added field to annotation format

q2_amr/amrfinderplus/types/_format.py

@@ -97,6 +97,7 @@ def _validate(self, n_records=None):
             "Name of closest sequence",
             "HMM id",
             "HMM description",
+            "Hierarchy node",
         ]
         header = header_coordinates[:1] + header_coordinates[5:]
         header_obs = pd.read_csv(str(self), sep="\t", nrows=0).columns.tolist()

q2_amr/amrfinderplus/types/tests/data/annotation/coordinates/e026af61-d911-4de3-a957-7e8bf837f30d/amr_annotation.tsv

@@ -1,3 +1,3 @@
-Protein identifier	Contig id	Start	Stop	Strand	Gene symbol	Sequence name	Scope	Element type	Element subtype	Class	Subclass	Method	Target length	Reference sequence length	% Coverage of reference sequence	% Identity to reference sequence	Alignment length	Accession of closest sequence	Name of closest sequence	HMM id	HMM description
-NA	contig01	101	958	+	blaTEM-156	class A beta-lactamase TEM-156	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	ALLELEX	286	286	100.00	100.00	286	WP_061158039.1	class A beta-lactamase TEM-156	NA	NA
-NA	contig02	1	1191	+	blaPDC	PDC family class C beta-lactamase	core	AMR	AMR	BETA-LACTAM	CEPHALOSPORIN	BLASTX	397	397	100.00	99.75	397	WP_061189306.1	class C beta-lactamase PDC-114	NA	NA
+Protein identifier	Gene symbol	Sequence name	Scope	Element type	Element subtype	Class	Subclass	Method	Target length	Reference sequence length	% Coverage of reference sequence	% Identity to reference sequence	Alignment length	Accession of closest sequence	Name of closest sequence	HMM id	HMM description	Hierarchy node
+aph3pp-Ib_partial_5p_neg	aph(3'')-Ib	aminoglycoside O-phosphotransferase APH(3'')-Ib	core	AMR	AMR	AMINOGLYCOSIDE	STREPTOMYCIN	PARTIALP	225	267	81.27	100.00	217	WP_001082319.1	aminoglycoside O-phosphotransferase APH(3'')-Ib	NF032896.1	APH(3'') family aminoglycoside O-phosphotransferase	aph(3'')-Ib
+blaOXA-436_partial	blaOXA	OXA-48 family class D beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALP	233	265	87.92	100.00	233	WP_058842180.1	OXA-48 family carbapenem-hydrolyzing class D beta-lactamase OXA-436	NF012161.0	class D beta-lactamase	blaOXA-48_fam

q2_amr/amrfinderplus/types/tests/data/annotation/no_coordinates/aa447c99-ecd9-4c4a-a53b-4df6999815dd/amr_annotation.tsv

@@ -1,3 +1,3 @@
-Protein identifier	Gene symbol	Sequence name	Scope	Element type	Element subtype	Class	Subclass	Method	Target length	Reference sequence length	% Coverage of reference sequence	% Identity to reference sequence	Alignment length	Accession of closest sequence	Name of closest sequence	HMM id	HMM description
-aph3pp-Ib_partial_5p_neg	aph(3'')-Ib	aminoglycoside O-phosphotransferase APH(3'')-Ib	core	AMR	AMR	AMINOGLYCOSIDE	STREPTOMYCIN	PARTIALP	225	267	81.27	100.00	217	WP_001082319.1	aminoglycoside O-phosphotransferase APH(3'')-Ib	NF032896.1	APH(3'') family aminoglycoside O-phosphotransferase
-blaOXA-436_partial	blaOXA	OXA-48 family class D beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALP	233	265	87.92	100.00	233	WP_058842180.1	OXA-48 family carbapenem-hydrolyzing class D beta-lactamase OXA-436	NF012161.0	class D beta-lactamase
+Protein identifier	Gene symbol	Sequence name	Scope	Element type	Element subtype	Class	Subclass	Method	Target length	Reference sequence length	% Coverage of reference sequence	% Identity to reference sequence	Alignment length	Accession of closest sequence	Name of closest sequence	HMM id	HMM description	Hierarchy node
+aph3pp-Ib_partial_5p_neg	aph(3'')-Ib	aminoglycoside O-phosphotransferase APH(3'')-Ib	core	AMR	AMR	AMINOGLYCOSIDE	STREPTOMYCIN	PARTIALP	225	267	81.27	100.00	217	WP_001082319.1	aminoglycoside O-phosphotransferase APH(3'')-Ib	NF032896.1	APH(3'') family aminoglycoside O-phosphotransferase	aph(3'')-Ib
+blaOXA-436_partial	blaOXA	OXA-48 family class D beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALP	233	265	87.92	100.00	233	WP_058842180.1	OXA-48 family carbapenem-hydrolyzing class D beta-lactamase OXA-436	NF012161.0	class D beta-lactamase	blaOXA-48_fam