├── .appveyor.yml ├── .codecov.yml ├── .github └── workflows │ └── build.yml ├── .gitignore ├── LICENSE.md ├── MANIFEST.in ├── README.md ├── codecov.yml ├── docs ├── Detection-of-GFF3-format-errors.md ├── Detection-of-GFF3-format-errors.rst ├── ERROR_TAG_Location.md ├── FAQ.md ├── I5KNAL_gff-merge_part1.png ├── I5KNAL_gff-merge_part2.png ├── I5KNAL_gff-merge_part3.png ├── Makefile ├── Merge-two-GFF3-files.md ├── conf.py ├── gff3_QC.md ├── gff3_fix.md ├── gff3_fix.py-documentation.md ├── gff3_fix.py-documentation.rst ├── gff3_merge.md ├── gff3_sort.md ├── gff3_to_fasta.md ├── index.rst └── make.bat ├── example_file ├── example.gff3 ├── new_models.gff3 ├── new_models_w_replace.gff3 ├── reference.fa ├── reference.gff3 ├── u1.txt └── u2.txt ├── gff3tool ├── __init__.py ├── bin │ ├── __init__.py │ ├── gff3_QC.py │ ├── gff3_fix.py │ ├── gff3_merge.py │ ├── gff3_sort.py │ ├── gff3_to_fasta.py │ └── version.py ├── lib.md └── lib │ ├── ERROR │ ├── ERROR.py │ └── __init__.py │ ├── __init__.py │ ├── auto_assignment │ ├── create_annotation_summaries_nov21-7.pl │ ├── find_match.pl │ └── gen_spreadsheet.pl │ ├── check_gene_parent │ └── find_wrongly_split_gene_parent.pl │ ├── function4gff │ ├── __init__.py │ └── function4gff.py │ ├── gff3 │ ├── __init__.py │ └── gff3.py │ ├── gff3_ID_generator.py │ ├── gff3_fix │ ├── __init__.py │ └── fix.py │ ├── gff3_merge │ ├── __init__.py │ ├── auto_replace_tag.py │ ├── merge.py │ └── revision.py │ ├── id_processor.py │ ├── inter_model │ ├── __init__.py │ └── inter_model.py │ ├── intra_model │ ├── __init__.py │ └── intra_model.py │ ├── replace_OGS.py │ ├── single_feature │ ├── __init__.py │ └── single_feature.py │ └── utils.py ├── setup.cfg ├── setup.py ├── tests.py └── tests.sh /.appveyor.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NAL-i5K/GFF3toolkit/HEAD/.appveyor.yml -------------------------------------------------------------------------------- /.codecov.yml: 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