LICENSE
MANIFEST.in
PUBLISHING.md
README.md
install_lactoscfa_linux.sh
pyproject.toml
examples/example_hits.tsv
examples/metadata.tsv
examples/test_quickstart/README.md
examples/test_quickstart/hits.tsv
examples/test_quickstart/metadata.tsv
examples/test_quickstart/run_test_example.sh
lactoscfa/__init__.py
lactoscfa/__main__.py
lactoscfa/acid_sets.py
lactoscfa/annotation_scan.py
lactoscfa/benchmark.py
lactoscfa/cli.py
lactoscfa/config.py
lactoscfa/db.py
lactoscfa/env.py
lactoscfa/explain.py
lactoscfa/external.py
lactoscfa/io_utils.py
lactoscfa/manifest.py
lactoscfa/matrix.py
lactoscfa/parse.py
lactoscfa/plot.py
lactoscfa/profile.py
lactoscfa/report.py
lactoscfa/rules.py
lactoscfa/workflow.py
lactoscfa/data/db_v2/acids.tsv
lactoscfa/data/db_v2/evidence_sources.tsv
lactoscfa/data/db_v2/family_aliases.tsv
lactoscfa/data/db_v2/gene_families.tsv
lactoscfa/data/db_v2/manifest.json
lactoscfa/data/db_v2/pathways.toml
lactoscfa/data/db_v2/reference_ec_kegg_crosswalk.tsv
lactoscfa/data/db_v2/reference_proteins.faa
lactoscfa/data/db_v2/reference_proteins.provenance.tsv
lactoscfa/data/db_v2/reference_proteins.summary.tsv
lactoscfa/data/db_v2/reference_query_plan.resolved.tsv
lactoscfa/data/db_v2/thresholds.tsv
scripts/build_reference_db_v2.py
scripts/dev_smoke_test.ps1
scripts/dev_smoke_test.sh
scripts/plot_external_validation_figure.py
scripts/plot_faa117_pathway_schematic.py
scripts/run_faa117_diamond_profile.sh
scripts/run_faa117_diamond_profile_v2.sh
scripts/server_smoke_test.sh
tests/test_score.py