# HG changeset patch # User bgruening # Date 1729258482 0 # Node ID d6ede73082da923b1fc681bfff774cd502e82170 # Parent e7449b2c14bf2255dfbf7b70315d7ff60fbe07ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit df456b8d319fd0a629829fba0f5819117b7936d3 diff -r e7449b2c14bf -r d6ede73082da agat.xml --- a/agat.xml Wed Aug 07 20:54:27 2024 +0000 +++ b/agat.xml Fri Oct 18 13:34:42 2024 +0000 @@ -143,12 +143,19 @@ --config '$agat_configfile' --output ./output && cat ./output > '${annotation}' + #else if $tool.selector == 'fix_overlapping_genes' + @input_annotation_single@ + agat_sp_fix_overlaping_genes.pl + --gff '$input_annotation' + --config '$agat_configfile' + --output ./output && + cat ./output > '${annotation}' #end if ]]> Merge annotations (agat_sp_merge_annotations.pl) + @@ -333,6 +341,10 @@ + + + + @@ -343,7 +355,7 @@ tool['selector'] == 'convert_GFF2GTF' - tool['selector'] in ['fix','merge_annotations','complement','filter_feature_fasta','splice_sites','bam2gff','keep_longest_isoform'] + tool['selector'] in ['fix','merge_annotations','complement','filter_feature_fasta','splice_sites','bam2gff','keep_longest_isoform', 'fix_overlapping_genes'] @@ -566,6 +578,14 @@ + + + + + + + + 1.4.0 - 0 + 1 agat diff -r e7449b2c14bf -r d6ede73082da test-data/functional_annot/report.txt --- a/test-data/functional_annot/report.txt Wed Aug 07 20:54:27 2024 +0000 +++ b/test-data/functional_annot/report.txt Fri Oct 18 13:34:42 2024 +0000 @@ -1,5 +1,5 @@ -08/07/2024 -usage: /usr/local/bin/agat_sp_manage_functional_annotation.pl --gff annotation.gff3 --interpro /tmp/tmpfrax2fi0/files/1/a/8/dataset_1a8bf643-33d2-43bd-b647-4dc301ad8c40.dat -pe 5 -o galaxy_functional_annot +10/18/2024 +usage: /usr/local/bin/agat_sp_manage_functional_annotation.pl --gff annotation.gff3 --interpro /tmp/tmp710ob4jc/files/9/4/a/dataset_94a00ae6-101b-4441-816d-7fe1c480f05b.dat -pe 5 -o galaxy_functional_annot -------------------------------------------------------------------------------- ------------------------------------- mrna ------------------------------------- diff -r e7449b2c14bf -r d6ede73082da test-data/test01_plot1.pdf Binary file test-data/test01_plot1.pdf has changed diff -r e7449b2c14bf -r d6ede73082da test-data/test16.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test16.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 diff -r e7449b2c14bf -r d6ede73082da test-data/test16_input.gff --- /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