Allow REST to show presence of GENCODE Primary attribute (#636)

* Allow REST to return boolean value for presence of GENCODE Primary attribute

* Update lookup test with new attribute

* Update expected test result to false

* Update test db data relating to GENCODE primary attribute

* Remove gencode_primary from lookup test to debug

* Fix gencode_primary tests. Fix transcript id typo.

lib/EnsEMBL/REST/Model/Lookup.pm

@@ -515,6 +515,7 @@ sub features_as_hash {
       if (lc($object_type) eq 'transcript') {
         $features->{is_canonical} = $obj->is_canonical;
         $features->{length} = $obj->length;
+        $features->{gencode_primary} = $obj->gencode_primary; # boolean value for having GENCODE Primary attrib
       }
       if (lc($object_type) eq 'gene') {
         $features->{canonical_transcript} = $obj->canonical_transcript->stable_id.".".$obj->canonical_transcript->version;

t/lookup.t

@@ -109,7 +109,7 @@ $full_response = {
   %{$condensed_response},
   Parent => 'ENSG00000176515', start => 1080164, end => 1105181, strand => 1, version => 1, seq_region_name => '6', assembly_name => 'GRCh37',
   biotype => 'protein_coding', display_name => 'AL033381.1-201', logic_name => 'ensembl', source => 'ensembl',
-  is_canonical => 1, length => 3435,
+  is_canonical => 1, length => 3435, gencode_primary => 0,
 };
 cmp_deeply(json_GET("/lookup/$basic_id",'lookup transcript'), $full_response, 'Full response contains all Transcript information');
 
@@ -151,7 +151,7 @@ $full_response = {
   %{$condensed_response},
   Parent => 'ENSG00000164379', start => 1312675, end => 1314992, strand => 1, version => 2, seq_region_name => '6', assembly_name => 'GRCh37',
   biotype => 'protein_coding', display_name => 'FOXQ1-001', logic_name => 'ensembl_havana_transcript', source => 'ensembl',
-  is_canonical => 1, length => 2318,
+  is_canonical => 1, length => 2318, gencode_primary => 1,
 };
 cmp_deeply(json_GET("/lookup/$basic_id",'lookup transcript'), $full_response, 'Full response contains all Transcript information');
 

t/test-genome-DBs/homo_sapiens/core/attrib_type.txt

@@ -230,3 +230,4 @@
 405	ref_length	Golden Path Length	Length of the primary assembly
 406	total_length	Base Pairs	Total length of the assembly
 535	MANE_Select	MANE Select v0.92	MANE Select (v0.92) is the preliminary release (phase 7) of the MANE Select data set. The Matched Annotation from NCBI and EMBL-EBI project (MANE) is a collaboration between Ensembl-GENCODE and RefSeq to select a default transcript per human protein coding locus that is representative of biology, well-supported, expressed and conserved. This transcript set matches GRCh38 and is 100% identical between RefSeq and Ensembl-GENCODE for 5' UTR, CDS, splicing and 3' UTR.
+576	gencode_primary	GENCODE primary annotation	Gencode Primary replaces Gencode Basic for protein coding genes as the set of the most biologically relevant transcripts. Protein coding transcripts are compared to MANE Select or to Ensembl Canonical where MANE Select is not yet defined. The features (exons and introns) that are novel to the reference transcript are filtered and assessed for biological relevance using conservation and expression data. The transcripts having the filtered features are retained for the set. For noncoding genes, the Gencode Primary set is identical to the Gencode Basic set.

t/test-genome-DBs/homo_sapiens/core/transcript_attrib.txt

@@ -272,3 +272,4 @@
 1385028	52	Havana
 1385028	53	v@somewhere.com
 1384971	535	NM_033260.4
+1384971	576	GENCODE primary
\ No newline at end of file