From d755a1b3b6ace5be649a2455dcc456417a390784 Mon Sep 17 00:00:00 2001
From: Will Spooner <whs@sanger.ac.uk>
Date: Fri, 9 Feb 2007 17:22:11 +0000
Subject: [PATCH] Added store_mapping_path method to add assembly.mapping
entries to the meta table
---
.../Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm | 103 +++++++++++++++++-
1 file changed, 101 insertions(+), 2 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
index c0d9d1cb01..c2c5c19323 100644
--- a/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm
@@ -183,13 +183,19 @@ sub new {
}
$sth->finish();
+ $self->_cache_mapping_paths;
+ return $self;
+}
+
+sub _cache_mapping_paths{
#
# Retrieve a list of available mappings from the meta table.
# this may eventually be moved a table of its own if this proves too
# cumbersome
#
+ my $self = shift;
my %mapping_paths;
my $mc = $self->db()->get_MetaContainer();
@@ -252,11 +258,10 @@ sub new {
$self->{'_mapping_paths'} = \%mapping_paths;
- return $self;
+ return 1;
}
-
=head2 fetch_all
Arg [1] : none
@@ -666,6 +671,100 @@ sub get_mapping_path {
return $path || [];
}
+=head2 store_mapping_path
+
+ Arg [1] : Bio::EnsEMBL::CoordSystem $cs1
+ Arg [2] : Bio::EnsEMBL::CoordSystem $cs2
+ Arg [3..n] : Bio::EnsEMBL::CoordSystems $cs3..$csN
+ Example : my $pathref = $csa->store_mapping_path($cs1,$cs2);
+ Description: Given two or more coordinate systems this will store
+ mapping paths between them in the database.
+
+ The 'rank' attrib of the CoordSystems is used to
+ determine the assembled/component relationships between
+ them.
+
+ For example, if $cs1 represents chrs of version
+ V1, $cs2 represents contigs, and $cs3 clones then, unless
+ they already exist, the following entries will be created
+ in the meta table;
+ +------------------+---------------------+
+ | meta_key | meta_value |
+ +------------------+---------------------+
+ | assembly.mapping | chr:V1|clone |
+ | assembly.mapping | clone|contig |
+ | assembly.mapping | chr:V1|clone|contig |
+ +------------------+---------------------+
+
+
+ For a one-step mapping path to be valid there needs to be
+ a relationship between the two coordinate systems defined in
+ the assembly table. Two step mapping paths work by building
+ on the one-step mapping paths which are already defined.
+
+ The first coordinate system in a one step mapping path must
+ be the assembled coordinate system and the second must be
+ the component.
+
+ Returntype : reference to a list of lists of new meta_value mapping strings
+ created for assembly.mapping
+ Exceptions : CoordSystems with no rank/duplicated rank
+ Caller : general
+ Status : Experimental
+
+=cut
+
+sub store_mapping_path{
+ my $self = shift;
+ my @csystems = @_;
+
+ # Validate and sort the args
+ my %seen_ranks;
+ @csystems >= 2 or throw('Need two or more CoordSystems');
+ my $validate = sub{
+ ref($_[0]) && $_[0]->isa('Bio::EnsEMBL::CoordSystem') or
+ throw('CoordSystem argument expected.');
+ my $rank = $_[0]->rank ||
+ throw('CoordSystem has no rank: '.$_[0]->name);
+ $seen_ranks{$rank} &&
+ throw('CoordSystem '.$_[0]->name." shares rank $rank with ".
+ $seen_ranks{$rank}->name);
+ $seen_ranks{$rank} = $_[0];
+ };
+ @csystems = sort{$a->rank <=> $b->rank} map{&{$validate}($_)} @csystems;
+
+ # Get a list of all existing assembly.mappings
+ #my %mappings = map{$_=>1} @{$meta->list_value_by_key('assembly.mapping')};
+
+ # For each pair in the sorted list, store in the DB
+ my $meta = $self->db->get_MetaContainer;
+ my @retlist;
+ for( my $i=1; $i<@csystems; $i++ ){
+ for( my $j=0; $j<(@csystems-$i); $j++ ){
+ my $mapping = join( "|",
+ map{join( ':', $_->name, ($_->version||()) )}
+ @csystems[$j..$j+$i] );
+ my $mapping_key = join( "|",
+ map{join( ':', $_->name, ($_->version||'') )}
+ @csystems[$j..$j+$i] );
+ # Skip existing
+ next if $self->{'_mapping_paths'}->{$mapping_key};
+
+ # Update the database
+ $meta->store_key_value('assembly.mapping',$mapping);
+ push @retlist, $mapping;
+ }
+ }
+
+ if( @retlist ){
+ # Update mapping path cache
+ $self->_cache_mapping_paths;
+ }
+
+ # Return the mappings that we have just created
+ return [@retlist];
+}
+
sub _fetch_by_attrib {
my $self = shift;
--
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