├── .github └── workflows │ └── main.yml ├── .gitignore ├── LICENSE ├── MANIFEST.in ├── README.rst ├── deploy.sh ├── doc ├── Makefile ├── make.bat └── source │ ├── _templates │ └── class.rst │ ├── api.rst │ ├── attributes.rst │ ├── changelog.rst │ ├── conf.py │ ├── database-ids.rst │ ├── database-import.rst │ ├── database-schema.rst │ ├── developers.rst │ ├── dialect.rst │ ├── examples.rst │ ├── flybase-FBgn0031208.png │ ├── gtf.rst │ ├── index.rst │ ├── installation.rst │ ├── intro_docs_example.gff │ └── meta.rst ├── docs-requirements.txt ├── gffutils ├── __init__.py ├── attributes.py ├── bins.py ├── biopython_integration.py ├── constants.py ├── contrib │ ├── __init__.py │ └── plotting.py ├── convert.py ├── create.py ├── exceptions.py ├── feature.py ├── gffwriter.py ├── helpers.py ├── inspect.py ├── interface.py ├── iterators.py ├── merge_criteria.py ├── parser.py ├── pybedtools_integration.py ├── scripts │ ├── gffutils-cli │ └── gffutils-flybase-convert.py ├── test │ ├── __init__.py │ ├── attr_test_cases.py │ ├── conftest.py │ ├── data │ │ ├── F3-unique-3.v2.gff │ │ ├── FBgn0031208.gff │ │ ├── FBgn0031208.gtf │ │ ├── Saccharomyces_cerevisiae.R64-1-1.83.5000_gene_ids.txt │ │ ├── Saccharomyces_cerevisiae.R64-1-1.83.5000_transcript_ids.txt │ │ ├── Saccharomyces_cerevisiae.R64-1-1.83.chromsizes.txt │ │ ├── c_elegans_WS199_ann_gff.txt │ │ ├── c_elegans_WS199_dna_shortened.fa │ │ ├── c_elegans_WS199_shortened_gff.txt │ │ ├── dm6-chr2L.fa │ │ ├── dmel-all-no-analysis-r5.49_50k_lines.gff │ │ ├── download-large-annotation-files.sh │ │ ├── ensembl_gtf.txt │ │ ├── gencode-v19.gtf │ │ ├── gencode.vM8.5000_gene_ids.txt │ │ ├── gencode.vM8.5000_transcript_ids.txt │ │ ├── gencode.vM8.chromsizes.txt │ │ ├── gff_example1.gff3 │ │ ├── gff_example1.gff3.gz │ │ ├── glimmer_nokeyval.gff3 │ │ ├── gms2_example.gff3 │ │ ├── hybrid1.gff3 │ │ ├── intro_docs_example.gff │ │ ├── issue167.gff │ │ ├── issue174.gtf │ │ ├── issue_197.gff │ │ ├── jgi_gff2.txt │ │ ├── keep-order-test.gtf │ │ ├── keyval_sep_in_attrs.gff │ │ ├── mouse_extra_comma.gff3 │ │ ├── ncbi_gff3.txt │ │ ├── nonascii │ │ ├── random-chr.gff │ │ ├── sharr.gtf │ │ ├── synthetic.gff3 │ │ ├── unsanitized.gff │ │ ├── wormbase_gff2.txt │ │ └── wormbase_gff2_alt.txt │ ├── expected.py │ ├── feature_test.py │ ├── from-prev-version │ ├── helpers_test.py │ ├── parser_test.py │ ├── performance_evaluation.py │ ├── synth_test_base.py │ ├── test_1.py │ ├── test_biopython_integration.py │ ├── test_cli.py │ ├── test_issues.py │ ├── test_iterators.py │ ├── test_merge.py │ └── test_merge_all.py └── version.py ├── optional-requirements.txt ├── requirements.txt └── setup.py /.github/workflows/main.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/daler/gffutils/HEAD/.github/workflows/main.yml -------------------------------------------------------------------------------- /.gitignore: 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