├── .github ├── ISSUE_TEMPLATE.md └── workflows │ ├── pythonpackage.yml │ └── pythonpublish.yml ├── .gitignore ├── AUTHORS.rst ├── CHANGELOG.md ├── LICENSE ├── README.rst ├── emapper2gbk ├── __init__.py ├── __main__.py ├── emapper2gbk.py ├── genes_to_gbk.py ├── genomes_to_gbk.py └── utils.py ├── pictures ├── emapper2gbk_genes.svg └── emapper2gbk_genomes.svg ├── pyproject.toml ├── requirements.txt └── tests ├── __init__.py ├── go-basic.obo ├── test_data ├── ann │ ├── gene_1781.tsv │ ├── gene_1887.tsv │ ├── gene_2441.tsv │ └── genes_3987_3988.tsv ├── ann_genomes │ ├── gene_1781.tsv │ ├── gene_1887.tsv │ ├── gene_2441.tsv │ └── genes_3987_3988.tsv ├── betaox_annotation.tsv ├── betaox_annotation_genomes.tsv ├── betaox_from_gff.gbk ├── betaox_genes.faa ├── betaox_genes.fna ├── betaox_genomes.faa ├── betaox_genomes.fna ├── betaox_genomes.gff ├── betaox_no_gff.gbk ├── betaox_no_gff_merged.gbk ├── betaox_v2.emapper.annotations ├── data_eggnog │ ├── eggnog_expected.gbk │ ├── out.emapper.annotations │ ├── out.emapper.decorated.gff │ ├── out.emapper.genepred.fasta │ ├── out.emapper.genepred.gff │ └── queries.fasta ├── data_gff_type_accession │ ├── betaox_genomes_CDS.gff │ ├── betaox_genomes_gene.gff │ └── betaox_genomes_mRNA.gff ├── data_gmove │ ├── betaox_genomes.faa │ ├── betaox_genomes.fna │ ├── betaox_genomes.gff │ └── betaox_v2.emapper.annotations ├── faa │ ├── gene_1781.faa │ ├── gene_1887.faa │ ├── gene_2441.faa │ └── genes_3987_3988.faa ├── faa_genomes │ ├── gene_1781.faa │ ├── gene_1887.faa │ ├── gene_2441.faa │ └── genes_3987_3988.faa ├── fna │ ├── gene_1781.fna │ ├── gene_1887.fna │ ├── gene_2441.fna │ └── genes_3987_3988.fna ├── fna_genomes_mode │ ├── gene_1781.fna │ ├── gene_1887.fna │ ├── gene_2441.fna │ └── genes_3987_3988.fna ├── gff │ ├── gene_1781.gff │ ├── gene_1887.gff │ ├── gene_2441.gff │ └── genes_3987_3988.gff ├── numeric │ ├── betaox.gbk │ ├── betaox_annotation.tsv │ ├── betaox_genes.faa │ ├── betaox_genes.fna │ ├── 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