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Commit 507e3329 authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
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In generate_similarity_events(): Tighten rules for when to generate 

similarity events.  Require similarity events to be within 1.5% (not 2%)
of top score.

Reformat routine while here.
parent 3c97511c
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Showing with 78 additions and 76 deletions
modules/Bio/EnsEMBL/IdMapping/StableIdMapper.pm
View file @ 507e3329
......@@ -357,19 +357,18 @@ sub map_stable_ids {
sub generate_similarity_events {
my $self = shift;
my $mappings = shift;
my $scores = shift;
my $type = shift;
my ( $self, $mappings, $scores, $type ) = @_;
# argument checks
unless ($mappings and
$mappings->isa('Bio::EnsEMBL::IdMapping::MappingList')) {
unless ( $mappings and
$mappings->isa('Bio::EnsEMBL::IdMapping::MappingList') )
{
throw('Need a gene Bio::EnsEMBL::IdMapping::MappingList.');
}
unless ($scores and
$scores->isa('Bio::EnsEMBL::IdMapping::ScoredMappingMatrix')) {
unless ( $scores and
$scores->isa('Bio::EnsEMBL::IdMapping::ScoredMappingMatrix') )
{
throw('Need a Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
}
......@@ -380,99 +379,102 @@ sub generate_similarity_events {
#
# add similarities for mapped entries
#
foreach my $e (@{ $mappings->get_all_Entries }) {
foreach my $e ( @{ $mappings->get_all_Entries } ) {
# create lookup hash for mapped sources and targets; we'll need this
# later
$mapped->{'source'}->{ $e->source } = 1;
$mapped->{'target'}->{ $e->target } = 1;
# create lookup hash for mapped sources and targets; we'll need this later
$mapped->{'source'}->{$e->source} = 1;
$mapped->{'target'}->{$e->target} = 1;
# loop over all other entries which contain either source or target;
# add similarity if score is within 2% of this entry (which is the top
# scorer)
my @others = @{ $scores->get_Entries_for_target($e->target) };
push @others, @{ $scores->get_Entries_for_source($e->source) };
while (my $e2 = shift(@others)) {
# add similarity if score is within 1.5% of this entry (which is the
# top scorer)
my @others = @{ $scores->get_Entries_for_target( $e->target ) };
push @others, @{ $scores->get_Entries_for_source( $e->source ) };
while ( my $e2 = shift(@others) ) {
# skip self
next if (($e->source eq $e2->source) and ($e->target eq $e2->target));
if ( ( $e->source eq $e2->source ) and
( $e->target eq $e2->target ) )
{
next;
}
if ( $e2->score > ( $e->score*0.985 ) ) {
my $s_obj =
$self->cache->get_by_key( "${type}s_by_id", 'source',
$e2->source );
my $t_obj =
$self->cache->get_by_key( "${type}s_by_id", 'target',
$e2->target );
my $key = join( "\t",
$s_obj->stable_id, $s_obj->version,
$t_obj->stable_id, $t_obj->version,
$self->mapping_session_id, $type,
$e2->score );
$self->add_stable_id_event( 'similarity', $key );
if ($e2->score > ($e->score * 0.98)) {
my $s_obj = $self->cache->get_by_key("${type}s_by_id", 'source',
$e2->source);
my $t_obj = $self->cache->get_by_key("${type}s_by_id", 'target',
$e2->target);
my $key = join("\t",
$s_obj->stable_id,
$s_obj->version,
$t_obj->stable_id,
$t_obj->version,
$self->mapping_session_id,
$type,
$e2->score
);
$self->add_stable_id_event('similarity', $key);
}
# [todo] add overlap hack here? (see Java code)
# probably better solution: let synteny rescoring affect this decision
}
# probably better solution: let synteny rescoring affect this
# decision
} ## end while ( my $e2 = shift(@others...))
}
} ## end foreach my $e ( @{ $mappings...})
#
# similarities for other entries
#
foreach my $dbtype (keys %$mapped) {
foreach my $dbtype ( keys %$mapped ) {
# note: $dbtype will be either 'source' or 'target'
my $m1 = "get_all_${dbtype}s";
my $m2 = "get_Entries_for_${dbtype}";
foreach my $id (@{ $scores->$m1 }) {
foreach my $id ( @{ $scores->$m1 } ) {
# skip if this is a mapped source/target
next if ($mapped->{$dbtype}->{$id});
my @entries = sort { $b->score <=> $a->score } @{ $scores->$m2($id) };
if ( $mapped->{$dbtype}->{$id} ) { next }
next unless (@entries);
my @entries =
sort { $b->score <=> $a->score } @{ $scores->$m2($id) };
# skip if top score < 0.7
unless (@entries) { next }
# skip if top score < 0.75
my $top_score = $entries[0]->score;
next if ($top_score < 0.7);
if ( $top_score < 0.75 ) { next }
# add similarities for all entries within 5% of top scorer
while (my $e = shift(@entries)) {
if ($e->score > ($top_score * 0.95)) {
my $s_obj = $self->cache->get_by_key("${type}s_by_id", 'source',
$e->source);
my $t_obj = $self->cache->get_by_key("${type}s_by_id", 'target',
$e->target);
my $key = join("\t",
$s_obj->stable_id,
$s_obj->version,
$t_obj->stable_id,
$t_obj->version,
$self->mapping_session_id,
$type,
$e->score
);
$self->add_stable_id_event('similarity', $key);
while ( my $e = shift(@entries) ) {
if ( $e->score > ( $top_score*0.95 ) ) {
my $s_obj =
$self->cache->get_by_key( "${type}s_by_id", 'source',
$e->source );
my $t_obj =
$self->cache->get_by_key( "${type}s_by_id", 'target',
$e->target );
my $key = join( "\t",
$s_obj->stable_id, $s_obj->version,
$t_obj->stable_id, $t_obj->version,
$self->mapping_session_id, $type,
$e->score );
$self->add_stable_id_event( 'similarity', $key );
}
}
}
}
}
} ## end foreach my $id ( @{ $scores...})
} ## end foreach my $dbtype ( keys %$mapped)
} ## end sub generate_similarity_events
sub filter_same_gene_transcript_similarities {
......
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