Skip to content
Snippets Groups Projects
Commit c2c738dd authored by Patrick Meidl's avatar Patrick Meidl
Browse files

set dbID and adaptor for stored genes before storing xrefs; pass... 

set dbID and adaptor for stored genes before storing xrefs; pass DBEntryAdaptor->store a Transcript object rather than a dbID
parent 4de2fab1
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
+ 152
− 148
View file @ c2c738dd
......@@ -566,153 +566,158 @@ sub store {
$tst->bind_param(7,$transcript->status,SQL_VARCHAR);
$tst->bind_param(8,$transcript->description,SQL_LONGVARCHAR);
$tst->execute();
$tst->execute();
$tst->finish();
$tst->finish();
my $transc_dbID = $tst->{'mysql_insertid'};
# set dbID and adaptor of transcript here - you'll need this when storing
# xrefs
$transcript->dbID($transc_dbID);
$transcript->adaptor($self);
my $transc_dbID = $tst->{'mysql_insertid'};
#
# store translation
#
my $translation = $transcript->translation();
if( defined $translation ) {
#make sure that the start and end exon are set correctly
my $start_exon = $translation->start_Exon();
my $end_exon = $translation->end_Exon();
if(!$start_exon) {
throw("Translation does not define a start exon.");
}
#
# store translation
#
my $translation = $transcript->translation();
if( defined $translation ) {
#make sure that the start and end exon are set correctly
my $start_exon = $translation->start_Exon();
my $end_exon = $translation->end_Exon();
if(!$start_exon) {
throw("Translation does not define a start exon.");
}
if(!$end_exon) {
throw("Translation does not defined an end exon.");
}
#If the dbID is not set, this means the exon must have been a different
#object in memory than the the exons of the transcript. Try to find the
#matching exon in all of the exons we just stored
if(!$start_exon->dbID()) {
my $key = $start_exon->hashkey();
($start_exon) = grep {$_->hashkey() eq $key} @$exons;
if($start_exon) {
$translation->start_Exon($start_exon);
} else {
throw("Translation's start_Exon does not appear to be one of the " .
"exons in its associated Transcript");
}
}
if(!$end_exon->dbID()) {
my $key = $end_exon->hashkey();
($end_exon) = grep {$_->hashkey() eq $key} @$exons;
if($start_exon) {
$translation->end_Exon($end_exon);
} else {
throw("Translation's end_Exon does not appear to be one of the " .
"exons in its associated Transcript.");
}
}
$db->get_TranslationAdaptor()->store( $translation, $transc_dbID );
# set values of the original translation, we may have copied it
# when we transformed the transcript
$original_translation->dbID($translation->dbID());
$original_translation->adaptor($translation->adaptor());
}
if(!$end_exon) {
throw("Translation does not defined an end exon.");
}
#
# store the xrefs/object xref mapping
#
my $dbEntryAdaptor = $db->get_DBEntryAdaptor();
#If the dbID is not set, this means the exon must have been a different
#object in memory than the the exons of the transcript. Try to find the
#matching exon in all of the exons we just stored
if(!$start_exon->dbID()) {
my $key = $start_exon->hashkey();
($start_exon) = grep {$_->hashkey() eq $key} @$exons;
if($start_exon) {
$translation->start_Exon($start_exon);
} else {
throw("Translation's start_Exon does not appear to be one of the " .
"exons in its associated Transcript");
}
}
foreach my $dbe ( @{$transcript->get_all_DBEntries} ) {
$dbEntryAdaptor->store( $dbe, $transc_dbID, "Transcript" );
}
if(!$end_exon->dbID()) {
my $key = $end_exon->hashkey();
($end_exon) = grep {$_->hashkey() eq $key} @$exons;
#
# Update transcript to point to display xref if it is set
#
if(my $dxref = $transcript->display_xref) {
my $dxref_id;
if($dxref->is_stored($db)) {
$dxref_id = $dxref->dbID();
} else {
$dxref_id = $dbEntryAdaptor->exists($dxref);
}
if(defined($dxref_id)) {
my $sth = $self->prepare( "update transcript set display_xref_id = ?".
" where transcript_id = ?");
$sth->bind_param(1,$dxref_id,SQL_INTEGER);
$sth->bind_param(2,$transc_dbID,SQL_INTEGER);
$sth->execute();
$dxref->dbID($dxref_id);
$dxref->adaptor($dbEntryAdaptor);
$sth->finish();
} else {
warning("Display_xref ".$dxref->dbname().":".$dxref->display_id() .
" is not stored in database.\nNot storing " .
"relationship to this transcript.");
$dxref->dbID(undef);
$dxref->adaptor(undef);
}
}
if($start_exon) {
$translation->end_Exon($end_exon);
} else {
throw("Translation's end_Exon does not appear to be one of the " .
"exons in its associated Transcript.");
}
}
#
# Link transcript to exons in exon_transcript table
#
my $etst =
$self->prepare("insert into exon_transcript (exon_id,transcript_id,rank)"
." values (?,?,?)");
my $rank = 1;
foreach my $exon ( @{$transcript->get_all_Exons} ) {
$etst->bind_param(1,$exon->dbID,SQL_INTEGER);
$etst->bind_param(2,$transc_dbID,SQL_INTEGER);
$etst->bind_param(3,$rank,SQL_INTEGER);
$etst->execute();
$rank++;
}
$db->get_TranslationAdaptor()->store( $translation, $transc_dbID );
# set values of the original translation, we may have copied it
# when we transformed the transcript
$original_translation->dbID($translation->dbID());
$original_translation->adaptor($translation->adaptor());
}
$etst->finish();
#
# store the xrefs/object xref mapping
#
my $dbEntryAdaptor = $db->get_DBEntryAdaptor();
foreach my $dbe ( @{$transcript->get_all_DBEntries} ) {
$dbEntryAdaptor->store( $dbe, $transcript, "Transcript" );
}
#
# Update transcript to point to display xref if it is set
#
if(my $dxref = $transcript->display_xref) {
my $dxref_id;
if($dxref->is_stored($db)) {
$dxref_id = $dxref->dbID();
} else {
$dxref_id = $dbEntryAdaptor->exists($dxref);
}
if(defined($dxref_id)) {
my $sth = $self->prepare( "update transcript set display_xref_id = ?".
" where transcript_id = ?");
$sth->bind_param(1,$dxref_id,SQL_INTEGER);
$sth->bind_param(2,$transc_dbID,SQL_INTEGER);
$sth->execute();
$dxref->dbID($dxref_id);
$dxref->adaptor($dbEntryAdaptor);
$sth->finish();
} else {
warning("Display_xref ".$dxref->dbname().":".$dxref->display_id() .
" is not stored in database.\nNot storing " .
"relationship to this transcript.");
$dxref->dbID(undef);
$dxref->adaptor(undef);
}
}
#
# Link transcript to exons in exon_transcript table
#
my $etst =
$self->prepare("insert into exon_transcript (exon_id,transcript_id,rank)"
." values (?,?,?)");
my $rank = 1;
foreach my $exon ( @{$transcript->get_all_Exons} ) {
$etst->bind_param(1,$exon->dbID,SQL_INTEGER);
$etst->bind_param(2,$transc_dbID,SQL_INTEGER);
$etst->bind_param(3,$rank,SQL_INTEGER);
$etst->execute();
$rank++;
}
$etst->finish();
#
# Store stable_id
#
if (defined($transcript->stable_id)) {
if (!defined($transcript->version)) {
throw("Trying to store incomplete stable id information for " .
"transcript");
}
my $statement =
"INSERT INTO transcript_stable_id ".
"SET transcript_id = ?, ".
" stable_id = ?, ".
"version = ?, ";
if( $transcript->created_date() ) {
$statement .= "created_date = from_unixtime( ".$transcript->created_date()."),";
} else {
$statement .= "created_date = \"0000-00-00 00:00:00\",";
}
if( $transcript->modified_date() ) {
$statement .= "modified_date = from_unixtime( ".$transcript->modified_date().")";
} else {
$statement .= "modified_date = \"0000-00-00 00:00:00\"";
}
my $sth = $self->prepare($statement);
$sth->bind_param(1,$transc_dbID,SQL_INTEGER);
$sth->bind_param(2,$transcript->stable_id,SQL_VARCHAR);
$sth->bind_param(3,$transcript->version,SQL_INTEGER);
$sth->execute();
$sth->finish();
}
#
# Store stable_id
#
if (defined($transcript->stable_id)) {
if (!defined($transcript->version)) {
throw("Trying to store incomplete stable id information for " .
"transcript");
}
my $statement =
"INSERT INTO transcript_stable_id ".
"SET transcript_id = ?, ".
" stable_id = ?, ".
"version = ?, ";
if( $transcript->created_date() ) {
$statement .= "created_date = from_unixtime( ".$transcript->created_date()."),";
} else {
$statement .= "created_date = \"0000-00-00 00:00:00\",";
}
if( $transcript->modified_date() ) {
$statement .= "modified_date = from_unixtime( ".$transcript->modified_date().")";
} else {
$statement .= "modified_date = \"0000-00-00 00:00:00\"";
}
my $sth = $self->prepare($statement);
$sth->bind_param(1,$transc_dbID,SQL_INTEGER);
$sth->bind_param(2,$transcript->stable_id,SQL_VARCHAR);
$sth->bind_param(3,$transcript->version,SQL_INTEGER);
$sth->execute();
$sth->finish();
}
# Now the supporting evidence
......@@ -752,18 +757,17 @@ sub store {
#update the original transcript object - not the transfered copy that
#we might have created
$original->dbID( $transc_dbID );
$original->adaptor( $self );
# store transcript attributes if there are any
my $attr_adaptor = $db->get_AttributeAdaptor();
$attr_adaptor->store_on_Transcript($transcript,
$transcript->get_all_Attributes);
#update the original transcript object - not the transfered copy that
#we might have created
$original->dbID( $transc_dbID );
$original->adaptor( $self );
# store transcript attributes if there are any
my $attr_adaptor = $db->get_AttributeAdaptor();
$attr_adaptor->store_on_Transcript($transcript,
$transcript->get_all_Attributes);
return $transc_dbID;
return $transc_dbID;
}
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment