From 4312cdc1025633cf533857a594e9bb344d81cfab Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Fri, 12 Nov 2010 09:54:09 +0000
Subject: [PATCH] Allow multiple assembly exceptions and store synonyms of
slice (seq region synonym) if they exist
---
modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm | 82 +++++++++++++++++------
1 file changed, 63 insertions(+), 19 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
index 98bd045b33..3ce885ff4c 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
@@ -290,6 +290,20 @@ sub fetch_by_region {
if ( $sth->rows() == 0 ) {
$sth->finish();
+
+ # try synonyms
+ my $syn_sql_sth = $self->prepare("select s.name from seq_region s, seq_region_synonym ss where s.seq_region_id = ss.seq_region_id and ss.synonym = ?");
+ $syn_sql_sth->bind_param(1, $seq_region_name, SQL_VARCHAR);
+ $syn_sql_sth->execute();
+ my $new_name;
+ $syn_sql_sth->bind_columns( \$new_name);
+ if($syn_sql_sth->fetch){
+ $syn_sql_sth->finish;
+ return $self->fetch_by_region($coord_system_name, $new_name, $start, $end, $strand, $version, $no_fuzz);
+ }
+ $syn_sql_sth->finish;
+
+
if ($no_fuzz) { return undef }
# Do fuzzy matching, assuming that we are just missing a version
@@ -1374,40 +1388,62 @@ sub fetch_normalized_slice_projection {
}
my @syms;
- if( @haps > 1 ) {
+ if( @haps >= 1 ) {
my @sort_haps = sort { $a->[1] <=> $b->[1] } @haps;
- throw( "More than one HAP region not supported yet" );
- } elsif( @haps == 1 ) {
- my $hap = $haps[0];
- my $seq_reg_slice = $self->fetch_by_seq_region_id($slice_seq_region_id);
- my $exc_slice = $self->fetch_by_seq_region_id( $hap->[2] );
+ my $count =0;
+ my $chr_start = 1;
+ my $hap_start = 1;
+ my $last = 0;
- #
- # lengths of haplotype and reference in db may be different
- # we want to use the maximum possible length for the mapping
- # between the two systems
- #
+ my $seq_reg_slice = $self->fetch_by_seq_region_id($slice_seq_region_id);
+ my $exc_slice = $self->fetch_by_seq_region_id( $sort_haps[0][2] );
my $len1 = $seq_reg_slice->length();
my $len2 = $exc_slice->length();
my $max_len = ($len1 > $len2) ? $len1 : $len2;
- #the inserted region can differ in length, but mapped sections
- #need to be same lengths
- my $diff = $hap->[4] - $hap->[1];
+ while($count <= scalar(@sort_haps) and !$last){
+ my $chr_end;
+ my $hap_end;
+ if(defined($sort_haps[$count]) and defined($sort_haps[$count][0]) ){
+ $hap_end = $sort_haps[$count][0]-1;
+ $chr_end = $sort_haps[$count][3]-1
+ }
+ else{
+ $last = 1;
+ $hap_end = $len1;
+ $chr_end = $len2;
+ my $diff = ($hap_end-$hap_start)-($chr_end-$chr_start);
+ if($diff > 0){
+ push( @syms, [ $hap_start, $hap_end, $sort_haps[0][2], $chr_start, $chr_end+$diff] );
+ }
+ elsif($diff < 0){
+ push( @syms, [ $hap_start, $hap_end+$diff, $sort_haps[0][2], $chr_start, $chr_end] );
+ }
+ else{
+ push( @syms, [ $hap_start, $hap_end, $sort_haps[0][2], $chr_start, $chr_end] );
+ }
+ next;
+ }
+ if($hap_end and $hap_start < $len1){ # if hap at start or end of chromosome
+ push( @syms, [ $hap_start, $hap_end, $sort_haps[0][2], $chr_start, $chr_end] );
+ }
+ $chr_start = $chr_end + ($sort_haps[$count][4]-$sort_haps[$count][3]) + 2;
+ $hap_start = $hap_end + ($sort_haps[$count][1]-$sort_haps[$count][0]) + 2;
+ $count++;
+ }
+
- # we want the region of the haplotype INVERTED
- push( @syms, [ 1, $hap->[0]-1, $hap->[2], 1, $hap->[3] - 1 ] );
- push( @syms, [ $hap->[1]+1, $max_len - $diff,
- $hap->[2], $hap->[4] + 1, $max_len ] );
}
+
# for now haps and pars should not be both there, but in theory we
# could handle it here by cleverly merging the pars into the existing syms,
# for now just:
push( @syms, @pars );
my $mapper = Bio::EnsEMBL::Mapper->new( "sym", "org" );
+ my $count = 0;
for my $sym ( @syms ) {
$mapper->add_map_coordinates( $slice_seq_region_id, $sym->[0], $sym->[1],
1, $sym->[2], $sym->[3], $sym->[4] );
@@ -1581,6 +1617,15 @@ sub store {
$seq_adaptor->store($seq_region_id, $$seqref);
}
+ #synonyms
+ if(defined($slice->{'synonym'})){
+ foreach my $syn (@{$slice->{'synonym'}} ){
+ $syn->seq_region_id($seq_region_id); # set the seq_region_id
+ $syn->adaptor->store($syn);
+ }
+ }
+
+
$slice->adaptor($self);
return $seq_region_id;
@@ -1819,7 +1864,6 @@ LSQL
} ## end sub cache_toplevel_seq_mappings
-
#####################################
# sub DEPRECATED METHODs
#####################################
--
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