Commit 040a03e9 authored by Andy Yates's avatar Andy Yates
Browse files

Explaining that the fetch_by_X_id methods will return a slice on the forward strand

parent 00eedb68
......@@ -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
......
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