pcrxn / antismash_gbk_to_table

antismash_gbk_to_table

Installation

pip install https://github.com/socialgene/antismash_gbk_to_table/archive/main.tar.gz

Usage

wget https://antismash-db.secondarymetabolites.org/output/GCF_004339725.1/GCF_004339725.1.zip
mkdir GCF_004339725
unzip -n -d GCF_004339725 GCF_004339725.1.zip

antismash_gbk_to_table --input ./GCF_004339725/*.region*.gbk --output GCF_004339725_table.tsv --header true

Results

cat GCF_004339725_table.tsv

locus	tool	type	start	end	strand	category	contig_edge	neighbouring	product	protocluster_number	candidate_cluster_number	candidate_cluster_numbers	region_number	kind
NZ_SMGK01000001	antismash	protocluster	22733	45843	1		False		LAP	1
NZ_SMGK01000001	antismash	proto_core	32733	35843	1				LAP	1
NZ_SMGK01000001	antismash	cand_cluster	22733	45843	1		False		LAP		1			single
NZ_SMGK01000001	antismash	region	22733	45843	1		False		LAP			1	1
NZ_SMGK01000001	antismash	cand_cluster	558000	645023	1		False		NRPS; T1PKS; NRPS-like		1			neighbouring
NZ_SMGK01000001	antismash	region	558000	645023	1		False		NRPS; T1PKS; NRPS-like			1; 2; 3	2
NZ_SMGK01000001	antismash	protocluster	558000	610087	1		False		NRPS	1
NZ_SMGK01000001	antismash	proto_core	578000	590087	1				NRPS	1
NZ_SMGK01000001	antismash	cand_cluster	558000	610087	1		False		NRPS; T1PKS		2			chemical_hybrid
NZ_SMGK01000001	antismash	protocluster	559358	607310	1		False		T1PKS	2
NZ_SMGK01000001	antismash	proto_core	579358	587310	-1				T1PKS	2
NZ_SMGK01000001	antismash	protocluster	603188	645023	1		False		NRPS-like	3
NZ_SMGK01000001	antismash	proto_core	623188	625023	1				NRPS-like	3
NZ_SMGK01000001	antismash	cand_cluster	603188	645023	1		False		NRPS-like		3			single
NZ_SMGK01000001	antismash	cand_cluster	1172805	1235383	1		False		T3PKS; terpene		1			neighbouring
NZ_SMGK01000001	antismash	region	1172805	1235383	1		False		T3PKS; terpene			1; 2; 3	3
NZ_SMGK01000001	antismash	protocluster	1172805	1213854	1		False		T3PKS	1
NZ_SMGK01000001	antismash	proto_core	1192805	1193854	1				T3PKS	1
NZ_SMGK01000001	antismash	cand_cluster	1172805	1213854	1		False		T3PKS		2			single
NZ_SMGK01000001	antismash	protocluster	1213380	1235383	1		False		terpene	2
NZ_SMGK01000001	antismash	proto_core	1223380	1225383	1				terpene	2
NZ_SMGK01000001	antismash	cand_cluster	1213380	1235383	1		False		terpene		3			single
NZ_SMGK01000002	antismash	protocluster	34229	76787	1		False		NRPS-like	1
NZ_SMGK01000002	antismash	proto_core	54229	56787	-1				NRPS-like	1
NZ_SMGK01000002	antismash	cand_cluster	34229	76787	1		False		NRPS-like		1			single
NZ_SMGK01000002	antismash	region	34229	76787	1		False		NRPS-like			1	1
NZ_SMGK01000002	antismash	protocluster	640246	662158	1		False		terpene	1
NZ_SMGK01000002	antismash	proto_core	650246	652158	1				terpene	1
NZ_SMGK01000002	antismash	cand_cluster	640246	662158	1		False		terpene		1			single
NZ_SMGK01000002	antismash	region	640246	662158	1		False		terpene			1	2
NZ_SMGK01000008	antismash	protocluster	82608	93489	1		False		bacteriocin	1
NZ_SMGK01000008	antismash	proto_core	87608	88489	1				bacteriocin	1
NZ_SMGK01000008	antismash	cand_cluster	82608	93489	1		False		bacteriocin		1			single
NZ_SMGK01000008	antismash	region	82608	93489	1		False		bacteriocin			1	1