From 040a03e92760b65567f29355045a377f04d72acd Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Fri, 23 Mar 2012 11:13:52 +0000
Subject: [PATCH] Explaining that the fetch_by_X_id methods will return a slice
on the forward strand
---
modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm | 16 +++++++++++++---
1 file changed, 13 insertions(+), 3 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
index 1809db2068..a9af3fbb7b 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
--
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