Mercurial > repos > bgruening > agat

diff test-data/test16_input.gff @ 6:d6ede73082da draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit df456b8d319fd0a629829fba0f5819117b7936d3
author bgruening
date Fri, 18 Oct 2024 13:34:42 +0000
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test16_input.gff	Fri Oct 18 13:34:42 2024 +0000
@@ -0,0 +1,54 @@
+##gff-version 3
+##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	.	+	.	ID=nbis-gene-2;Name=dnaN;gbkey=Gene;gene=dnaN;gene_biotype=protein_coding;gene_id=nbis-gene-2;locus_tag=C7A06_RS00010
+NZ_CP027599.1	RefSeq	transcript	1052	2152	.	+	.	ID=gene-C7A06_RS00010;Parent=nbis-gene-2;Name=dnaN;gbkey=Gene;gene=dnaN;gene_biotype=protein_coding;gene_id=nbis-gene-2;locus_tag=C7A06_RS00010;original_biotype=mrna;transcript_id=gene-C7A06_RS00010
+NZ_CP027599.1	Protein Homology	exon	1052	2152	.	+	.	ID=nbis-exon-2;Parent=gene-C7A06_RS00010;Dbxref=Genbank:WP_000673464.1;Name=WP_000673464.1;Ontology_term=GO:0006260,GO:0003887,GO:0009360;gbkey=CDS;gene=dnaN;gene_id=nbis-gene-2;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;transcript_id=gene-C7A06_RS00010;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	1052	2152	.	+	0	ID=cds-WP_000673464.1;Parent=gene-C7A06_RS00010;Dbxref=Genbank:WP_000673464.1;Name=WP_000673464.1;Ontology_term=GO:0006260,GO:0003887,GO:0009360;gbkey=CDS;gene=dnaN;gene_id=nbis-gene-2;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;transcript_id=gene-C7A06_RS00010;transl_table=11
+NZ_CP027599.1	RefSeq	gene	2152	3225	.	+	.	ID=nbis-gene-3;Name=recF;gbkey=Gene;gene=recF;gene_biotype=protein_coding;gene_id=nbis-gene-3;locus_tag=C7A06_RS00015
+NZ_CP027599.1	RefSeq	transcript	2152	3225	.	+	.	ID=gene-C7A06_RS00015;Parent=nbis-gene-3;Name=recF;gbkey=Gene;gene=recF;gene_biotype=protein_coding;gene_id=nbis-gene-3;locus_tag=C7A06_RS00015;original_biotype=mrna;transcript_id=gene-C7A06_RS00015
+NZ_CP027599.1	Protein Homology	exon	2152	3225	.	+	.	ID=nbis-exon-3;Parent=gene-C7A06_RS00015;Dbxref=Genbank:WP_000060112.1;Name=WP_000060112.1;Ontology_term=GO:0006281,GO:0003697,GO:0005524;gbkey=CDS;gene=recF;gene_id=nbis-gene-3;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;transcript_id=gene-C7A06_RS00015;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	2152	3225	.	+	0	ID=cds-WP_000060112.1;Parent=gene-C7A06_RS00015;Dbxref=Genbank:WP_000060112.1;Name=WP_000060112.1;Ontology_term=GO:0006281,GO:0003697,GO:0005524;gbkey=CDS;gene=recF;gene_id=nbis-gene-3;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;transcript_id=gene-C7A06_RS00015;transl_table=11
+NZ_CP027599.1	RefSeq	gene	3254	5668	.	+	.	ID=nbis-gene-4;Name=gyrB;gbkey=Gene;gene=gyrB;gene_biotype=protein_coding;gene_id=nbis-gene-4;locus_tag=C7A06_RS00020
+NZ_CP027599.1	RefSeq	transcript	3254	5668	.	+	.	ID=gene-C7A06_RS00020;Parent=nbis-gene-4;Name=gyrB;gbkey=Gene;gene=gyrB;gene_biotype=protein_coding;gene_id=nbis-gene-4;locus_tag=C7A06_RS00020;original_biotype=mrna;transcript_id=gene-C7A06_RS00020
+NZ_CP027599.1	Protein Homology	exon	3254	5668	.	+	.	ID=nbis-exon-4;Parent=gene-C7A06_RS00020;Dbxref=Genbank:WP_000072067.1;Name=WP_000072067.1;Ontology_term=GO:0006265,GO:0003918,GO:0009330;gbkey=CDS;gene=gyrB;gene_id=nbis-gene-4;go_component=DNA topoisomerase type II (double strand cut%2C ATP-hydrolyzing) complex|0009330||IEA;go_function=DNA topoisomerase type II (double strand cut%2C 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;transcript_id=gene-C7A06_RS00020;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	3254	5668	.	+	0	ID=cds-WP_000072067.1;Parent=gene-C7A06_RS00020;Dbxref=Genbank:WP_000072067.1;Name=WP_000072067.1;Ontology_term=GO:0006265,GO:0003918,GO:0009330;gbkey=CDS;gene=gyrB;gene_id=nbis-gene-4;go_component=DNA topoisomerase type II (double strand cut%2C ATP-hydrolyzing) complex|0009330||IEA;go_function=DNA topoisomerase type II (double strand cut%2C 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;transcript_id=gene-C7A06_RS00020;transl_table=11
+NZ_CP027599.1	RefSeq	gene	5908	6306	.	+	.	ID=nbis-gene-5;Name=yidB;gbkey=Gene;gene=yidB;gene_biotype=protein_coding;gene_id=nbis-gene-5;locus_tag=C7A06_RS00025
+NZ_CP027599.1	RefSeq	transcript	5908	6306	.	+	.	ID=gene-C7A06_RS00025;Parent=nbis-gene-5;Name=yidB;gbkey=Gene;gene=yidB;gene_biotype=protein_coding;gene_id=nbis-gene-5;locus_tag=C7A06_RS00025;original_biotype=mrna;transcript_id=gene-C7A06_RS00025
+NZ_CP027599.1	Protein Homology	exon	5908	6306	.	+	.	ID=nbis-exon-5;Parent=gene-C7A06_RS00025;Dbxref=Genbank:WP_000522208.1;Name=WP_000522208.1;gbkey=CDS;gene=yidB;gene_id=nbis-gene-5;inference=COORDINATES: similar to AA sequence:RefSeq:NP_418153.4;locus_tag=C7A06_RS00025;product=YidB family protein;protein_id=WP_000522208.1;transcript_id=gene-C7A06_RS00025;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	5908	6306	.	+	0	ID=cds-WP_000522208.1;Parent=gene-C7A06_RS00025;Dbxref=Genbank:WP_000522208.1;Name=WP_000522208.1;gbkey=CDS;gene=yidB;gene_id=nbis-gene-5;inference=COORDINATES: similar to AA sequence:RefSeq:NP_418153.4;locus_tag=C7A06_RS00025;product=YidB family protein;protein_id=WP_000522208.1;transcript_id=gene-C7A06_RS00025;transl_table=11
+NZ_CP027599.1	RefSeq	gene	6421	7233	.	+	.	ID=nbis-gene-6;Name=yidA;gbkey=Gene;gene=yidA;gene_biotype=protein_coding;gene_id=nbis-gene-6;locus_tag=C7A06_RS00030
+NZ_CP027599.1	RefSeq	transcript	6421	7233	.	+	.	ID=gene-C7A06_RS00030;Parent=nbis-gene-6;Name=yidA;gbkey=Gene;gene=yidA;gene_biotype=protein_coding;gene_id=nbis-gene-6;locus_tag=C7A06_RS00030;original_biotype=mrna;transcript_id=gene-C7A06_RS00030
+NZ_CP027599.1	Protein Homology	exon	6421	7233	.	+	.	ID=nbis-exon-6;Parent=gene-C7A06_RS00030;Dbxref=Genbank:WP_000985541.1;Name=WP_000985541.1;Ontology_term=GO:0016787;gbkey=CDS;gene=yidA;gene_id=nbis-gene-6;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;transcript_id=gene-C7A06_RS00030;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	6421	7233	.	+	0	ID=cds-WP_000985541.1;Parent=gene-C7A06_RS00030;Dbxref=Genbank:WP_000985541.1;Name=WP_000985541.1;Ontology_term=GO:0016787;gbkey=CDS;gene=yidA;gene_id=nbis-gene-6;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;transcript_id=gene-C7A06_RS00030;transl_table=11
+NZ_CP027599.1	RefSeq	gene	7279	7935	.	-	.	ID=nbis-gene-7;Name=C7A06_RS00035;gbkey=Gene;gene_biotype=protein_coding;gene_id=nbis-gene-7;locus_tag=C7A06_RS00035
+NZ_CP027599.1	RefSeq	transcript	7279	7935	.	-	.	ID=gene-C7A06_RS00035;Parent=nbis-gene-7;Name=C7A06_RS00035;gbkey=Gene;gene_biotype=protein_coding;gene_id=nbis-gene-7;locus_tag=C7A06_RS00035;original_biotype=mrna;transcript_id=gene-C7A06_RS00035
+NZ_CP027599.1	Protein Homology	exon	7279	7935	.	-	.	ID=nbis-exon-7;Parent=gene-C7A06_RS00035;Dbxref=Genbank:WP_000772931.1;Name=WP_000772931.1;gbkey=CDS;gene_id=nbis-gene-7;inference=COORDINATES: similar to AA sequence:RefSeq:NP_709504.1;locus_tag=C7A06_RS00035;product=hypothetical protein;protein_id=WP_000772931.1;transcript_id=gene-C7A06_RS00035;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	7279	7935	.	-	0	ID=cds-WP_000772931.1;Parent=gene-C7A06_RS00035;Dbxref=Genbank:WP_000772931.1;Name=WP_000772931.1;gbkey=CDS;gene_id=nbis-gene-7;inference=COORDINATES: similar to AA sequence:RefSeq:NP_709504.1;locus_tag=C7A06_RS00035;product=hypothetical protein;protein_id=WP_000772931.1;transcript_id=gene-C7A06_RS00035;transl_table=11
+NZ_CP027599.1	RefSeq	gene	8213	8902	.	+	.	ID=nbis-gene-8;Name=dgoR;gbkey=Gene;gene=dgoR;gene_biotype=protein_coding;gene_id=nbis-gene-8;locus_tag=C7A06_RS00040
+NZ_CP027599.1	RefSeq	transcript	8213	8902	.	+	.	ID=gene-C7A06_RS00040;Parent=nbis-gene-8;Name=dgoR;gbkey=Gene;gene=dgoR;gene_biotype=protein_coding;gene_id=nbis-gene-8;locus_tag=C7A06_RS00040;original_biotype=mrna;transcript_id=gene-C7A06_RS00040
+NZ_CP027599.1	Protein Homology	exon	8213	8902	.	+	.	ID=nbis-exon-8;Parent=gene-C7A06_RS00040;Dbxref=Genbank:WP_000174305.1;Name=WP_000174305.1;gbkey=CDS;gene=dgoR;gene_id=nbis-gene-8;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;transcript_id=gene-C7A06_RS00040;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	8213	8902	.	+	0	ID=cds-WP_000174305.1;Parent=gene-C7A06_RS00040;Dbxref=Genbank:WP_000174305.1;Name=WP_000174305.1;gbkey=CDS;gene=dgoR;gene_id=nbis-gene-8;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;transcript_id=gene-C7A06_RS00040;transl_table=11
+NZ_CP027599.1	RefSeq	gene	8899	9777	.	+	.	ID=nbis-gene-9;Name=dgoK;gbkey=Gene;gene=dgoK;gene_biotype=protein_coding;gene_id=nbis-gene-9;locus_tag=C7A06_RS00045
+NZ_CP027599.1	RefSeq	transcript	8899	9777	.	+	.	ID=gene-C7A06_RS00045;Parent=nbis-gene-9;Name=dgoK;gbkey=Gene;gene=dgoK;gene_biotype=protein_coding;gene_id=nbis-gene-9;locus_tag=C7A06_RS00045;original_biotype=mrna;transcript_id=gene-C7A06_RS00045
+NZ_CP027599.1	Protein Homology	exon	8899	9777	.	+	.	ID=nbis-exon-9;Parent=gene-C7A06_RS00045;Dbxref=Genbank:WP_000127112.1;Name=WP_000127112.1;gbkey=CDS;gene=dgoK;gene_id=nbis-gene-9;inference=COORDINATES: similar to AA sequence:RefSeq:NP_709506.1;locus_tag=C7A06_RS00045;product=2-dehydro-3-deoxygalactonokinase;protein_id=WP_000127112.1;transcript_id=gene-C7A06_RS00045;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	8899	9777	.	+	0	ID=cds-WP_000127112.1;Parent=gene-C7A06_RS00045;Dbxref=Genbank:WP_000127112.1;Name=WP_000127112.1;gbkey=CDS;gene=dgoK;gene_id=nbis-gene-9;inference=COORDINATES: similar to AA sequence:RefSeq:NP_709506.1;locus_tag=C7A06_RS00045;product=2-dehydro-3-deoxygalactonokinase;protein_id=WP_000127112.1;transcript_id=gene-C7A06_RS00045;transl_table=11
+NZ_CP027599.1	RefSeq	gene	9761	10378	.	+	.	ID=nbis-gene-10;Name=dgoA;gbkey=Gene;gene=dgoA;gene_biotype=protein_coding;gene_id=nbis-gene-10;locus_tag=C7A06_RS00050
+NZ_CP027599.1	RefSeq	transcript	9761	10378	.	+	.	ID=gene-C7A06_RS00050;Parent=nbis-gene-10;Name=dgoA;gbkey=Gene;gene=dgoA;gene_biotype=protein_coding;gene_id=nbis-gene-10;locus_tag=C7A06_RS00050;original_biotype=mrna;transcript_id=gene-C7A06_RS00050
+NZ_CP027599.1	Protein Homology	exon	9761	10378	.	+	.	ID=nbis-exon-10;Parent=gene-C7A06_RS00050;Dbxref=Genbank:WP_001198699.1;Name=WP_001198699.1;gbkey=CDS;gene=dgoA;gene_id=nbis-gene-10;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;transcript_id=gene-C7A06_RS00050;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	9761	10378	.	+	0	ID=cds-WP_001198699.1;Parent=gene-C7A06_RS00050;Dbxref=Genbank:WP_001198699.1;Name=WP_001198699.1;gbkey=CDS;gene=dgoA;gene_id=nbis-gene-10;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;transcript_id=gene-C7A06_RS00050;transl_table=11
+NZ_CP027599.1	RefSeq	gene	10375	11523	.	+	.	ID=nbis-gene-11;Name=dgoD;gbkey=Gene;gene=dgoD;gene_biotype=protein_coding;gene_id=nbis-gene-11;locus_tag=C7A06_RS00055
+NZ_CP027599.1	RefSeq	transcript	10375	11523	.	+	.	ID=gene-C7A06_RS00055;Parent=nbis-gene-11;Name=dgoD;gbkey=Gene;gene=dgoD;gene_biotype=protein_coding;gene_id=nbis-gene-11;locus_tag=C7A06_RS00055;original_biotype=mrna;transcript_id=gene-C7A06_RS00055
+NZ_CP027599.1	Protein Homology	exon	10375	11523	.	+	.	ID=nbis-exon-11;Parent=gene-C7A06_RS00055;Dbxref=Genbank:WP_000705001.1;Name=WP_000705001.1;Ontology_term=GO:0009063,GO:0008869;gbkey=CDS;gene=dgoD;gene_id=nbis-gene-11;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;transcript_id=gene-C7A06_RS00055;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	10375	11523	.	+	0	ID=cds-WP_000705001.1;Parent=gene-C7A06_RS00055;Dbxref=Genbank:WP_000705001.1;Name=WP_000705001.1;Ontology_term=GO:0009063,GO:0008869;gbkey=CDS;gene=dgoD;gene_id=nbis-gene-11;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;transcript_id=gene-C7A06_RS00055;transl_table=11
+NZ_CP027599.1	RefSeq	gene	11598	12935	.	+	.	ID=nbis-gene-12;Name=dgoT;gbkey=Gene;gene=dgoT;gene_biotype=protein_coding;gene_id=nbis-gene-12;locus_tag=C7A06_RS00060
+NZ_CP027599.1	RefSeq	transcript	11598	12935	.	+	.	ID=gene-C7A06_RS00060;Parent=nbis-gene-12;Name=dgoT;gbkey=Gene;gene=dgoT;gene_biotype=protein_coding;gene_id=nbis-gene-12;locus_tag=C7A06_RS00060;original_biotype=mrna;transcript_id=gene-C7A06_RS00060
+NZ_CP027599.1	Protein Homology	exon	11598	12935	.	+	.	ID=nbis-exon-12;Parent=gene-C7A06_RS00060;Dbxref=Genbank:WP_000253455.1;Name=WP_000253455.1;gbkey=CDS;gene=dgoT;gene_id=nbis-gene-12;inference=COORDINATES: similar to AA sequence:RefSeq:NP_709507.1;locus_tag=C7A06_RS00060;product=MFS transporter;protein_id=WP_000253455.1;transcript_id=gene-C7A06_RS00060;transl_table=11
+NZ_CP027599.1	Protein Homology	CDS	11598	12935	.	+	0	ID=cds-WP_000253455.1;Parent=gene-C7A06_RS00060;Dbxref=Genbank:WP_000253455.1;Name=WP_000253455.1;gbkey=CDS;gene=dgoT;gene_id=nbis-gene-12;inference=COORDINATES: similar to AA sequence:RefSeq:NP_709507.1;locus_tag=C7A06_RS00060;product=MFS transporter;protein_id=WP_000253455.1;transcript_id=gene-C7A06_RS00060;transl_table=11