diff --git a/modules/Bio/EnsEMBL/Map/DBSQL/DitagFeatureAdaptor.pm b/modules/Bio/EnsEMBL/Map/DBSQL/DitagFeatureAdaptor.pm
index fe832c96ddf5a08632529de49250057d6dee97ef..4dc83812366f972e053046e7530fe6a4135ef4dd 100644
--- a/modules/Bio/EnsEMBL/Map/DBSQL/DitagFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Map/DBSQL/DitagFeatureAdaptor.pm
@@ -170,6 +170,7 @@ sub fetch_all_by_type {
Example : $tags = $ditagfeature_adaptor->fetch_all_by_Slice($slice, "SME005");
Description: Retrieves ditagFeatures from the database overlapping a specific region
and (optional) of a specific ditag type or analysis.
+ Start & end locations are returned in slice coordinates, now.
Returntype : listref of Bio::EnsEMBL::Map::DitagFeatures
Caller : general
@@ -232,7 +233,7 @@ sub fetch_all_by_Slice {
WHERE ditag_feature_id IN(".$ids_to_fetch.")" );
$sth->execute();
- my $result = $self->_fetch($sth);
+ my $result = $self->_fetch($sth, $slice);
push(@result, @$result);
}
@@ -240,9 +241,77 @@ sub fetch_all_by_Slice {
}
+=head2 fetch_pairs_by_Slice
+
+ Arg [1] : Bio::EnsEMBL::Slice
+ Arg [2] : (optional) ditag type (specific library)
+ Arg [3] : (optional) analysis logic_name
+ Example : my $ditagfeatures = $dfa->fetch_pairs_by_Slice($slice);
+ foreach my $ditagfeature (@$ditagfeatures){
+ $minstart = $$ditagfeature2{'start'};
+ $maxend = $$ditagfeature2{'end'};
+ $bothstrand = $$ditagfeature2{'strand'};
+ $tag_count = $$ditagfeature2{'tag_count'};
+ print "$minstart, $maxend, $bothstrand, $tag_count\n";
+ }
+ Description: Retrieves ditagFeature information in pairs from the database overlapping a specific region
+ and (optional) of a specific ditag type or analysis. The absotute start and end points are
+ fetched.
+ Slices should be SMALL!
+ Returntype : array ref with hash ref of artifical DitagFeature object
+ Caller : general
+
+=cut
+
+sub fetch_pairs_by_Slice {
+ my ($self, $slice, $tagtype, $logic_name) = @_;
+ my ($tag_id, $pair_id, $seq_region_id, $start, $end, $strand, $analysis_id, $tag_count);
+ my @result;
+
+ my $sql = "SELECT df.ditag_id, df.ditag_pair_id, df.seq_region_id, MIN(df.seq_region_start), ".
+ "MAX(df.seq_region_end), df.seq_region_strand, df.analysis_id, d.tag_count ".
+ "FROM ditag_feature df, ditag d ".
+ "WHERE df.ditag_id=d.ditag_id ";
+ if($tagtype){
+ $sql .= "AND d.type = \"".$tagtype."\"";
+ }
+ $sql .= " AND df.seq_region_id = ".$slice->get_seq_region_id.
+ " AND df.seq_region_start <= ".$slice->end.
+ " AND df.seq_region_end >= ".$slice->start;
+ if($logic_name){
+ my $analysis = $self->db->get_AnalysisAdaptor->fetch_by_logic_name($logic_name);
+ if(!$analysis) {
+ return undef;
+ }
+ $sql .= " AND df.analysis_id = ".$analysis->dbID();
+ }
+ $sql .= " GROUP BY df.ditag_id, df.ditag_pair_id;";
+
+ my $sth = $self->prepare($sql);
+ $sth->execute();
+ $sth->bind_columns( \$tag_id, \$pair_id, \$seq_region_id, \$start, \$end, \$strand, \$analysis_id ,\$tag_count);
+ while ( $sth->fetch ) {
+ my %ditag_pair = (
+ ditag => $tag_id,
+ pair_id => $pair_id,
+ region => $seq_region_id,
+ start => $start,
+ end => $end,
+ strand => $strand,
+ analysis => $analysis_id,
+ tag_count => $tag_count
+ );
+ push(@result, \%ditag_pair);
+ }
+
+ return \@result;
+}
+
+
=head2 _fetch
Arg [1] : statement handler
+ Arg [2] : (optional) target-slice for the feature
Description: generic sql-fetch function for the DitagFeature fetch methods
Returntype : listref of Bio::EnsEMBL::Map::DitagFeatures
Caller : private
@@ -250,7 +319,7 @@ sub fetch_all_by_Slice {
=cut
sub _fetch {
- my ($self, $sth) = @_;
+ my ($self, $sth, $dest_slice) = @_;
my ( $tag_id, $mothertag_id, $seqreg, $seqstart, $seqend, $strand, $analysis_id, $hit_start,
$hit_end, $hit_strand, $cigar_line, $ditag_side, $ditag_pair_id );
@@ -260,13 +329,36 @@ sub _fetch {
\$hit_strand, \$cigar_line, \$ditag_side,
\$ditag_pair_id );
- my @ditags;
+ my @ditag_features;
+ my $dest_slice_start;
+ my $dest_slice_end;
+ my $dest_slice_strand;
+ if($dest_slice) {
+ $dest_slice_start = $dest_slice->start();
+ $dest_slice_end = $dest_slice->end();
+ $dest_slice_strand = $dest_slice->strand();
+ }
while ( $sth->fetch ) {
my $analysis_obj = $self->db->get_AnalysisAdaptor->fetch_by_dbID($analysis_id);
my $slice = $self->db->get_SliceAdaptor->fetch_by_seq_region_id($seqreg);
- push @ditags,
+ if($dest_slice) {
+ if($dest_slice_start != 1 || $dest_slice_strand != 1) {
+ if($dest_slice_strand == 1) {
+ $seqstart = $seqstart - $dest_slice_start + 1;
+ $seqend = $seqend - $dest_slice_start + 1;
+ } else {
+ my $tmp_seq_region_start = $seqstart;
+ $seqstart = $dest_slice_end - $seqend + 1;
+ $seqend = $dest_slice_end - $tmp_seq_region_start + 1;
+ $strand *= -1;
+ }
+ $slice = $dest_slice;
+ }
+ }
+
+ push @ditag_features,
Bio::EnsEMBL::Map::DitagFeature->new( -dbid => $tag_id,
-slice => $slice,
-start => $seqstart,
@@ -280,11 +372,12 @@ sub _fetch {
-cigar_line => $cigar_line,
-ditag_side => $ditag_side,
-ditag_pair_id => $ditag_pair_id,
+ -ditag => undef,
-adaptor => $self,
);
}
- return \@ditags;
+ return \@ditag_features;
}
diff --git a/modules/Bio/EnsEMBL/Map/DitagFeature.pm b/modules/Bio/EnsEMBL/Map/DitagFeature.pm
index 7f85fcc7a27ffe650c9aa6b8c306c232f3086309..cc0b4bbf9cf2f0762ad852aa5fe465b50fa255d5 100644
--- a/modules/Bio/EnsEMBL/Map/DitagFeature.pm
+++ b/modules/Bio/EnsEMBL/Map/DitagFeature.pm
@@ -67,6 +67,7 @@ use Bio::EnsEMBL::Utils::Argument qw( rearrange );
Arg [15] : (optional) int tag_count, only used for imported mappings where
identical positions where collapsed into into one feature.
Default: 1
+ Arg [16] : (optional) ditag object
Example : $ditag = Bio::EnsEMBL::Map::DitagFeature->new
(-dbID => 123, -adaptor => $adaptor, ...);
@@ -79,9 +80,9 @@ use Bio::EnsEMBL::Utils::Argument qw( rearrange );
sub new {
my ($caller, @args) = @_;
my ( $dbID, $adaptor, $start, $end, $strand, $slice, $analysis, $hit_start, $hit_end,
- $hit_strand, $ditag_id, $ditag_side, $cigar_line, $ditag_pair_id, $tag_count ) = rearrange(
- [ 'dbid', 'adaptor' ,'start', 'end', 'strand', 'slice', 'analysis', 'hit_start',
- 'hit_end', 'hit_strand', 'ditag_id', 'ditag_side', 'cigar_line', 'ditag_pair_id' ,'tag_count'],
+ $hit_strand, $ditag_id, $ditag_side, $cigar_line, $ditag_pair_id, $tag_count, $ditag ) =
+ rearrange( [ 'dbid', 'adaptor' ,'start', 'end', 'strand', 'slice', 'analysis', 'hit_start',
+ 'hit_end', 'hit_strand', 'ditag_id', 'ditag_side', 'cigar_line', 'ditag_pair_id' ,'tag_count', 'ditag'],
@args );
my $class = ref($caller) || $caller;
@@ -131,6 +132,7 @@ sub new {
'ditag_side' => $ditag_side,
'cigar_line' => $cigar_line,
'tag_count' => $tag_count,
+ 'ditag' => $ditag,
}, $class);
return $self;
@@ -139,21 +141,37 @@ sub new {
=head2 fetch_ditag
- Arg [1] : none
- Description: Get the ditag object of this DitagFeature
+ Description: Deprecated, use ditag() instead
+
+=cut
+
+sub fetch_ditag {
+ throw("Deprecated method, please use ditag() instead.\n")
+}
+
+
+=head2 ditag
+
+ Arg [1] : (optional) ditag object
+ Description: Get/Set the ditag object of this DitagFeature
Returntype : Bio::EnsEMBL::Map::Ditag
Exceptions : none
Caller : general
=cut
-sub fetch_ditag {
+sub ditag {
my $self = shift;
- my $ditag_adaptor = $self->adaptor->db->get_DitagAdaptor;
- my $ditag = $ditag_adaptor->fetch_by_dbID($self->ditag_id);
+ if(@_) {
+ $self->{'ditag'} = shift;
+ } elsif(!$self->{'ditag'} && $self->{'adaptor'} && $self->{'ditag_id'}) {
+ #lazy load the ditag
+ my $ditag_adaptor = $self->adaptor->db->get_DitagAdaptor;
+ $self->{'ditag'} = $ditag_adaptor->fetch_by_dbID($self->ditag_id);
+ }
- return $ditag;
+ return $self->{'ditag'};
}