From addf3b991dcba9af6a5e9cfc09ac277e383fb9c7 Mon Sep 17 00:00:00 2001
From: Mark Quinton-Tulloch <markquintontulloch@gmail.com>
Date: Fri, 19 Apr 2024 08:12:01 +0100
Subject: [PATCH] Add ENSEMBL xrefs

---
 .../make_agr_gene_json.pl                     | 82 ++++++++++++++++++-
 1 file changed, 79 insertions(+), 3 deletions(-)

diff --git a/scripts/AGR/curation_db_submissions/make_agr_gene_json.pl b/scripts/AGR/curation_db_submissions/make_agr_gene_json.pl
index 374753ba3..cd5be828e 100755
--- a/scripts/AGR/curation_db_submissions/make_agr_gene_json.pl
+++ b/scripts/AGR/curation_db_submissions/make_agr_gene_json.pl
@@ -9,7 +9,7 @@
 use Wormbase;
 
 my ($help, $debug, $test, $verbose, $store, $wormbase, $schema);
-my ($outfile, $acedbpath, $ws_version, $out_fh);
+my ($outfile, $acedbpath, $ws_version, $out_fh, $gtf_file);
 
 const my $LINKML_SCHEMA => 'v2.2.3';
 
@@ -40,7 +40,8 @@
 	    "store:s"     => \$store,
 	    "database:s"  => \$acedbpath,
 	    "outfile:s"   => \$outfile,
-            "wsversion=s" => \$ws_version
+            "wsversion=s" => \$ws_version,
+	    "gtf=s"       => \$gtf_file
 	    );
 
 if ( $store ) {
@@ -61,6 +62,8 @@
 
 my @genes;
 
+my $locs = get_location_data($db, $gtf_file);
+
 my $it = $db->fetch_many(-query => $query);
 
 while (my $obj = $it->next) {
@@ -133,7 +136,7 @@
     my @baseXrefs = qw(gene gene/expression gene/references);
     push @baseXrefs, 'gene/phenotypes' if ($obj->Allele and $obj->Allele->Phenotype) || ($obj->RNAi_result and $obj->RNAi_result->Phenotype);
     push @baseXrefs, 'gene/expression_images' if ($obj->Expr_pattern && grep {$_->Picture} $obj->Expr_pattern);
-    
+
     for my $baseXref (@baseXrefs) {
 	push @xrefs, {
 	    referenced_curie => 'WB:' . $obj->name,
@@ -153,6 +156,16 @@
 	};
     }
 
+    # Ensembl xrefs, only for genomically placed genes
+    if (defined $locs and exists $locs->{$obj->name}) {
+	push @xrefs, {
+	    referenced_curie => 'ENSEMBL:' . $obj->name,
+	    page_area => 'default',
+	    display_name => 'ENSEMBL:' . $obj->name,
+	    prefix => 'ENSEMBL'
+	};
+    }
+    
 
 
     my $is_obsolete = $obj->Status && $obj->Status->name eq 'Dead' ? JSON::true : JSON::false;
@@ -341,4 +354,67 @@ sub get_paper {
     return $publication_id;
 }
 
+
+
+sub get_location_data {
+  my ($acedb, $gtf) = @_;
+
+  # get the assembly name for the canonical bioproject
+  my ($assembly_name, $fh, %locs);
+  
+  my $species_obj = $acedb->fetch(-class => 'Species', -name => $wormbase->full_name);
+  my @seq_col = $species_obj->at('Assembly');
+        
+  foreach my $seq_col_name (@seq_col) {
+    my ($bioproj);
+
+    my $seq_col = $seq_col_name->fetch;
+    my $this_assembly_name = $seq_col->Name;
+
+    my @db = $seq_col->at('Origin.DB_info.Database');
+    foreach my $db (@db) {
+      if ($db->name eq 'NCBI_BioProject') {
+        $bioproj = $db->right->right->name;
+      }
+    }
+    
+    if (defined $bioproj and $wormbase->ncbi_bioproject eq $bioproj) {
+      $assembly_name = $this_assembly_name->name;
+      last;
+    }
+  }
+    
+  if (not defined $assembly_name) {
+    die "Could not find name of current assembly for " . $wormbase->species() . "\n";
+  }
+
+  # parse the GTF
+  if ($gtf =~ /\.gz$/) {
+    open( $fh, "gunzip -c $gtf |") 
+        or die "Could not open gunzip stream GTF file $gtf\n";
+  } else {
+    open( $fh, $gtf) 
+        or die "Could not open GTF file $gtf\n";
+  }
+
+  while(<$fh>) {
+    /^\#/ and next;
+    
+    my @l = split(/\t/, $_);
+    next if $l[2] ne "gene";
+
+    my ($wbgid) = $l[8] =~ /gene_id\s+\"(\S+)\"/; 
+
+    $locs{$wbgid} = {
+      assembly       => $assembly_name,
+      chromosome     => $l[0],
+      startPosition  => $l[3] + 0, 
+      endPosition    => $l[4] + 0,
+      strand         => $l[6],
+    };
+  }
+      
+  return \%locs;
+}
+
 1;