diff test-data/annotation_dup.gff @ 4:abba05ead5d7 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 85b3b324f510d5f3c9322ecbdd9636e0c2cb8c07
author bgruening
date Fri, 26 Jul 2024 15:21:48 +0000
parents
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotation_dup.gff	Fri Jul 26 15:21:48 2024 +0000
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+##gtf-version 3
+#!gff-spec-version 1.21
+#!processor NCBI annotwriter
+#!genome-build ASM301845v1
+#!genome-build-accession NCBI_Assembly:GCF_003018455.1
+#!annotation-date 05/25/2022 04:54:31
+#!annotation-source NCBI RefSeq 
+##sequence-region NZ_CP027599.1 1 5942969
+##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=562
+NZ_CP027599.1	RefSeq	gene	1052	2152	.	+	.	gene_id "nbis-gene-2"; ID "nbis-gene-2"; Name "dnaN"; gbkey "Gene"; gene "dnaN"; gene_biotype "protein_coding"; locus_tag "C7A06_RS00010";
+NZ_CP027599.1	RefSeq	transcript	1052	2152	.	+	.	gene_id "nbis-gene-2"; transcript_id "gene-C7A06_RS00010"; ID "gene-C7A06_RS00010"; Name "dnaN"; Parent "nbis-gene-2"; gbkey "Gene"; gene "dnaN"; gene_biotype "protein_coding"; locus_tag "C7A06_RS00010"; original_biotype "mrna";
+NZ_CP027599.1	Protein Homology	exon	1052	2152	.	+	.	gene_id "nbis-gene-2"; transcript_id "gene-C7A06_RS00010"; Dbxref "Genbank:WP_000673464.1"; ID "nbis-exon-2"; Name "WP_000673464.1"; Ontology_term "GO:0006260" "GO:0003887" "GO:0009360"; Parent "gene-C7A06_RS00010"; gbkey "CDS"; gene "dnaN"; go_component "DNA polymerase III complex|0009360||IEA"; go_function "DNA-directed DNA polymerase activity|0003887||IEA"; go_process "DNA replication|0006260||IEA"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_006177590.1"; locus_tag "C7A06_RS00010"; product "DNA polymerase III subunit beta"; protein_id "WP_000673464.1"; transl_table "11";
+NZ_CP027599.1	Protein Homology	CDS	1052	2152	.	+	0	gene_id "nbis-gene-2"; transcript_id "gene-C7A06_RS00010"; Dbxref "Genbank:WP_000673464.1"; ID "cds-WP_000673464.1"; Name "WP_000673464.1"; Ontology_term "GO:0006260" "GO:0003887" "GO:0009360"; Parent "gene-C7A06_RS00010"; gbkey "CDS"; gene "dnaN"; go_component "DNA polymerase III complex|0009360||IEA"; go_function "DNA-directed DNA polymerase activity|0003887||IEA"; go_process "DNA replication|0006260||IEA"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_006177590.1"; locus_tag "C7A06_RS00010"; product "DNA polymerase III subunit beta"; protein_id "WP_000673464.1"; transl_table "11";
+NZ_CP027599.1	RefSeq	transcript	1052	2152	.	+	.	gene_id "nbis-gene-2"; transcript_id "gene-C7A06_RS00011"; ID "gene-C7A06_RS00010"; Name "dnaN"; Parent "nbis-gene-2"; gbkey "Gene"; gene "dnaN"; gene_biotype "protein_coding"; locus_tag "C7A06_RS00010"; original_biotype "mrna";
+NZ_CP027599.1	Protein Homology	exon	1052	2152	.	+	.	gene_id "nbis-gene-2"; transcript_id "gene-C7A06_RS00011"; Dbxref "Genbank:WP_000673464.1"; ID "nbis-exon-2b"; Name "WP_000673464.1"; Ontology_term "GO:0006260" "GO:0003887" "GO:0009360"; Parent "gene-C7A06_RS00010"; gbkey "CDS"; gene "dnaN"; go_component "DNA polymerase III complex|0009360||IEA"; go_function "DNA-directed DNA polymerase activity|0003887||IEA"; go_process "DNA replication|0006260||IEA"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_006177590.1"; locus_tag "C7A06_RS00010"; product "DNA polymerase III subunit beta"; protein_id "WP_000673464.1"; transl_table "11";
+NZ_CP027599.1	Protein Homology	CDS	1052	2152	.	+	0	gene_id "nbis-gene-2"; transcript_id "gene-C7A06_RS00011"; Dbxref "Genbank:WP_000673464.1"; ID "cds-WP_000673464.2"; Name "WP_000673464.2"; Ontology_term "GO:0006260" "GO:0003887" "GO:0009360"; Parent "gene-C7A06_RS00010"; gbkey "CDS"; gene "dnaN"; go_component "DNA polymerase III complex|0009360||IEA"; go_function "DNA-directed DNA polymerase activity|0003887||IEA"; go_process "DNA replication|0006260||IEA"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_006177590.1"; locus_tag "C7A06_RS00010"; product "DNA polymerase III subunit beta"; protein_id "WP_000673464.1"; transl_table "11";
+NZ_CP027599.1	RefSeq	gene	2152	3225	.	+	.	gene_id "nbis-gene-3"; ID "nbis-gene-3"; Name "recF"; gbkey "Gene"; gene "recF"; gene_biotype "protein_coding"; locus_tag "C7A06_RS00015";
+NZ_CP027599.1	RefSeq	transcript	2152	3225	.	+	.	gene_id "nbis-gene-3"; transcript_id "gene-C7A06_RS00015"; ID "gene-C7A06_RS00015"; Name "recF"; Parent "nbis-gene-3"; gbkey "Gene"; gene "recF"; gene_biotype "protein_coding"; locus_tag "C7A06_RS00015"; original_biotype "mrna";
+NZ_CP027599.1	Protein Homology	exon	2152	3225	.	+	.	gene_id "nbis-gene-3"; transcript_id "gene-C7A06_RS00015"; Dbxref "Genbank:WP_000060112.1"; ID "nbis-exon-3"; Name "WP_000060112.1"; Ontology_term "GO:0006281" "GO:0003697" "GO:0005524"; Parent "gene-C7A06_RS00015"; gbkey "CDS"; gene "recF"; go_function "single-stranded DNA binding|0003697||IEA" "ATP binding|0005524||IEA"; go_process "DNA repair|0006281||IEA"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_005121479.1"; locus_tag "C7A06_RS00015"; product "DNA replication/repair protein RecF"; protein_id "WP_000060112.1"; transl_table "11";
+NZ_CP027599.1	Protein Homology	CDS	2152	3225	.	+	0	gene_id "nbis-gene-3"; transcript_id "gene-C7A06_RS00015"; Dbxref "Genbank:WP_000060112.1"; ID "cds-WP_000060112.1"; Name "WP_000060112.1"; Ontology_term "GO:0006281" "GO:0003697" "GO:0005524"; Parent "gene-C7A06_RS00015"; gbkey "CDS"; gene "recF"; go_function "single-stranded DNA binding|0003697||IEA" "ATP binding|0005524||IEA"; go_process "DNA repair|0006281||IEA"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_005121479.1"; locus_tag "C7A06_RS00015"; product "DNA replication/repair protein RecF"; protein_id "WP_000060112.1"; transl_table "11";
+NZ_CP027599.1	RefSeq	gene	3254	5668	.	+	.	gene_id "nbis-gene-4"; ID "nbis-gene-4"; Name "gyrB"; gbkey "Gene"; gene "gyrB"; gene_biotype "protein_coding"; locus_tag "C7A06_RS00020";
+NZ_CP027599.1	RefSeq	transcript	3254	5668	.	+	.	gene_id "nbis-gene-4"; transcript_id "gene-C7A06_RS00020"; ID "gene-C7A06_RS00020"; Name "gyrB"; Parent "nbis-gene-4"; gbkey "Gene"; gene "gyrB"; gene_biotype "protein_coding"; locus_tag "C7A06_RS00020"; original_biotype "mrna";
+NZ_CP027599.1	Protein Homology	exon	3254	5668	.	+	.	gene_id "nbis-gene-4"; transcript_id "gene-C7A06_RS00020"; Dbxref "Genbank:WP_000072067.1"; ID "nbis-exon-4"; Name "WP_000072067.1"; Ontology_term "GO:0006265" "GO:0003918" "GO:0009330"; Parent "gene-C7A06_RS00020"; gbkey "CDS"; gene "gyrB"; go_component "DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex|0009330||IEA"; go_function "DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity|0003918||IEA"; go_process "DNA topological change|0006265||IEA"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_005121480.1"; locus_tag "C7A06_RS00020"; product "DNA topoisomerase (ATP-hydrolyzing) subunit B"; protein_id "WP_000072067.1"; transl_table "11";
+NZ_CP027599.1	Protein Homology	CDS	3254	5668	.	+	0	gene_id "nbis-gene-4"; transcript_id "gene-C7A06_RS00020"; Dbxref "Genbank:WP_000072067.1"; ID "cds-WP_000072067.1"; Name "WP_000072067.1"; Ontology_term "GO:0006265" "GO:0003918" "GO:0009330"; Parent "gene-C7A06_RS00020"; gbkey "CDS"; gene "gyrB"; go_component "DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex|0009330||IEA"; go_function "DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity|0003918||IEA"; go_process "DNA topological change|0006265||IEA"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_005121480.1"; locus_tag "C7A06_RS00020"; product "DNA topoisomerase (ATP-hydrolyzing) subunit B"; protein_id "WP_000072067.1"; transl_table "11";
+NZ_CP027599.1	RefSeq	gene	5908	6306	.	+	.	gene_id "nbis-gene-5"; ID "nbis-gene-5"; Name "yidB"; gbkey "Gene"; gene "yidB"; gene_biotype "protein_coding"; locus_tag "C7A06_RS00025";
+NZ_CP027599.1	RefSeq	transcript	5908	6306	.	+	.	gene_id "nbis-gene-5"; transcript_id "gene-C7A06_RS00025"; ID "gene-C7A06_RS00025"; Name "yidB"; Parent "nbis-gene-5"; gbkey "Gene"; gene "yidB"; gene_biotype "protein_coding"; locus_tag "C7A06_RS00025"; original_biotype "mrna";
+NZ_CP027599.1	Protein Homology	exon	5908	6306	.	+	.	gene_id "nbis-gene-5"; transcript_id "gene-C7A06_RS00025"; Dbxref "Genbank:WP_000522208.1"; ID "nbis-exon-5"; Name "WP_000522208.1"; Parent "gene-C7A06_RS00025"; gbkey "CDS"; gene "yidB"; inference "COORDINATES: similar to AA sequence:RefSeq:NP_418153.4"; locus_tag "C7A06_RS00025"; product "YidB family protein"; protein_id "WP_000522208.1"; transl_table "11";
+NZ_CP027599.1	Protein Homology	CDS	5908	6306	.	+	0	gene_id "nbis-gene-5"; transcript_id "gene-C7A06_RS00025"; Dbxref "Genbank:WP_000522208.1"; ID "cds-WP_000522208.1"; Name "WP_000522208.1"; Parent "gene-C7A06_RS00025"; gbkey "CDS"; gene "yidB"; inference "COORDINATES: similar to AA sequence:RefSeq:NP_418153.4"; locus_tag "C7A06_RS00025"; product "YidB family protein"; protein_id "WP_000522208.1"; transl_table "11";
+NZ_CP027599.1	RefSeq	gene	6421	7233	.	+	.	gene_id "nbis-gene-6"; ID "nbis-gene-6"; Name "yidA"; gbkey "Gene"; gene "yidA"; gene_biotype "protein_coding"; locus_tag "C7A06_RS00030";
+NZ_CP027599.1	RefSeq	transcript	6421	7233	.	+	.	gene_id "nbis-gene-6"; transcript_id "gene-C7A06_RS00030"; ID "gene-C7A06_RS00030"; Name "yidA"; Parent "nbis-gene-6"; gbkey "Gene"; gene "yidA"; gene_biotype "protein_coding"; locus_tag "C7A06_RS00030"; original_biotype "mrna";
+NZ_CP027599.1	Protein Homology	exon	6421	7233	.	+	.	gene_id "nbis-gene-6"; transcript_id "gene-C7A06_RS00030"; Dbxref "Genbank:WP_000985541.1"; ID "nbis-exon-6"; Name "WP_000985541.1"; Ontology_term "GO:0016787"; Parent "gene-C7A06_RS00030"; gbkey "CDS"; gene "yidA"; go_function "hydrolase activity|0016787||IEA"; inference "COORDINATES: similar to AA sequence:RefSeq:NP_418152.1"; locus_tag "C7A06_RS00030"; product "sugar-phosphatase"; protein_id "WP_000985541.1"; transl_table "11";
+NZ_CP027599.1	Protein Homology	CDS	6421	7233	.	+	0	gene_id "nbis-gene-6"; transcript_id "gene-C7A06_RS00030"; Dbxref "Genbank:WP_000985541.1"; ID "cds-WP_000985541.1"; Name "WP_000985541.1"; Ontology_term "GO:0016787"; Parent "gene-C7A06_RS00030"; gbkey "CDS"; gene "yidA"; go_function "hydrolase activity|0016787||IEA"; inference "COORDINATES: similar to AA sequence:RefSeq:NP_418152.1"; locus_tag "C7A06_RS00030"; product "sugar-phosphatase"; protein_id "WP_000985541.1"; transl_table "11";
+NZ_CP027599.1	RefSeq	gene	7279	7935	.	-	.	gene_id "nbis-gene-7"; ID "nbis-gene-7"; Name "C7A06_RS00035"; gbkey "Gene"; gene_biotype "protein_coding"; locus_tag "C7A06_RS00035";
+NZ_CP027599.1	RefSeq	transcript	7279	7935	.	-	.	gene_id "nbis-gene-7"; transcript_id "gene-C7A06_RS00035"; ID "gene-C7A06_RS00035"; Name "C7A06_RS00035"; Parent "nbis-gene-7"; gbkey "Gene"; gene_biotype "protein_coding"; locus_tag "C7A06_RS00035"; original_biotype "mrna";
+NZ_CP027599.1	Protein Homology	exon	7279	7935	.	-	.	gene_id "nbis-gene-7"; transcript_id "gene-C7A06_RS00035"; Dbxref "Genbank:WP_000772931.1"; ID "nbis-exon-7"; Name "WP_000772931.1"; Parent "gene-C7A06_RS00035"; gbkey "CDS"; inference "COORDINATES: similar to AA sequence:RefSeq:NP_709504.1"; locus_tag "C7A06_RS00035"; product "hypothetical protein"; protein_id "WP_000772931.1"; transl_table "11";
+NZ_CP027599.1	Protein Homology	CDS	7279	7935	.	-	0	gene_id "nbis-gene-7"; transcript_id "gene-C7A06_RS00035"; Dbxref "Genbank:WP_000772931.1"; ID "cds-WP_000772931.1"; Name "WP_000772931.1"; Parent "gene-C7A06_RS00035"; gbkey "CDS"; inference "COORDINATES: similar to AA sequence:RefSeq:NP_709504.1"; locus_tag "C7A06_RS00035"; product "hypothetical protein"; protein_id "WP_000772931.1"; transl_table "11";
+NZ_CP027599.1	RefSeq	gene	8213	8902	.	+	.	gene_id "nbis-gene-8"; ID "nbis-gene-8"; Name "dgoR"; gbkey "Gene"; gene "dgoR"; gene_biotype "protein_coding"; locus_tag "C7A06_RS00040";
+NZ_CP027599.1	RefSeq	transcript	8213	8902	.	+	.	gene_id "nbis-gene-8"; transcript_id "gene-C7A06_RS00040"; ID "gene-C7A06_RS00040"; Name "dgoR"; Parent "nbis-gene-8"; gbkey "Gene"; gene "dgoR"; gene_biotype "protein_coding"; locus_tag "C7A06_RS00040"; original_biotype "mrna";
+NZ_CP027599.1	Protein Homology	exon	8213	8902	.	+	.	gene_id "nbis-gene-8"; transcript_id "gene-C7A06_RS00040"; Dbxref "Genbank:WP_000174305.1"; ID "nbis-exon-8"; Name "WP_000174305.1"; Parent "gene-C7A06_RS00040"; gbkey "CDS"; gene "dgoR"; inference "COORDINATES: similar to AA sequence:RefSeq:NP_709505.1"; locus_tag "C7A06_RS00040"; product "D-galactonate utilization transcriptional regulator DgoR"; protein_id "WP_000174305.1"; transl_table "11";
+NZ_CP027599.1	Protein Homology	CDS	8213	8902	.	+	0	gene_id "nbis-gene-8"; transcript_id "gene-C7A06_RS00040"; Dbxref "Genbank:WP_000174305.1"; ID "cds-WP_000174305.1"; Name "WP_000174305.1"; Parent "gene-C7A06_RS00040"; gbkey "CDS"; gene "dgoR"; inference "COORDINATES: similar to AA sequence:RefSeq:NP_709505.1"; locus_tag "C7A06_RS00040"; product "D-galactonate utilization transcriptional regulator DgoR"; protein_id "WP_000174305.1"; transl_table "11";
+NZ_CP027599.1	RefSeq	gene	8899	9777	.	+	.	gene_id "nbis-gene-9"; ID "nbis-gene-9"; Name "dgoK"; gbkey "Gene"; gene "dgoK"; gene_biotype "protein_coding"; locus_tag "C7A06_RS00045";
+NZ_CP027599.1	RefSeq	transcript	8899	9777	.	+	.	gene_id "nbis-gene-9"; transcript_id "gene-C7A06_RS00045"; ID "gene-C7A06_RS00045"; Name "dgoK"; Parent "nbis-gene-9"; gbkey "Gene"; gene "dgoK"; gene_biotype "protein_coding"; locus_tag "C7A06_RS00045"; original_biotype "mrna";
+NZ_CP027599.1	Protein Homology	exon	8899	9777	.	+	.	gene_id "nbis-gene-9"; transcript_id "gene-C7A06_RS00045"; Dbxref "Genbank:WP_000127112.1"; ID "nbis-exon-9"; Name "WP_000127112.1"; Parent "gene-C7A06_RS00045"; gbkey "CDS"; gene "dgoK"; inference "COORDINATES: similar to AA sequence:RefSeq:NP_709506.1"; locus_tag "C7A06_RS00045"; product "2-dehydro-3-deoxygalactonokinase"; protein_id "WP_000127112.1"; transl_table "11";
+NZ_CP027599.1	Protein Homology	CDS	8899	9777	.	+	0	gene_id "nbis-gene-9"; transcript_id "gene-C7A06_RS00045"; Dbxref "Genbank:WP_000127112.1"; ID "cds-WP_000127112.1"; Name "WP_000127112.1"; Parent "gene-C7A06_RS00045"; gbkey "CDS"; gene "dgoK"; inference "COORDINATES: similar to AA sequence:RefSeq:NP_709506.1"; locus_tag "C7A06_RS00045"; product "2-dehydro-3-deoxygalactonokinase"; protein_id "WP_000127112.1"; transl_table "11";
+NZ_CP027599.1	RefSeq	gene	9761	10378	.	+	.	gene_id "nbis-gene-10"; ID "nbis-gene-10"; Name "dgoA"; gbkey "Gene"; gene "dgoA"; gene_biotype "protein_coding"; locus_tag "C7A06_RS00050";
+NZ_CP027599.1	RefSeq	transcript	9761	10378	.	+	.	gene_id "nbis-gene-10"; transcript_id "gene-C7A06_RS00050"; ID "gene-C7A06_RS00050"; Name "dgoA"; Parent "nbis-gene-10"; gbkey "Gene"; gene "dgoA"; gene_biotype "protein_coding"; locus_tag "C7A06_RS00050"; original_biotype "mrna";
+NZ_CP027599.1	Protein Homology	exon	9761	10378	.	+	.	gene_id "nbis-gene-10"; transcript_id "gene-C7A06_RS00050"; Dbxref "Genbank:WP_001198699.1"; ID "nbis-exon-10"; Name "WP_001198699.1"; Parent "gene-C7A06_RS00050"; gbkey "CDS"; gene "dgoA"; inference "COORDINATES: similar to AA sequence:RefSeq:YP_026238.1"; locus_tag "C7A06_RS00050"; product "2-dehydro-3-deoxy-6-phosphogalactonate aldolase"; protein_id "WP_001198699.1"; transl_table "11";
+NZ_CP027599.1	Protein Homology	CDS	9761	10378	.	+	0	gene_id "nbis-gene-10"; transcript_id "gene-C7A06_RS00050"; Dbxref "Genbank:WP_001198699.1"; ID "cds-WP_001198699.1"; Name "WP_001198699.1"; Parent "gene-C7A06_RS00050"; gbkey "CDS"; gene "dgoA"; inference "COORDINATES: similar to AA sequence:RefSeq:YP_026238.1"; locus_tag "C7A06_RS00050"; product "2-dehydro-3-deoxy-6-phosphogalactonate aldolase"; protein_id "WP_001198699.1"; transl_table "11";
+NZ_CP027599.1	RefSeq	gene	10375	11523	.	+	.	gene_id "nbis-gene-11"; ID "nbis-gene-11"; Name "dgoD"; gbkey "Gene"; gene "dgoD"; gene_biotype "protein_coding"; locus_tag "C7A06_RS00055";
+NZ_CP027599.1	RefSeq	transcript	10375	11523	.	+	.	gene_id "nbis-gene-11"; transcript_id "gene-C7A06_RS00055"; ID "gene-C7A06_RS00055"; Name "dgoD"; Parent "nbis-gene-11"; gbkey "Gene"; gene "dgoD"; gene_biotype "protein_coding"; locus_tag "C7A06_RS00055"; original_biotype "mrna";
+NZ_CP027599.1	Protein Homology	exon	10375	11523	.	+	.	gene_id "nbis-gene-11"; transcript_id "gene-C7A06_RS00055"; Dbxref "Genbank:WP_000705001.1"; ID "nbis-exon-11"; Name "WP_000705001.1"; Ontology_term "GO:0009063" "GO:0008869"; Parent "gene-C7A06_RS00055"; gbkey "CDS"; gene "dgoD"; go_function "galactonate dehydratase activity|0008869||IEA"; go_process "cellular amino acid catabolic process|0009063||IEA"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_020077623.1"; locus_tag "C7A06_RS00055"; product "galactonate dehydratase"; protein_id "WP_000705001.1"; transl_table "11";
+NZ_CP027599.1	Protein Homology	CDS	10375	11523	.	+	0	gene_id "nbis-gene-11"; transcript_id "gene-C7A06_RS00055"; Dbxref "Genbank:WP_000705001.1"; ID "cds-WP_000705001.1"; Name "WP_000705001.1"; Ontology_term "GO:0009063" "GO:0008869"; Parent "gene-C7A06_RS00055"; gbkey "CDS"; gene "dgoD"; go_function "galactonate dehydratase activity|0008869||IEA"; go_process "cellular amino acid catabolic process|0009063||IEA"; inference "COORDINATES: similar to AA sequence:RefSeq:WP_020077623.1"; locus_tag "C7A06_RS00055"; product "galactonate dehydratase"; protein_id "WP_000705001.1"; transl_table "11";