From b06b9c6d7cfd6aba8ebaf419dafbd704659c447f Mon Sep 17 00:00:00 2001
From: Stefano Giorgetti <sgiorgetti@ebi.ac.uk>
Date: Fri, 20 Sep 2024 15:29:58 +0000
Subject: [PATCH] Revert regulatory summary and filter EMARs
---
lib/EnsEMBL/REST/Model/Overlap.pm | 13 ++++---------
t/overlap.t | 8 ++++----
2 files changed, 8 insertions(+), 13 deletions(-)
diff --git a/lib/EnsEMBL/REST/Model/Overlap.pm b/lib/EnsEMBL/REST/Model/Overlap.pm
index 9c64fe72..2f1da502 100644
--- a/lib/EnsEMBL/REST/Model/Overlap.pm
+++ b/lib/EnsEMBL/REST/Model/Overlap.pm
@@ -160,15 +160,7 @@ sub to_hash {
my ($self, $features, $feature_type) = @_;
my @hashed;
foreach my $feature (@{$features}) {
-
- my $hash;
-
- if (lc($feature_type) eq 'regulatory') {
- $hash = $feature->summary_as_hash_2();
- } else {
- $hash = $feature->summary_as_hash();
- }
-
+ my $hash = $feature->summary_as_hash();
foreach my $key (@KNOWN_NUMERICS) {
my $v = $hash->{$key};
$hash->{$key} = ($v*1) if defined $v;
@@ -189,6 +181,9 @@ sub to_hash {
$hash->{description} = $feature->{$feature_type}->{hdescription} if defined($feature->{$feature_type}->{hdescription});
}
}
+ if (lc($feature_type) eq 'regulatory') {
+ next if ($hash->{description} eq 'Epigenetically modified accessible region');
+ }
push(@hashed, $hash);
}
return \@hashed;
diff --git a/t/overlap.t b/t/overlap.t
index 85ad58dc..34b064fd 100644
--- a/t/overlap.t
+++ b/t/overlap.t
@@ -304,13 +304,13 @@ my $base = '/overlap/region/homo_sapiens';
my $region = '1:76429380..76430144';
cmp_deeply(json_GET("$base/$region?feature=regulatory", 'Get regulatory_feature'), [{
id => 'ENSR00000105157',
- extended_end => 76430144,
- extended_start => 76429380,
- description => 'open_chromatin_region',
+ bound_end => 76430144,
+ bound_start => 76429380,
+ description => 'Open chromatin region',
end => 76430144,
feature_type => 'regulatory',
seq_region_name => 1,
- source => 'Ensembl',
+ source => 'Regulatory_Build',
start => 76429380,
strand => 0
}], 'Getting regulatory_feature as JSON');
--
GitLab