Commit 47ff4b54 authored by Graham McVicker's avatar Graham McVicker
Browse files

perform fuzzy matching of seq_region versions if no exact matching seq_region is found

parent 6b51d267
......@@ -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();
......
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