diff --git a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm index 1809db206850dda667aa1e71f194217be58b0c6e..a9af3fbb7bf4577c2c73f050d05366e5f5a75692 100644 --- a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm +++ b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm @@ -1222,8 +1222,10 @@ sub fetch_by_chr_band { Example : $slc = $sa->fetch_by_exon_stable_id('ENSE00000302930',10); Description: Creates a slice around the region of the specified exon. If a context size is given, the slice is extended by that - number of basepairs on either side of the - transcript. + number of basepairs on either side of the exon. + + The slice will be created in the exon's native coordinate system + and in the forward orientation. Returntype : Bio::EnsEMBL::Slice Exceptions : Thrown if the exon is not in the database. Caller : general @@ -1257,6 +1259,9 @@ sub fetch_by_exon_stable_id{ If a context size is given, the slice is extended by that number of basepairs on either side of the transcript. + + The slice will be created in the transcript's native coordinate + system and in the forward orientation. Returntype : Bio::EnsEMBL::Slice Exceptions : Thrown if the transcript is not in the database. Caller : general @@ -1292,6 +1297,9 @@ sub fetch_by_transcript_stable_id{ If a context size is given, the slice is extended by that number of basepairs on either side of the transcript. + + The slice will be created in the transcript's native coordinate + system and in the forward orientation. Returntype : Bio::EnsEMBL::Slice Exceptions : throw on incorrect args throw if transcript is not in database @@ -1327,7 +1335,9 @@ sub fetch_by_transcript_id { Description: Creates a slice around the region of the specified gene. If a context size is given, the slice is extended by that number of basepairs on either side of the gene. - The slice will be created in the genes native coordinate system. + + The slice will be created in the gene's native coordinate system + and in the forward orientation. Returntype : Bio::EnsEMBL::Slice Exceptions : throw on incorrect args throw if transcript does not exist