$a} keys %splice_site) { # We start from the end
next if (defined($splice_site{$pep_len}{'overlap'}));
next if ($pep_len > length($sequence)); # Get rid of 1 codon STOP exons in the protein
$splice++;
my $length = $pep_len;
$length-- if (defined($splice_site{$pep_len}{'phase'}) && 1 == $splice_site{$pep_len}{'phase'});
my $peptide;
$peptide = substr($sequence,$length,length($sequence),'');
$peptide = lc($peptide) unless ($splice % 2); # Even splice lower-cased
$seqsplice = $peptide . $seqsplice;
}
$seqsplice = $sequence . $seqsplice; # First exon AS IS
return $seqsplice;
}
# GJ 2008-11-17
# Returns the amino acid sequence with exon boundaries denoted as O, B, or J depending on the phase (O=0, B=1, J=2)
sub get_exon_bounded_sequence {
my $self = shift;
my $numbers = shift;
my $transcript = $self->get_Transcript;
# The get_all_translateable_exons creates a list of reformatted "translateable" exon sequences.
# When the exon phase is 1 or 2, there will be duplicated residues at the end and start of exons.
# We'll deal with this during the exon loop.
my @exons = @{$transcript->get_all_translateable_Exons};
my $seq_string = "";
for my $ex (@exons) {
my $seq = $ex->peptide($transcript)->seq;
# PHASE HANDLING
my $phase = $ex->phase;
my $end_phase = $ex->end_phase;
# First, cut off repeated end residues.
if ($end_phase == 1) {
# We only own 1/3, so drop the last residue.
$seq = substr($seq,0,-1);
}
# Now cut off repeated start residues.
if ($phase == 2) {
# We only own 1/3, so drop the first residue.
$seq = substr($seq, 1);
}
if ($end_phase > -1) {
$seq = $seq . 'o' if ($end_phase == 0);
$seq = $seq . 'b' if ($end_phase == 1);
$seq = $seq . 'j' if ($end_phase == 2);
}
#print "Start_phase: $phase End_phase: $end_phase\t$seq\n";
$seq_string .= $seq;
}
if (defined $numbers) {
$seq_string =~ s/o/0/g; $seq_string =~ s/b/1/g; $seq_string =~ s/j/2/g;
}
return $seq_string;
}
=head2 seq_length
Example : my $seq_length = $member->seq_length;
Description: get the sequence length of this member
Returntype : int
Exceptions : none
Caller : general
=cut
sub seq_length {
my $self = shift;
unless(defined($self->{'_seq_length'})) {
#need to check case if user is calling seq_length first
#call $self->sequence (to lazy load if needed)
my $seq = $self->sequence;
$self->{'_seq_length'} = length($seq) if(defined($seq));
}
return $self->{'_seq_length'};
}
=head2 sequence_id
Arg [1] : int $sequence_id
Example : my $sequence_id = $member->sequence_id;
Description: Extracts the sequence_id of this member
Returntype : int
Exceptions : none
Caller : general
=cut
sub sequence_id {
my $self = shift;
$self->{'_sequence_id'} = shift if(@_);
if(!defined($self->{'_sequence_id'})) { $self->{'_sequence_id'}=0; }
return $self->{'_sequence_id'};
}
=head2 gene_member_id
Arg [1] : int $gene_member_id
Example : my $gene_member_id = $member->gene_member_id;
Description: Gene_member_id of this protein member
Returntype : int
Exceptions : none
Caller : general
=cut
sub gene_member_id {
my $self = shift;
$self->{'_gene_member_id'} = shift if(@_);
return $self->{'_gene_member_id'};
}
=head2 bioseq
Args : none
Example : my $primaryseq = $member->primaryseq;
Description: returns sequence this member as a Bio::Seq object
Returntype : Bio::Seq object
Exceptions : none
Caller : general
=cut
sub bioseq {
my $self = shift;
throw("Member stable_id undefined") unless defined($self->stable_id());
throw("No sequence for member " . $self->stable_id()) unless defined($self->sequence());
my $seqname;
if (defined($self->genome_db_id) and defined($self->dbID)) {
$seqname = "IDs:" . $self->genome_db_id . ":" . $self->dbID . " " .
$self->source_name . ":" . $self->stable_id;
} else {
$seqname = $self->source_name . ":" . $self->stable_id;
}
my $seq = Bio::Seq->new(-seq => $self->sequence(),
-primary_id => "member_id_".$self->dbID,
-display_id => "member_id_".$self->dbID,
-desc => $seqname ."|". $self->description(),
);
return $seq;
}
=head2 gene_member
Arg[1] : Bio::EnsEMBL::Compara::Member $geneMember (optional)
Example : my $gene_member = $member->gene_member;
Description: returns gene member object for this protein member
Returntype : Bio::EnsEMBL::Compara::Member object
Exceptions : if arg[0] is not a Bio::EnsEMBL::Compara::Member object
Caller : MemberAdaptor(set), general
=cut
sub gene_member {
my $self = shift;
my $gene_member = shift;
if ($gene_member) {
throw("arg must be a [Bio::EnsEMBL::Compara::Member] not a [$gene_member]")
unless ($gene_member->isa('Bio::EnsEMBL::Compara::Member'));
$self->{'_gene_member'} = $gene_member;
}
if(!defined($self->{'_gene_member'}) and
defined($self->adaptor) and $self->dbID)
{
$self->{'_gene_member'} = $self->adaptor->fetch_gene_for_peptide_member_id($self->dbID);
}
return $self->{'_gene_member'};
}
=head2 print_member
Arg[1] : string $postfix
Example : $member->print_member("BRH");
Description: used for debugging, prints out key descriptive elements
of member
Returntype : none
Exceptions : none
Caller : general
=cut
sub print_member
{
my $self = shift;
my $postfix = shift;
printf(" %s %s(%d)\t%s : %d-%d",$self->source_name, $self->stable_id,
$self->dbID,$self->chr_name,$self->chr_start, $self->chr_end);
if($postfix) { print(" $postfix"); }
else { print("\n"); }
}
=head2 get_Gene
Args : none
Example : $gene = $member->get_Gene
Description: if member is an 'ENSEMBLGENE' returns Bio::EnsEMBL::Gene object
by connecting to ensembl genome core database
REQUIRES properly setup Registry conf file or
manually setting genome_db->db_adaptor for each genome.
Returntype : Bio::EnsEMBL::Gene or undef
Exceptions : none
Caller : general
=cut
sub get_Gene {
my $self = shift;
return $self->{'core_gene'} if($self->{'core_gene'});
unless($self->genome_db and
$self->genome_db->db_adaptor and
$self->genome_db->db_adaptor->isa('Bio::EnsEMBL::DBSQL::DBAdaptor'))
{
throw("unable to connect to core ensembl database: missing registry and genome_db.locator");
}
my $coreDBA = $self->genome_db->db_adaptor;
if($self->source_name eq 'ENSEMBLGENE') {
$self->{'core_gene'} = $coreDBA->get_GeneAdaptor->fetch_by_stable_id($self->stable_id);
}
if($self->source_name eq 'ENSEMBLPEP') {
$self->{'core_gene'} = $coreDBA->get_GeneAdaptor->fetch_by_stable_id($self->gene_member->stable_id);
}
return $self->{'core_gene'};
}
=head2 get_Transcript
Args : none
Example : $transcript = $member->get_Transcript
Description: if member is an 'ENSEMBLPEP' returns Bio::EnsEMBL::Transcript object
by connecting to ensembl genome core database
REQUIRES properly setup Registry conf file or
manually setting genome_db->db_adaptor for each genome.
Returntype : Bio::EnsEMBL::Transcript or undef
Exceptions : none
Caller : general
=cut
sub get_Transcript {
my $self = shift;
return undef unless($self->source_name eq 'ENSEMBLPEP');
return $self->{'core_transcript'} if($self->{'core_transcript'});
unless($self->genome_db and
$self->genome_db->db_adaptor and
$self->genome_db->db_adaptor->isa('Bio::EnsEMBL::DBSQL::DBAdaptor'))
{
throw("unable to connect to core ensembl database: missing registry and genome_db.locator");
}
my $coreDBA = $self->genome_db->db_adaptor;
$self->{'core_transcript'} = $coreDBA->get_TranscriptAdaptor->fetch_by_translation_stable_id($self->stable_id);
return $self->{'core_transcript'};
}
=head2 get_Translation
Args : none
Example : $translation = $member->get_Translation
Description: if member is an 'ENSEMBLPEP' returns Bio::EnsEMBL::Translation object
by connecting to ensembl genome core database
REQUIRES properly setup Registry conf file or
manually setting genome_db->db_adaptor for each genome.
Returntype : Bio::EnsEMBL::Gene or undef
Exceptions : none
Caller : general
=cut
sub get_Translation {
my $self = shift;
return $self->get_Transcript->translation if($self->get_Transcript);
return undef;
}
sub gene {
my $self = shift;
return $self->get_Gene;
}
sub transcript {
my $self = shift;
return $self->get_Transcript;
}
sub translation {
my $self = shift;
return $self->get_Translation;
}
=head2 get_longest_peptide_Member
Args : none
Example : $longestPepMember = $member->get_longest_peptide_Member
Description: if member is an "ENSEMBLGENE" it will return the longest peptide member
if member is an 'ENSEMBLPEP' it will get its gene member and have it
return the longest peptide (which could be the same as the starting member)
Returntype : Bio::EnsEMBL::Compara::Member or undef
Exceptions : none
Caller : general
=cut
sub get_longest_peptide_Member {
my $self = shift;
return undef unless($self->adaptor);
my $longestPep = undef;
if($self->source_name eq 'ENSEMBLGENE') {
$longestPep = $self->adaptor->fetch_longest_peptide_member_for_gene_member_id($self->dbID);
}
if($self->source_name eq 'ENSEMBLPEP') {
my $geneMember = $self->gene_member;
return undef unless($geneMember);
$longestPep = $self->adaptor->fetch_longest_peptide_member_for_gene_member_id($geneMember->dbID);
}
return $longestPep;
}
=head2 get_all_peptide_Members
Args : none
Example : $pepMembers = $gene_member->get_all_peptide_Members
Description: return listref of all peptide members of this gene_member
Returntype : array ref of Bio::EnsEMBL::Compara::Member
Exceptions : throw if not an ENSEMBLGENE
Caller : general
=cut
sub get_all_peptide_Members {
my $self = shift;
throw("adaptor undefined, can access database") unless($self->adaptor);
throw("not an ENSEMBLGENE member") if($self->source_name ne 'ENSEMBLGENE');
return $self->adaptor->fetch_peptides_for_gene_member_id($self->dbID);
}
# DEPRECATED METHODS
####################
sub source_id {
my $self = shift;
throw("Method deprecated. You can now get the source_name by directly calling source_name method\n");
}
1;
]]>