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Commit d43a18d0 authored by Felix Kokocinski's avatar Felix Kokocinski
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ditag code changes for havana

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modules/Bio/EnsEMBL/Map/DBSQL/DitagFeatureAdaptor.pm
+ 98
− 5
View file @ d43a18d0
......@@ -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;
}
......
modules/Bio/EnsEMBL/Map/DitagFeature.pm
+ 27
− 9
View file @ d43a18d0
......@@ -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'};
}
......
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