.gitignore
.readthedocs.yaml
CHANGELOG.md
Dockerfile
LICENSE
MANIFEST.in
README.md
environment.yml
logging_config.ini
pyproject.toml
pytest.ini
requirements.txt
tox.ini
.github/CONTRIBUTING.md
.github/workflows/pypi_publish.yml
.github/workflows/python_lint.yml
.github/workflows/tests.yml
assets/allele_calling.png
assets/benchmark.ipynb
assets/blast_id_dist.py
assets/mash_blast_correlation.ipynb
assets/mash_blast_correlation.py
assets/requirements_assets.txt
assets/taranis_schema.png
docs/requirements.txt
img/allele_calling_folder.png
img/taranis_diagram_identify_alleles.jpg
taranys/__init__.py
taranys/__main__.py
taranys/allele_calling.py
taranys/analyze_schema.py
taranys/blast.py
taranys/clustering.py
taranys/distance.py
taranys/eval_cluster.py
taranys/inferred_alleles.py
taranys/reference_alleles.py
taranys/seq_cluster.py
taranys/utils.py
taranys.egg-info/PKG-INFO
taranys.egg-info/SOURCES.txt
taranys.egg-info/dependency_links.txt
taranys.egg-info/entry_points.txt
taranys.egg-info/requires.txt
taranys.egg-info/top_level.txt
test/__init__.py
test/MLST_listeria/analyze_schema/lm0002.fasta
test/MLST_listeria/analyze_schema/lmo0011.fasta
test/MLST_listeria/analyze_schema/lmo0019.fasta
test/MLST_listeria/reference_allele/lmo1762.fasta
test/MLST_listeria/reference_allele/lmo1784.fasta
test/profile_MLST_listeria/profiles_csv.csv
test/reference_alleles_mlst_listeria/abcZ.fasta
test/reference_alleles_mlst_listeria/bglA.fasta
test/reference_alleles_mlst_listeria/cat.fasta
test/reference_alleles_mlst_listeria/dapE.fasta
test/reference_alleles_mlst_listeria/dat.fasta
test/reference_alleles_mlst_listeria/ldh.fasta
test/reference_alleles_mlst_listeria/lhkA.fasta
test/reference_listeria/GCF_002213505.1_ASM221350v1_genomic.fna
test/samples_listeria/4122_S1_paired_assembly.fasta
test/samples_listeria/4123_S2_paired_assembly.fasta