diff --git a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm index 3a064390b326d2cd0d8e160f440f74bf787f2907..fb8c5d99746134b60304d176e07d9037552e6438 100644 --- a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm +++ b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm @@ -516,13 +516,12 @@ sub fetch_by_toplevel_location { If we are unsuccessful at retriving a location retry taking any possible chr prefix into account e.g. chrX and X are treated as equivalents - Example : my $slice = $sa->fetch_by_toplevel_location('X:1-10000') - my $slice = $sa->fetch_by_toplevel_location('X:1-10000:-1') + Example : my $slice = $sa->fetch_by_location('X:1-10000','chromosome') + my $slice = $sa->fetch_by_location('X:1-10000:-1','toplevel') Description : Converts an Ensembl location/region into the sequence region name, start and end and passes them onto C<fetch_by_region()>. - The code assumes that the required slice is on the top level - coordinate system. The code assumes that location formatting - is not perfect and will perform basic cleanup before parsing. + The code assumes that location formatting is not perfect and + will perform basic cleanup before parsing. Returntype : Bio::EnsEMBL::Slice Exceptions : If $location or coordinate system is false otherwise see C<fetch_by_region()>