├── .github └── workflows │ └── test-shigatyper.yml ├── LICENSE ├── MANIFEST.in ├── README.md ├── environment.yaml ├── requirements.txt ├── setup.py └── shigatyper ├── __init__.py ├── resources ├── ShigellaRef5.fasta ├── ShigellaRef5.fasta.fai └── ShigellaRef5.mmi └── shigatyper.py /.github/workflows/test-shigatyper.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CFSAN-Biostatistics/shigatyper/HEAD/.github/workflows/test-shigatyper.yml -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CFSAN-Biostatistics/shigatyper/HEAD/LICENSE -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- 1 | shigatyper/resources/ShigellaRef5.fasta 2 | README.md -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CFSAN-Biostatistics/shigatyper/HEAD/README.md -------------------------------------------------------------------------------- /environment.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CFSAN-Biostatistics/shigatyper/HEAD/environment.yaml -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CFSAN-Biostatistics/shigatyper/HEAD/requirements.txt -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CFSAN-Biostatistics/shigatyper/HEAD/setup.py -------------------------------------------------------------------------------- /shigatyper/__init__.py: -------------------------------------------------------------------------------- 1 | __version__ = '2.0.5' 2 | -------------------------------------------------------------------------------- /shigatyper/resources/ShigellaRef5.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CFSAN-Biostatistics/shigatyper/HEAD/shigatyper/resources/ShigellaRef5.fasta -------------------------------------------------------------------------------- /shigatyper/resources/ShigellaRef5.fasta.fai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CFSAN-Biostatistics/shigatyper/HEAD/shigatyper/resources/ShigellaRef5.fasta.fai -------------------------------------------------------------------------------- /shigatyper/resources/ShigellaRef5.mmi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CFSAN-Biostatistics/shigatyper/HEAD/shigatyper/resources/ShigellaRef5.mmi -------------------------------------------------------------------------------- /shigatyper/shigatyper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CFSAN-Biostatistics/shigatyper/HEAD/shigatyper/shigatyper.py --------------------------------------------------------------------------------