From 5b4a40539785c721defc3fda1c727b1c79e9617c Mon Sep 17 00:00:00 2001
From: Ewan Birney <birney@sanger.ac.uk>
Date: Wed, 17 Oct 2001 13:57:41 +0000
Subject: [PATCH] updates to Mapper. Now looks more sensible wrt API. Works for
alignment mapping at least
---
modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm | 4 +++-
modules/Bio/EnsEMBL/Mapper.pm | 10 +++++++++-
modules/t/mapper.t | 2 +-
3 files changed, 13 insertions(+), 3 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
index d3b0e0d40e..aaf6859f88 100644
--- a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
@@ -194,6 +194,7 @@ sub fetch_by_dbID {
return $gene;
}
+
=head2 fetch_by_stable_id
Title : fetch_by_stable_id
@@ -244,12 +245,13 @@ sub fetch_by_contig_list{
$str =~ s/\,$//g;
$str = "($str)";
+
#
# this is non-optimised, because we are going to make multiple
# trips to the database. should fix here
#
- my $sth = $self->prepare("select distinct(t.gene_id) from transcript t,exon_transcript et,exon e,contig c where c.id in $str and c.internal_id = e.contig and et.exon_id = e.exon_id and et.transcript_id = t.transcript_id");
+ my $sth = $self->prepare("select distinct(t.gene_id) from transcript t,exon_transcript et,exon e,contig c where c.id in $str and c.internal_id = e.contig_id and et.exon_id = e.exon_id and et.transcript_id = t.transcript_id");
$sth->execute;
my @out;
diff --git a/modules/Bio/EnsEMBL/Mapper.pm b/modules/Bio/EnsEMBL/Mapper.pm
index d845a9d42f..d5940d94f5 100644
--- a/modules/Bio/EnsEMBL/Mapper.pm
+++ b/modules/Bio/EnsEMBL/Mapper.pm
@@ -67,11 +67,15 @@ use Bio::EnsEMBL::Mapper::Gap;
sub new {
my($class,@args) = @_;
- my $to = shift @args;
my $from = shift @args;
+ my $to = shift @args;
my $self = {};
bless $self,$class;
+
+ if( !defined $to ) {
+ $self->throw("Must supply from and to tags");
+ }
$self->{'_pair_hash_to'} = {};
$self->{'_pair_hash_from'} = {};
@@ -239,6 +243,10 @@ sub map_coordinates{
sub add_map_coordinates{
my ($self,$contig_start,$contig_end,$contig_id,$chr_start,$chr_end,$chr_name,$contig_ori) = @_;
+ if( !defined $contig_ori ) {
+ $self->throw("Need 7 arguments!");
+ }
+
if( $contig_start !~ /\d+/ || $chr_start !~ /\d+/ ) {
$self->throw("Not doable - $contig_start as start or $chr_start as start?");
}
diff --git a/modules/t/mapper.t b/modules/t/mapper.t
index 5ee3bb02bf..df95e28f62 100644
--- a/modules/t/mapper.t
+++ b/modules/t/mapper.t
@@ -35,7 +35,7 @@ use Bio::EnsEMBL::Mapper;
# testing the Bio::EnsEMBL::Mapper module
-$mapper = Bio::EnsEMBL::Mapper->new( "virtualcontig", "rawcontig" );
+$mapper = Bio::EnsEMBL::Mapper->new( "rawcontig", "virtualcontig" );
load_sgp_dump( $mapper );
$mapper->_freeze;
--
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