Coordinates of Pfam domains are not correctly reported due to splicing

[dariober]

If I'm not mistaken, there is a problem with the integration of Pfam domains into the final GFF file. It seems that when a transcript contains introns, the coordinates of the domain are not correctly spliced and offset.

Below is an example:

There are 3 Pfam domains in a transcript with multiple exons. The first domain, PF02861, has coordinates 277134-277217 and sits between the first intron and the second CDS (277188-277561). The 3rd domain, PF00004, is fully contained in an intron. I think a protein domain can include only CDS regions (possibly more than one).

These are all the features of this gene:

grep 'Tgondii_000009000.1' scaffold.out.gff3 
TgRH.10_pilon_pilon	AUGUSTUS	mRNA	276645	280440	0.92	+	.	ID=Tgondii_000009000.1;Parent=Tgondii_000009000
TgRH.10_pilon_pilon	AUGUSTUS	CDS	276645	276885	1	+	0	ID=Tgondii_000009000.1:CDS:1;Parent=Tgondii_000009000.1
TgRH.10_pilon_pilon	AUGUSTUS	CDS	277188	277561	0.93	+	2	ID=Tgondii_000009000.1:CDS:2;Parent=Tgondii_000009000.1
TgRH.10_pilon_pilon	AUGUSTUS	CDS	278836	279009	1	+	0	ID=Tgondii_000009000.1:CDS:3;Parent=Tgondii_000009000.1
TgRH.10_pilon_pilon	AUGUSTUS	CDS	279671	279944	1	+	0	ID=Tgondii_000009000.1:CDS:4;Parent=Tgondii_000009000.1
TgRH.10_pilon_pilon	AUGUSTUS	CDS	280220	280440	0.99	+	2	ID=Tgondii_000009000.1:CDS:5;Parent=Tgondii_000009000.1
TgRH.10_pilon_pilon	.	polypeptide	276645	280440	.	+	.	ID=Tgondii_000009000.1:pep;Derives_from=Tgondii_000009000.1;orthologous_to=Tgondii_000248400.1,Tgondii_000874000.1,TGME49_257990_t26_1,TGME49_275690_t26_1,TGME49_268650_t26_1,Tgondii_000009100.1;ortholog_cluster=ORTHOMCL32;product=term%3Dheat shock protein 101%2C putative%3Bevidence%3DIEA%3Bwith%3DGeneDB:TGME49_257990_t26_1%3Bis_preferred%3Dtrue,term%3Dchaperone clpB protein%2C putative%3Bevidence%3DIEA%3Bwith%3DGeneDB:TGME49_268650_t26_1%3Brank%3D1,term%3DClpB%2C putative%3Bevidence%3DIEA%3Bwith%3DGeneDB:TGME49_275690_t26_1%3Brank%3D1;Ontology_term=GO:0005524,GO:0019538
TgRH.10_pilon_pilon	Pfam	protein_match	277134	277217	.	+	.	Parent=Tgondii_000009000.1:pep;Name=PF02861;signature_desc=Clp amino terminal domain%2C pathogenicity island component;Ontology_term=GO:0019538
TgRH.10_pilon_pilon	Pfam	protein_match	277254	277388	.	+	.	Parent=Tgondii_000009000.1:pep;Name=PF02861;signature_desc=Clp amino terminal domain%2C pathogenicity island component;Ontology_term=GO:0019538
TgRH.10_pilon_pilon	Pfam	protein_match	277572	277847	.	+	.	Parent=Tgondii_000009000.1:pep;Name=PF00004;signature_desc=ATPase family associated with various cellular activities (AAA);Ontology_term=GO:0005524
TgRH.10_pilon_pilon	.	polypeptide	280746	285473	.	+	.	ID=Tgondii_000009100.1:pep;Derives_from=Tgondii_000009100.1;orthologous_to=Tgondii_000248400.1,Tgondii_000874000.1,TGME49_257990_t26_1,TGME49_275690_t26_1,TGME49_268650_t26_1,Tgondii_000009000.1;ortholog_cluster=ORTHOMCL32;product=term%3Dheat shock protein 101%2C putative%3Bevidence%3DIEA%3Bwith%3DGeneDB:TGME49_257990_t26_1%3Bis_preferred%3Dtrue,term%3Dchaperone clpB protein%2C putative%3Bevidence%3DIEA%3Bwith%3DGeneDB:TGME49_268650_t26_1%3Brank%3D1,term%3DClpB%2C putative%3Bevidence%3DIEA%3Bwith%3DGeneDB:TGME49_275690_t26_1%3Brank%3D1
TgRH.1_pilon_pilon	.	polypeptide	7742535	7745808	.	+	.	ID=Tgondii_000248400.1:pep;Derives_from=Tgondii_000248400.1;orthologous_to=Tgondii_000874000.1,TGME49_257990_t26_1,TGME49_275690_t26_1,TGME49_268650_t26_1,Tgondii_000009000.1,Tgondii_000009100.1;ortholog_cluster=ORTHOMCL32;product=term%3Dheat shock protein 101%2C putative%3Bevidence%3DIEA%3Bwith%3DGeneDB:TGME49_257990_t26_1%3Bis_preferred%3Dtrue,term%3Dchaperone clpB protein%2C putative%3Bevidence%3DIEA%3Bwith%3DGeneDB:TGME49_268650_t26_1%3Brank%3D1,term%3DClpB%2C putative%3Bevidence%3DIEA%3Bwith%3DGeneDB:TGME49_275690_t26_1%3Brank%3D1;Ontology_term=GO:0019538,GO:0016887,GO:0005524
TgRH.8_pilon_pilon	.	polypeptide	3707700	3716669	.	+	.	ID=Tgondii_000874000.1:pep;Derives_from=Tgondii_000874000.1;orthologous_to=Tgondii_000248400.1,TGME49_257990_t26_1,TGME49_275690_t26_1,TGME49_268650_t26_1,Tgondii_000009000.1,Tgondii_000009100.1;ortholog_cluster=ORTHOMCL32;product=term%3Dheat shock protein 101%2C putative%3Bevidence%3DIEA%3Bwith%3DGeneDB:TGME49_257990_t26_1%3Bis_preferred%3Dtrue,term%3Dchaperone clpB protein%2C putative%3Bevidence%3DIEA%3Bwith%3DGeneDB:TGME49_268650_t26_1%3Brank%3D1,term%3DClpB%2C putative%3Bevidence%3DIEA%3Bwith%3DGeneDB:TGME49_275690_t26_1%3Brank%3D1;Ontology_term=GO:0019538,GO:0005524,GO:0016887,GO:0008134,GO:0006355

If any useful, this script https://github.com/glaParaBio/genomeAnnotationPipeline/blob/master/scripts/add_hmmsearch_to_gff.py should properly integrate the output of hmmsearch/hmmscan into a gff (not extensively tested!)