#Have to do this outside of the HERETO thanks to tabs
$expected.=join("\t",
qw/20 wibble region 30274334 30300924 . + ./,
'ID=gene:ENSG00000131044;Name=C20orf125;biotype=protein_coding;description=DJ310O13.1.2 (NOVEL PROTEIN SIMILAR DROSOPHILA PROTEIN CG7474%2C ISOFORM 2 ) (FRAGMENT). [Source:SPTREMBL%3BAcc:Q9BR18];gene_id=ENSG00000131044;logic_name=ensembl;version=1'
'ID=gene:ENSG00000131044;Name=C20orf125;biotype=protein_coding;description=DJ310O13.1.2 (NOVEL PROTEIN SIMILAR DROSOPHILA PROTEIN CG7474%2C ISOFORM 2 ) (FRAGMENT). [Source:SPTREMBL%3BAcc:Q9BR18];gene_id=ENSG00000131044;logic_name=ensembl;projection_parent_gene=ENSG_PARENT_GENE;version=1'
);
$expected.="\n";
assert_gff3($gene,$expected,'Gene with custom source serialises to GFF3 as expected. Source is wibble');
assert_gff3($gene->canonical_transcript(),$expected,'Transcript with custom source serialises to GFF3 as expected. Source is wibble');
...
...
@@ -206,7 +206,7 @@ OUT
#Have to do this outside of the HERETO thanks to tabs
$expected.=join("\t",
qw/20 ensembl region 30274334 30300924 . + ./,
'ID=gene:ENSG00000131044;Name=C20orf125;Dbxref=bibble,fibble;Ontology_term=GO:0001612;biotype=protein_coding;description=DJ310O13.1.2 (NOVEL PROTEIN SIMILAR DROSOPHILA PROTEIN CG7474%2C ISOFORM 2 ) (FRAGMENT). [Source:SPTREMBL%3BAcc:Q9BR18];gene_id=ENSG00000131044;logic_name=ensembl;version=1'
'ID=gene:ENSG00000131044;Name=C20orf125;Dbxref=bibble,fibble;Ontology_term=GO:0001612;biotype=protein_coding;description=DJ310O13.1.2 (NOVEL PROTEIN SIMILAR DROSOPHILA PROTEIN CG7474%2C ISOFORM 2 ) (FRAGMENT). [Source:SPTREMBL%3BAcc:Q9BR18];gene_id=ENSG00000131044;logic_name=ensembl;projection_parent_gene=ENSG_PARENT_GENE;version=1'
18 non_ref Non Reference Non Reference Sequence Region
19 karyotype_rank Rank in the karyotype For a given seq_region, if it is part of the species karyotype, will indicate its rank
20 proj_parent_g projection parent gene Stable identifier of the parent gene this gene was projected from (projection between different species and/or assemblies).
21 proj_parent_t projection parent transcript Stable identifier of the parent transcript this transcript was projected from (projection between different species and/or assemblies).