From 1ade13b08bab35fd7297605638a5d3785854d258 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Tue, 23 Oct 2007 11:32:52 +0000
Subject: [PATCH] Added another argument to fetch_by_region():
Arg [7] : boolean $no_fuzz
If true, do not use "fuzzy matching" (see below).
This was done to allow the user to by-pass the fuzzy matching code.
This will allow for some speed increases and to remove any ambiguity
around the results from this method.
Also inserted clarifying comment about stickleback DB ('groups' vs.
'chromosomes') from Anne.
---
modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm | 19 +++++++++++++++++--
1 file changed, 17 insertions(+), 2 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
index 202a313dd4..eb93cc412a 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
@@ -135,6 +135,8 @@ 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)
+ Arg [7] : boolean $no_fuzz
+ If true, do not use "fuzzy matching" (see below).
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
@@ -156,6 +158,9 @@ sub new {
example fetch_by_region('clone', 'AC008066') will
retrieve the sequence_region with name 'AC008066.4'.
+ The fuzzy matching can be turned off by setting the
+ $no_fuzz argument to a true value.
+
If the requested seq_region is not found in the database undef
is returned.
@@ -173,8 +178,9 @@ sub new {
# ARNE: This subroutine needs simplification!!
#
sub fetch_by_region {
- my ($self, $coord_system_name, $seq_region_name,
- $start, $end, $strand, $version) = @_;
+ my ( $self, $coord_system_name, $seq_region_name, $start, $end,
+ $strand, $version, $no_fuzz )
+ = @_;
$start = 1 if (!defined($start));
$strand = 1 if (!defined($strand));
@@ -188,6 +194,13 @@ sub fetch_by_region {
$cs = $csa->fetch_by_name($coord_system_name,$version);
## REMOVE THESE THREE LINES WHEN STICKLEBACK DB IS FIXED!
+ ## Anne/ap5 (2007-10-09):
+ # The problem was that the stickleback genebuild called the
+ # chromosomes 'groups', which meant they weren't being picked out by
+ # the karyotype drawing code. Apparently they are usually called
+ # 'groups' in the stickleback community, even though they really are
+ # chromosomes!
+
if( !$cs && $coord_system_name eq 'chromosome' ) {
$cs = $csa->fetch_by_name('group',$version);
}
@@ -255,6 +268,8 @@ sub fetch_by_region {
if ($sth->rows() == 0) {
$sth->finish();
+ if ($no_fuzz) { return undef }
+
# do fuzzy matching, assuming that we are just missing a version on
# the end of the seq_region name
--
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