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Commit 0cfbdb98 authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
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Support for canonical translations. 

The TranslationAdaptor now has a fetch_all_by_Transcript() method with
which it's possible to get all translations for a transcript.

The fetch_by_Transcript() method now uses the new
canonical_translation_id field in the transcript table to get the
canonical transcript.

For species without alternative initiation (all Core speaces today), the
semantics and the results are the same as before.

Using the API from now on, without patch_56_57_e.sql applied, will
result in SQL errors.
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modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
+ 164
− 58
View file @ 0cfbdb98
......@@ -79,6 +79,108 @@ use Bio::EnsEMBL::Utils::Exception qw( throw warning deprecate );
=head2 fetch_all_by_Transcript
Arg [1] : Bio::EnsEMBL::Transcript $transcript
Example :
@tl = @{ $translation_adaptor->fetch_by_Transcript($transcript) };
Description: Retrieves all Translation associated with a
particular transcript. If no Translation is found, a
reference to an empty list is returned.
Returntype : listref of Bio::EnsEMBL::Translation
Exceptions : throw on incorrect argument
Caller : Transcript
Status : Stable
=cut
sub fetch_all_by_Transcript {
my ( $self, $transcript ) = @_;
if (
!(
ref($transcript) && $transcript->isa('Bio::EnsEMBL::Transcript') )
)
{
throw('Bio::EnsEMBL::Transcript argument is required.');
}
my $lsi_created_date =
$self->db()->dbc()->from_date_to_seconds('tlsi.created_date');
my $lsi_modified_date =
$self->db()->dbc()->from_date_to_seconds('tlsi.modified_date');
my $sql =
sprintf( "SELECT tl.translation_id, tl.start_exon_id, "
. "tl.end_exon_id, tl.seq_start, tl.seq_end, "
. "tlsi.stable_id, tlsi.version, %s, %s "
. "FROM translation tl "
. "LEFT JOIN translation_stable_id tlsi "
. "ON (tlsi.translation_id = tl.translation_id) "
. "WHERE tl.transcript_id = ?",
$lsi_created_date, $lsi_modified_date );
my $transcript_id = $transcript->dbID();
my $sth = $self->prepare($sql);
$sth->bind_param( 1, $transcript_id, SQL_INTEGER );
$sth->execute();
my (
$translation_id, $start_exon_id, $end_exon_id,
$seq_start, $seq_end, $stable_id,
$version, $created_date, $modified_date
);
$sth->bind_columns(
\(
$translation_id, $start_exon_id, $end_exon_id,
$seq_start, $seq_end, $stable_id,
$version, $created_date, $modified_date
) );
my @translations = ();
while ( $sth->fetch() ) {
if ( !defined($translation_id) ) { next }
my ( $start_exon, $end_exon );
# this will load all the exons whenever we load the translation
# but I guess thats ok ....
foreach my $exon ( @{ $transcript->get_all_Exons() } ) {
if ( $exon->dbID() == $start_exon_id ) { $start_exon = $exon }
if ( $exon->dbID() == $end_exon_id ) { $end_exon = $exon }
}
if ( !( defined($start_exon) && defined($end_exon) ) ) {
throw(
sprintf(
"Could not find start or end exon in transcript_id=%d\n",
$transcript->dbID() ) );
}
push(
@translations,
Bio::EnsEMBL::Translation->new_fast( {
'dbID' => $translation_id,
'adaptor' => $self,
'start' => $seq_start,
'end' => $seq_end,
'start_exon' => $start_exon,
'end_exon' => $end_exon,
'stable_id' => $stable_id,
'version' => $version,
'created_date' => $created_date || undef,
'modified_date' => $modified_date || undef
} ) );
} ## end while ( $sth->fetch() )
return \@translations;
} ## end sub fetch_all_by_Transcript
=head2 fetch_by_Transcript
Arg [1] : Bio::EnsEMBL::Transcript $transcript
......@@ -95,73 +197,77 @@ use Bio::EnsEMBL::Utils::Exception qw( throw warning deprecate );
sub fetch_by_Transcript {
my ( $self, $transcript ) = @_;
if(!ref($transcript) || !$transcript->isa('Bio::EnsEMBL::Transcript')) {
throw("Bio::EnsEMBL::Transcript argument is required.");
if (
!(
ref($transcript) && $transcript->isa('Bio::EnsEMBL::Transcript') )
)
{
throw('Bio::EnsEMBL::Transcript argument is required.');
}
my $lsi_created_date = $self->db->dbc->from_date_to_seconds("tlsi.created_date");
my $lsi_modified_date = $self->db->dbc->from_date_to_seconds("tlsi.modified_date");
my $sql = "
SELECT tl.translation_id, tl.start_exon_id,
tl.end_exon_id, tl.seq_start, tl.seq_end,
tlsi.stable_id, tlsi.version, " . $lsi_created_date . ", ". $lsi_modified_date .
" FROM translation tl
LEFT JOIN translation_stable_id tlsi
ON tlsi.translation_id = tl.translation_id
WHERE tl.transcript_id = ?";
my $lsi_created_date =
$self->db()->dbc()->from_date_to_seconds('tlsi.created_date');
my $lsi_modified_date =
$self->db()->dbc()->from_date_to_seconds('tlsi.modified_date');
my $sql =
sprintf( "SELECT tl.translation_id, tl.start_exon_id, "
. "tl.end_exon_id, tl.seq_start, tl.seq_end, "
. "tlsi.stable_id, tlsi.version, %s, %s "
. "FROM translation tl "
. "JOIN transcript tr "
. "ON (tl.translation_id = tr.canonical_translation_id) "
. "LEFT JOIN translation_stable_id tlsi "
. "ON (tlsi.translation_id = tl.translation_id) "
. "WHERE tr.transcript_id = ?",
$lsi_created_date, $lsi_modified_date );
my $transcript_id = $transcript->dbID();
my $sth = $self->prepare($sql);
$sth->bind_param(1,$transcript_id,SQL_INTEGER);
my $sth = $self->prepare($sql);
$sth->bind_param( 1, $transcript_id, SQL_INTEGER );
$sth->execute();
my ( $translation_id, $start_exon_id, $end_exon_id,
$seq_start, $seq_end, $stable_id, $version, $created_date,
$modified_date ) =
$sth->fetchrow_array();
$sth->finish;
if( ! defined $translation_id ) {
return undef;
}
my (
$translation_id, $start_exon_id, $end_exon_id,
$seq_start, $seq_end, $stable_id,
$version, $created_date, $modified_date
) = $sth->fetchrow_array();
$sth->finish();
if ( !defined($translation_id) ) { return undef }
my ($start_exon, $end_exon);
my ( $start_exon, $end_exon );
# this will load all the exons whenever we load the translation
# but I guess thats ok ....
foreach my $exon (@{$transcript->get_all_Exons()}) {
if($exon->dbID() == $start_exon_id ) {
$start_exon = $exon;
}
if($exon->dbID() == $end_exon_id ) {
$end_exon = $exon;
}
foreach my $exon ( @{ $transcript->get_all_Exons() } ) {
if ( $exon->dbID() == $start_exon_id ) { $start_exon = $exon }
if ( $exon->dbID() == $end_exon_id ) { $end_exon = $exon }
}
unless($start_exon && $end_exon) {
throw("Could not find start or end exon in transcript_id=".$transcript->dbID."\n");
if ( !( defined($start_exon) && defined($end_exon) ) ) {
throw(
sprintf( "Could not find start or end exon in transcript_id=%d\n",
$transcript->dbID() ) );
}
my $translation = Bio::EnsEMBL::Translation->new_fast
({
'dbID' => $translation_id,
'adaptor' => $self,
'start' => $seq_start,
'end' => $seq_end,
'start_exon' => $start_exon,
'end_exon' => $end_exon,
'stable_id' => $stable_id,
'version' => $version,
'created_date' => $created_date || undef,
'modified_date' => $modified_date || undef
}
);
my $translation = Bio::EnsEMBL::Translation->new_fast( {
'dbID' => $translation_id,
'adaptor' => $self,
'start' => $seq_start,
'end' => $seq_end,
'start_exon' => $start_exon,
'end_exon' => $end_exon,
'stable_id' => $stable_id,
'version' => $version,
'created_date' => $created_date || undef,
'modified_date' => $modified_date || undef
} );
return $translation;
}
} ## end sub fetch_by_Transcript
......@@ -534,11 +640,11 @@ sub list_stable_ids {
Arg [1] : int $dbID
The internal identifier of the Translation to obtain
Example : $translation = $translation_adaptor->fetch_by_dbID(1234);
Description: This fetches a Translation object via its internal id. This
is only debatably useful since translations do not make much
sense outside of the context of their Translation. Consider
using fetch_by_Transcript instead.
Returntype : Bio::EnsEMBL::Translation or undef if the translation is not
Description: This fetches a Translation object via its internal id.
This is only debatably useful since translations do
not make much sense outside of the context of their
Transcript. Consider using fetch_by_Transcript instead.
Returntype : Bio::EnsEMBL::Translation, or undef if the translation is not
found.
Exceptions : warning if an additional (old style) Transcript argument is
provided
......@@ -573,10 +679,10 @@ sub fetch_by_dbID {
Arg [1] : string $stable_id
The stable identifier of the Translation to obtain
Example : $translation = $translation_adaptor->fetch_by_stable_id("ENSP00001");
Description: This fetches a Translation object via its stable id. This
is only debatably useful since translations do not make much
sense outside of the context of their Translation. Consider
using fetch_by_Transcript instead.
Description: This fetches a Translation object via its stable id.
This is only debatably useful since translations do
not make much sense outside of the context of their
Transcript. Consider using fetch_by_Transcript instead.
Returntype : Bio::EnsEMBL::Translation or undef if the translation is not
found.
Exceptions : warning if an additional (old style) Transcript argument is
......
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