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Commit 75b70e78 authored by Kevin Howe's avatar Kevin Howe
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On storage of supporting features, check that the feature isn't already 

present, and reuse it if it is.
parent 532fe594
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modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
+ 2
− 33
View file @ 75b70e78
......@@ -299,39 +299,8 @@ sub store {
}
# Now the supporting evidence
# should be stored from featureAdaptor
my $sql = "insert into supporting_feature (exon_id, feature_id, feature_type)
values(?, ?, ?)";
my $sf_sth = $self->prepare($sql);
my $anaAdaptor = $self->db->get_AnalysisAdaptor();
my $dna_adaptor = $self->db->get_DnaAlignFeatureAdaptor();
my $pep_adaptor = $self->db->get_ProteinAlignFeatureAdaptor();
my $type;
foreach my $sf (@{$exon->get_all_supporting_features}) {
if(!$sf->isa("Bio::EnsEMBL::BaseAlignFeature")){
throw("$sf must be an align feature otherwise" .
"it can't be stored");
}
if($sf->isa("Bio::EnsEMBL::DnaDnaAlignFeature")){
$dna_adaptor->store($sf);
$type = 'dna_align_feature';
}elsif($sf->isa("Bio::EnsEMBL::DnaPepAlignFeature")){
$pep_adaptor->store($sf);
$type = 'protein_align_feature';
} else {
warning("Supporting feature of unknown type. Skipping : [$sf]\n");
next;
}
$sf_sth->bind_param(1, $exonId, SQL_INTEGER);
$sf_sth->bind_param(2, $sf->dbID, SQL_INTEGER);
$sf_sth->bind_param(3, $type, SQL_VARCHAR);
$sf_sth->execute();
}
my $esf_adaptor = $db->get_SupportingFeatureAdaptor;
$esf_adaptor->store($exonId, $exon->get_all_supporting_features);
#
# Finally, update the dbID and adaptor of the exon (and any component exons)
......
modules/Bio/EnsEMBL/DBSQL/SupportingFeatureAdaptor.pm
+ 141
− 0
View file @ 75b70e78
......@@ -95,5 +95,146 @@ sub fetch_all_by_Exon {
return $out;
}
=head2 store
Arg [2] : Int $transID
The dbID of an EnsEMBL transcript to associate with supporting
features
Arg [1] : Ref to array of Bio::EnsEMBL::BaseAlignFeature (the support)
Example : $sfa->store($exon_id, \@features);
Description: Stores a set of alignment features and associates an EnsEMBL transcript
with them
Returntype : none
Exceptions : thrown when invalid dbID is passed to this method
Caller : TranscriptAdaptor
Status : Stable
=cut
sub store {
my ( $self, $exon_dbID, $aln_objs ) = @_;
my $pep_check_sql =
"SELECT protein_align_feature_id " .
"FROM protein_align_feature " .
"WHERE seq_region_id = ? " .
"AND seq_region_start = ? " .
"AND seq_region_end = ? " .
"AND seq_region_strand = ? " .
"AND hit_name = ? " .
"AND hit_start = ? " .
"AND hit_end = ? " .
"AND analysis_id = ? " .
"AND cigar_line = ? ";
my $dna_check_sql =
"SELECT dna_align_feature_id " .
"FROM dna_align_feature " .
"WHERE seq_region_id = ? " .
"AND seq_region_start = ? " .
"AND seq_region_end = ? " .
"AND seq_region_strand = ? " .
"AND hit_name = ? " .
"AND hit_start = ? " .
"AND hit_end = ? " .
"AND analysis_id = ? " .
"AND cigar_line = ? " .
"AND hit_strand = ? ";
my $assoc_check_sql =
"SELECT * " .
"FROM supporting_feature " .
"WHERE exon_id = $exon_dbID " .
"AND feature_type = ? " .
"AND feature_id = ? ";
my $assoc_write_sql = "INSERT into supporting_feature " .
"(exon_id, feature_id, feature_type) " .
"values(?, ?, ?)";
my $pep_check_sth = $self->prepare($pep_check_sql);
my $dna_check_sth = $self->prepare($dna_check_sql);
my $assoc_check_sth = $self->prepare($assoc_check_sql);
my $sf_sth = $self->prepare($assoc_write_sql);
my $dna_adaptor = $self->db->get_DnaAlignFeatureAdaptor();
my $pep_adaptor = $self->db->get_ProteinAlignFeatureAdaptor();
foreach my $f (@$aln_objs) {
# check that the feature is in toplevel coords
if($f->slice->start != 1 || $f->slice->strand != 1) {
#move feature onto a slice of the entire seq_region
my $tls = $self->db->get_sliceAdaptor->fetch_by_region($f->slice->coord_system->name(),
$f->slice->seq_region_name(),
undef, #start
undef, #end
undef, #strand
$f->slice->coord_system->version());
$f = $f->transfer($tls);
if(!$f) {
throw('Could not transfer Feature to slice of ' .
'entire seq_region prior to storing');
}
}
if(!$f->isa("Bio::EnsEMBL::BaseAlignFeature")){
throw("$f must be an align feature otherwise" .
"it can't be stored");
}
my ($sf_dbID, $type, $adap, $check_sth);
my @check_args = ($self->db->get_SliceAdaptor->get_seq_region_id($f->slice),
$f->start,
$f->end,
$f->strand,
$f->hseqname,
$f->hstart,
$f->hend,
$f->analysis->dbID,
$f->cigar_string);
if($f->isa("Bio::EnsEMBL::DnaDnaAlignFeature")){
$adap = $dna_adaptor;
$check_sth = $dna_check_sth;
$type = 'dna_align_feature';
push @check_args, $f->hstrand;
} elsif($f->isa("Bio::EnsEMBL::DnaPepAlignFeature")){
$adap = $pep_adaptor;
$check_sth = $pep_check_sth;
$type = 'protein_align_feature';
} else {
warning("Supporting feature of unknown type. Skipping : [$f]\n");
next;
}
$check_sth->execute(@check_args);
$sf_dbID = $check_sth->fetchrow_array;
if (not $sf_dbID) {
$adap->store($f);
$sf_dbID = $f->dbID;
}
# now check association
$assoc_check_sth->execute($type,
$sf_dbID);
if (not $assoc_check_sth->fetchrow_array) {
$sf_sth->bind_param(1, $exon_dbID, SQL_INTEGER);
$sf_sth->bind_param(2, $sf_dbID, SQL_INTEGER);
$sf_sth->bind_param(3, $type, SQL_VARCHAR);
$sf_sth->execute();
}
}
$dna_check_sth->finish;
$pep_check_sth->finish;
$assoc_check_sth->finish;
$sf_sth->finish;
}
1;
modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
+ 2
− 34
View file @ 75b70e78
......@@ -766,40 +766,8 @@ sub store {
}
# Now the supporting evidence
# should be stored from featureAdaptor
my $sql = "insert into transcript_supporting_feature
(transcript_id, feature_id, feature_type)
values(?, ?, ?)";
my $sf_sth = $self->prepare($sql);
my $anaAdaptor = $self->db->get_AnalysisAdaptor();
my $dna_adaptor = $self->db->get_DnaAlignFeatureAdaptor();
my $pep_adaptor = $self->db->get_ProteinAlignFeatureAdaptor();
my $type;
foreach my $sf (@{$transcript->get_all_supporting_features}) {
if(!$sf->isa("Bio::EnsEMBL::BaseAlignFeature")){
throw("$sf must be an align feature otherwise" .
"it can't be stored");
}
if($sf->isa("Bio::EnsEMBL::DnaDnaAlignFeature")){
$dna_adaptor->store($sf);
$type = 'dna_align_feature';
}elsif($sf->isa("Bio::EnsEMBL::DnaPepAlignFeature")){
$pep_adaptor->store($sf);
$type = 'protein_align_feature';
} else {
warning("Supporting feature of unknown type. Skipping : [$sf]\n");
next;
}
$sf_sth->bind_param(1, $transc_dbID, SQL_INTEGER);
$sf_sth->bind_param(2, $sf->dbID, SQL_INTEGER);
$sf_sth->bind_param(3, $type, SQL_VARCHAR);
$sf_sth->execute();
}
my $tsf_adaptor = $db->get_TranscriptSupportingFeatureAdaptor;
$tsf_adaptor->store($transc_dbID, $transcript->get_all_supporting_features);
# store transcript attributes if there are any
my $attr_adaptor = $db->get_AttributeAdaptor();
......
modules/Bio/EnsEMBL/DBSQL/TranscriptSupportingFeatureAdaptor.pm
+ 142
− 0
View file @ 75b70e78
......@@ -96,5 +96,147 @@ sub fetch_all_by_Transcript {
return $out;
}
=head2 store
Arg [2] : Int $transID
The dbID of an EnsEMBL transcript to associate with supporting
features
Arg [1] : Ref to array of Bio::EnsEMBL::BaseAlignFeature (the support)
Example : $dbea->store($transcript_id, \@features);
Description: Stores a set of alignment features and associates an EnsEMBL transcript
with them
Returntype : none
Exceptions : thrown when invalid dbID is passed to this method
Caller : TranscriptAdaptor
Status : Stable
=cut
sub store {
my ( $self, $tran_dbID, $aln_objs ) = @_;
my $pep_check_sql =
"SELECT protein_align_feature_id " .
"FROM protein_align_feature " .
"WHERE seq_region_id = ? " .
"AND seq_region_start = ? " .
"AND seq_region_end = ? " .
"AND seq_region_strand = ? " .
"AND hit_name = ? " .
"AND hit_start = ? " .
"AND hit_end = ? " .
"AND analysis_id = ? " .
"AND cigar_line = ? ";
my $dna_check_sql =
"SELECT dna_align_feature_id " .
"FROM dna_align_feature " .
"WHERE seq_region_id = ? " .
"AND seq_region_start = ? " .
"AND seq_region_end = ? " .
"AND seq_region_strand = ? " .
"AND hit_name = ? " .
"AND hit_start = ? " .
"AND hit_end = ? " .
"AND analysis_id = ? " .
"AND cigar_line = ? " .
"AND hit_strand = ? ";
my $assoc_check_sql =
"SELECT * " .
"FROM transcript_supporting_feature " .
"WHERE transcript_id = $tran_dbID " .
"AND feature_type = ? " .
"AND feature_id = ? ";
my $assoc_write_sql = "INSERT into transcript_supporting_feature " .
"(transcript_id, feature_id, feature_type) " .
"values(?, ?, ?)";
my $pep_check_sth = $self->prepare($pep_check_sql);
my $dna_check_sth = $self->prepare($dna_check_sql);
my $assoc_check_sth = $self->prepare($assoc_check_sql);
my $sf_sth = $self->prepare($assoc_write_sql);
my $dna_adaptor = $self->db->get_DnaAlignFeatureAdaptor();
my $pep_adaptor = $self->db->get_ProteinAlignFeatureAdaptor();
foreach my $f (@$aln_objs) {
# check that the feature is in toplevel coords
if($f->slice->start != 1 || $f->slice->strand != 1) {
#move feature onto a slice of the entire seq_region
my $tls = $self->db->get_sliceAdaptor->fetch_by_region($f->slice->coord_system->name(),
$f->slice->seq_region_name(),
undef, #start
undef, #end
undef, #strand
$f->slice->coord_system->version());
$f = $f->transfer($tls);
if(!$f) {
throw('Could not transfer Feature to slice of ' .
'entire seq_region prior to storing');
}
}
if(!$f->isa("Bio::EnsEMBL::BaseAlignFeature")){
throw("$f must be an align feature otherwise" .
"it can't be stored");
}
my ($sf_dbID, $type, $adap, $check_sth);
my @check_args = ($self->db->get_SliceAdaptor->get_seq_region_id($f->slice),
$f->start,
$f->end,
$f->strand,
$f->hseqname,
$f->hstart,
$f->hend,
$f->analysis->dbID,
$f->cigar_string);
if($f->isa("Bio::EnsEMBL::DnaDnaAlignFeature")){
$adap = $dna_adaptor;
$check_sth = $dna_check_sth;
$type = 'dna_align_feature';
push @check_args, $f->hstrand;
} elsif($f->isa("Bio::EnsEMBL::DnaPepAlignFeature")){
$adap = $pep_adaptor;
$check_sth = $pep_check_sth;
$type = 'protein_align_feature';
} else {
warning("Supporting feature of unknown type. Skipping : [$f]\n");
next;
}
$check_sth->execute(@check_args);
$sf_dbID = $check_sth->fetchrow_array;
if (not $sf_dbID) {
$adap->store($f);
$sf_dbID = $f->dbID;
}
# now check association
$assoc_check_sth->execute($type,
$sf_dbID);
if (not $assoc_check_sth->fetchrow_array) {
$sf_sth->bind_param(1, $tran_dbID, SQL_INTEGER);
$sf_sth->bind_param(2, $sf_dbID, SQL_INTEGER);
$sf_sth->bind_param(3, $type, SQL_VARCHAR);
$sf_sth->execute();
}
}
$dna_check_sth->finish;
$pep_check_sth->finish;
$assoc_check_sth->finish;
$sf_sth->finish;
}
1;
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