diff --git a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
index c6beb2eb1ae28efccafed7e547537f11896021c3..feff0405b4c55b491a576cb3ae6ab011cc95d68d 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
@@ -99,7 +99,7 @@ sub new {
'toplevel'.
Arg [2] : string $seq_region_name
The name of the sequence region that the slice will be
- created on
+ created on.
Arg [3] : int $start (optional, default = 1)
The start of the slice on the sequence region
Arg [4] : int $end (optional, default = seq_region length)
@@ -108,10 +108,25 @@ sub new {
The orientation of the slice on the sequence region
Arg [6] : string $version (optional, default = default version)
The version of the coordinate system to use (e.g. NCBI33)
- Example : $slice = $slice_adaptor->fetch_by_region('chromosome');
- Description: Creates a slice object on the given chromosome and coordinates.
- Returntype : Bio::EnsEMBL::Slice
- Exceptions : none
+ Example : $slice = $slice_adaptor->fetch_by_region('chromosome', 'X');
+ $slice = $slice_adaptor->fetch_by_region('clone', 'AC008066.4');
+ Description: Retrieves a slice on the requested region. At a minimum the
+ name of the coordinate system and the name of the seq_region to
+ fetch must be provided.
+
+ Some fuzzy matching is performed if no exact match for
+ the provided name is found. This allows clones to be
+ fetched even when their version is not known. For
+ example fetch_by_region('clone', 'AC008066') will
+ retrieve the sequence_region with name 'AC008066.4'.
+
+ If the requested seq_region is not found in the database undef
+ is returned.
+
+ Returntype : Bio::EnsEMBL::Slice or undef
+ Exceptions : throw if no seq_region_name is provided
+ throw if invalid coord_system_name is provided
+ throw if start > end is provided
Caller : general
=cut
@@ -120,7 +135,10 @@ sub fetch_by_region {
my ($self, $coord_system_name, $seq_region_name,
$start, $end, $strand, $version) = @_;
- throw('seq_region_name argument is required') if(!$seq_region_name);
+ $start = 1 if(!defined($start));
+ $strand = 1 if(!defined($strand));
+
+ throw('seq_region_name argument is required') if(!defined($seq_region_name));
my $csa = $self->db()->get_CoordSystemAdaptor();
my $coord_system = $csa->fetch_by_name($coord_system_name,$version);
@@ -143,29 +161,63 @@ sub fetch_by_region {
#force seq_region_name cast to string so mysql cannot treat as int
$sth->execute("$seq_region_name", $coord_system->dbID());
- if($sth->rows() != 1) {
- $version ||= '';
- $seq_region_name ||= '';
- $coord_system_name ||= '';
- throw("Cannot create slice on non-existant or ambigous seq_region:\n" .
- " coord_system=[$coord_system_name],\n" .
- " name=[$seq_region_name],\n" .
- " version=[$version]");
- }
+ if($sth->rows() == 0) {
+ $sth->finish();
- my $id;
- ($id, $length) = $sth->fetchrow_array();
- $sth->finish();
+ #do fuzzy matching, assuming that we are just missing a version on
+ #the end of the seq_region name
+
+ $sth = $self->prepare("SELECT name, seq_region_id, length " .
+ "FROM seq_region " .
+ "WHERE name LIKE ?" .
+ "AND coord_system_id = ?");
+
+ $sth->execute("$seq_region_name.%", $coord_system->dbID());
+
+ my $prefix_len = length($seq_region_name) + 1;
+ my $highest_version = undef;
+
+ # find the fuzzy-matched seq_region with the highest postfix (which ought
+ # to be a version)
+
+ my ($tmp_name, $id, $tmp_length);
+
+ while(($tmp_name, $id, $tmp_length) = $sth->fetchrow_array()) {
+ $key = lc(join(':',$tmp_name,
+ $coord_system->name(),
+ $coord_system->version));
+ $name_cache->{$key} = [$id,$tmp_length];
+ $self->{'_id_cache'}->{$id} = [$tmp_name,$tmp_length,$coord_system];
+
+ my $version = substr($tmp_name, $prefix_len);
+
+ #skip versions which are non-numeric and apparently not versions
+ next if($version !~ /^\d+$/);
+
+ if(!defined($highest_version) || ($version <=> $highest_version) > 0) {
+ $seq_region_name = $tmp_name;
+ $length = $tmp_length;
+ $highest_version = $version;
+ }
+ }
+ $sth->finish();
+
+ #return if we did not find any appropriate match:
+ return undef if(!defined($highest_version));
+ } else {
- #cache results to speed up future queries
- $name_cache->{$key} = [$id,$length];
- $self->{'_id_cache'}->{$id} = [$seq_region_name, $length, $coord_system];
+ my $id;
+ ($id, $length) = $sth->fetchrow_array();
+ $sth->finish();
+
+ #cache results to speed up future queries
+ $name_cache->{$key} = [$id,$length];
+ $self->{'_id_cache'}->{$id} = [$seq_region_name, $length, $coord_system];
+ }
}
- $start = 1 if(!defined($start));
- $strand = 1 if(!defined($strand));
$end = $length if(!defined($end));
-
+
if($end < $start) {
throw('start [$start] must be less than or equal to end [$end]');
}
@@ -193,7 +245,11 @@ sub fetch_by_region {
pass a slice over a network.
Slice::name allows you to serialise/marshall a slice and this
method allows you to deserialise/unmarshal it.
- Returntype : Bio::EnsEMBL::Slice
+
+ Returns undef if no seq_region with the provided name exists in
+ the database.
+
+ Returntype : Bio::EnsEMBL::Slice or undef
Exceptions : throw if incorrent arg provided
Caller : Pipeline
@@ -218,7 +274,7 @@ sub fetch_by_name {
return $self->fetch_by_region($cs_name,$seq_region, $start,
- $end, $strand, $cs_version);
+ $end, $strand, $cs_version);
}
@@ -231,7 +287,8 @@ sub fetch_by_name {
Example : $slice = $slice_adaptor->fetch_by_seq_region_id(34413);
Description: Creates a slice object of an entire seq_region using the
seq_region internal identifier to resolve the seq_region.
- Returntype : Bio::EnsEMBL::Slice
+ Returns undef if no such slice exists.
+ Returntype : Bio::EnsEMBL::Slice or undef
Exceptions : none
Caller : general
@@ -253,10 +310,7 @@ sub fetch_by_seq_region_id {
$sth->execute($seq_region_id);
- if($sth->rows() != 1) {
- throw("Cannot create slice on non-existant or ambigous seq_region:" .
- " seq_region_id=[$seq_region_id],\n");
- }
+ return undef if($sth->rows() == 0);
my $cs_id;
($name, $length, $cs_id) = $sth->fetchrow_array();