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Commit 0fa29252 authored by Monika Komorowska's avatar Monika Komorowska
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fix for ChainedAssemblyMapper to map using the destination slice if one is... 

fix for ChainedAssemblyMapper to map using the destination slice if one is provided http://www.ebi.ac.uk/panda/jira/browse/ENSCORESW-108
parent ad2b0516
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with 202 additions and 45 deletions
modules/Bio/EnsEMBL/DBSQL/DensityFeatureAdaptor.pm
+ 10
− 2
View file @ 0fa29252
......@@ -404,8 +404,16 @@ sub _objs_from_sth {
my $len = $seq_region_end - $seq_region_start + 1;
my @coords =
$mapper->map($sr_name, $seq_region_start, $seq_region_end,1, $sr_cs);
my @coords;
if (defined $dest_slice && $mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper') ) {
@coords = $mapper->map( $sr_name, $seq_region_start, $seq_region_end,
1, $sr_cs, 0, $dest_slice);
} else {
@coords = $mapper->map($sr_name, $seq_region_start, $seq_region_end,1, $sr_cs);
}
#filter out gaps
@coords = grep {!$_->isa('Bio::EnsEMBL::Mapper::Gap')} @coords;
......
modules/Bio/EnsEMBL/DBSQL/DnaAlignFeatureAdaptor.pm
+ 15
− 4
View file @ 0fa29252
......@@ -466,11 +466,22 @@ FEATURE:
# Remap the feature coordinates to another coord system
# if a mapper was provided.
if ( defined($mapper) ) {
( $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand )
=
$mapper->fastmap( $sr_name, $seq_region_start, $seq_region_end,
if (defined $dest_slice && $mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper') ) {
( $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand )
=
$mapper->map( $sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs, 1, $dest_slice);
} else {
( $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand )
=
$mapper->fastmap( $sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs );
}
# Skip features that map to gaps or coord system boundaries.
if ( !defined($seq_region_id) ) { next FEATURE }
......
modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
+ 14
− 3
View file @ 0fa29252
......@@ -617,11 +617,22 @@ FEATURE: while ( $sth->fetch() ) {
# was provided.
#
if ( defined($dest_mapper) ) {
( $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand )
= $dest_mapper->fastmap( $sr_name, $seq_region_start,
if (defined $dest_slice && $dest_mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper') ) {
( $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand )
=
$dest_mapper->map( $sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs, 1, $dest_slice);
} else {
( $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand )
= $dest_mapper->fastmap( $sr_name, $seq_region_start,
$seq_region_end, $seq_region_strand,
$sr_cs );
}
# Skip features that map to gaps or coord system boundaries.
if ( !defined($seq_region_id) ) { next FEATURE }
......
modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+ 15
− 3
View file @ 0fa29252
......@@ -1681,9 +1681,21 @@ sub _objs_from_sth {
#
if($mapper) {
($seq_region_id,$seq_region_start,$seq_region_end,$seq_region_strand) =
$mapper->fastmap($sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs);
if (defined $dest_slice && $mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper') ) {
( $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand )
=
$mapper->map( $sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs, 1, $dest_slice);
} else {
( $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand )
=
$mapper->fastmap( $sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs );
}
#skip features that map to gaps or coord system boundaries
next FEATURE if(!defined($seq_region_id));
......
modules/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm
+ 11
− 3
View file @ 0fa29252
......@@ -437,9 +437,17 @@ sub _objs_from_sth {
#
if ($mapper) {
($seq_region_id,$seq_region_start,$seq_region_end,$seq_region_strand) =
$mapper->fastmap($sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs);
if (defined $dest_slice && $mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper') ) {
( $seq_region_id, $seq_region_start,$seq_region_end, $seq_region_strand ) =
$mapper->map( $sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs, 1, $dest_slice);
} else {
( $seq_region_id, $seq_region_start,$seq_region_end, $seq_region_strand ) =
$mapper->fastmap( $sr_name, $seq_region_start, $seq_region_end,$seq_region_strand, $sr_cs );
}
#skip features that map to gaps or coord system boundaries
if(!defined($seq_region_id)) {
......
modules/Bio/EnsEMBL/DBSQL/OperonAdaptor.pm
+ 16
− 4
View file @ 0fa29252
......@@ -708,10 +708,22 @@ sub _objs_from_sth {
#
if ($mapper) {
( $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand )
= $mapper->fastmap( $sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs );
if (defined $dest_slice && $mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper') ) {
( $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand )
=
$mapper->map( $sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs, 1, $dest_slice);
} else {
( $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand )
=
$mapper->fastmap( $sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs );
}
#skip features that map to gaps or coord system boundaries
next OPERON if ( !defined($seq_region_id) );
......
modules/Bio/EnsEMBL/DBSQL/OperonTranscriptAdaptor.pm
+ 17
− 5
View file @ 0fa29252
......@@ -790,11 +790,23 @@ sub _objs_from_sth {
#
if ($mapper) {
( $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand )
= $mapper->fastmap( $sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs );
if (defined $dest_slice && $mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper') ) {
( $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand )
=
$mapper->map( $sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs, 1, $dest_slice);
} else {
( $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand )
=
$mapper->fastmap( $sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs );
}
#skip features that map to gaps or coord system boundaries
next OPERON if ( !defined($seq_region_id) );
......
modules/Bio/EnsEMBL/DBSQL/PredictionExonAdaptor.pm
+ 15
− 3
View file @ 0fa29252
......@@ -389,9 +389,21 @@ sub _objs_from_sth {
#
if($dest_mapper) {
($seq_region_id,$seq_region_start,$seq_region_end,$seq_region_strand) =
$dest_mapper->fastmap($sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs);
if (defined $dest_slice && $dest_mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper') ) {
( $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand )
=
$dest_mapper->map( $sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs, 1, $dest_slice);
} else {
( $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand )
= $dest_mapper->fastmap( $sr_name, $seq_region_start,
$seq_region_end, $seq_region_strand,
$sr_cs );
}
#skip features that map to gaps or coord system boundaries
next FEATURE if(!defined($seq_region_id));
......
modules/Bio/EnsEMBL/DBSQL/PredictionTranscriptAdaptor.pm
+ 15
− 3
View file @ 0fa29252
......@@ -351,9 +351,21 @@ sub _objs_from_sth {
#
if($mapper) {
($seq_region_id,$seq_region_start,$seq_region_end,$seq_region_strand) =
$mapper->fastmap($sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs);
if (defined $dest_slice && $mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper') ) {
( $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand )
=
$mapper->map( $sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs, 1, $dest_slice);
} else {
( $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand )
=
$mapper->fastmap( $sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs );
}
#skip features that map to gaps or coord system boundaries
next FEATURE if(!defined($seq_region_id));
......
modules/Bio/EnsEMBL/DBSQL/ProteinAlignFeatureAdaptor.pm
+ 15
− 3
View file @ 0fa29252
......@@ -255,9 +255,21 @@ sub _objs_from_sth {
#
if($mapper) {
($seq_region_id,$seq_region_start,$seq_region_end,$seq_region_strand) =
$mapper->fastmap($sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs);
if (defined $dest_slice && $mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper') ) {
( $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand )
=
$mapper->map( $sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs, 1, $dest_slice);
} else {
( $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand )
=
$mapper->fastmap( $sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs );
}
#skip features that map to gaps or coord system boundaries
next FEATURE if(!defined($seq_region_id));
......
modules/Bio/EnsEMBL/DBSQL/RepeatFeatureAdaptor.pm
+ 15
− 3
View file @ 0fa29252
......@@ -273,9 +273,21 @@ sub _objs_from_sth {
#
if($mapper) {
($seq_region_id,$seq_region_start,$seq_region_end,$seq_region_strand) =
$mapper->fastmap($sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs);
if (defined $dest_slice && $mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper') ) {
( $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand )
=
$mapper->map( $sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs, 1, $dest_slice);
} else {
( $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand )
=
$mapper->fastmap( $sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs );
}
#skip features that map to gaps or coord system boundaries
next FEATURE if(!defined($seq_region_id));
......
modules/Bio/EnsEMBL/DBSQL/SimpleFeatureAdaptor.pm
+ 15
− 3
View file @ 0fa29252
......@@ -260,9 +260,21 @@ sub _objs_from_sth {
#
if($mapper) {
($seq_region_id,$seq_region_start,$seq_region_end,$seq_region_strand) =
$mapper->fastmap($sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs);
if (defined $dest_slice && $mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper') ) {
( $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand )
=
$mapper->map( $sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs, 1, $dest_slice);
} else {
( $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand )
=
$mapper->fastmap( $sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs );
}
#skip features that map to gaps or coord system boundaries
next FEATURE if(!defined($seq_region_id));
......
modules/Bio/EnsEMBL/DBSQL/SplicingEventAdaptor.pm
+ 14
− 3
View file @ 0fa29252
......@@ -459,11 +459,22 @@ FEATURE:
# Remap the feature coordinates to another coord system if a mapper
# was provided.
if ( defined($dest_mapper) ) {
( $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand )
= $dest_mapper->fastmap( $sr_name, $seq_region_start,
if (defined $dest_slice && $dest_mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper') ) {
( $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand )
=
$dest_mapper->map( $sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs, 1, $dest_slice);
} else {
( $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand )
= $dest_mapper->fastmap( $sr_name, $seq_region_start,
$seq_region_end, $seq_region_strand,
$sr_cs );
}
# Skip features that map to gaps or coord system boundaries.
if ( !defined($seq_region_id) ) { next FEATURE }
......
modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
+ 15
− 3
View file @ 0fa29252
......@@ -1539,9 +1539,21 @@ sub _objs_from_sth {
#
if($dest_mapper) {
($seq_region_id,$seq_region_start,$seq_region_end,$seq_region_strand) =
$dest_mapper->fastmap($sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs);
if (defined $dest_slice && $dest_mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper') ) {
( $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand )
=
$dest_mapper->map( $sr_name, $seq_region_start, $seq_region_end,
$seq_region_strand, $sr_cs, 1, $dest_slice);
} else {
( $seq_region_id, $seq_region_start,
$seq_region_end, $seq_region_strand )
= $dest_mapper->fastmap( $sr_name, $seq_region_start,
$seq_region_end, $seq_region_strand,
$sr_cs );
}
#skip features that map to gaps or coord system boundaries
next FEATURE if(!defined($seq_region_id));
......
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