Mercurial > repos > bgruening > agat
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 | |
| children |
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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 @@ -0,0 +1,52 @@ +##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";