LICENSE
README.md
pyproject.toml
src/pufprobe/__init__.py
src/pufprobe/__main__.py
src/pufprobe/cli.py
src/pufprobe/config.py
src/pufprobe/externals.py
src/pufprobe/features.py
src/pufprobe/io_utils.py
src/pufprobe/logging_utils.py
src/pufprobe/models.py
src/pufprobe/ontology.py
src/pufprobe/ontology_names.py
src/pufprobe/workdir.py
src/pufprobe.egg-info/PKG-INFO
src/pufprobe.egg-info/SOURCES.txt
src/pufprobe.egg-info/dependency_links.txt
src/pufprobe.egg-info/entry_points.txt
src/pufprobe.egg-info/requires.txt
src/pufprobe.egg-info/top_level.txt
src/pufprobe/annotate/__init__.py
src/pufprobe/annotate/backfill.py
src/pufprobe/annotate/pipeline.py
src/pufprobe/clustering/__init__.py
src/pufprobe/clustering/mmseqs.py
src/pufprobe/clustering/pycluster.py
src/pufprobe/context/__init__.py
src/pufprobe/context/microsynteny.py
src/pufprobe/context/operons.py
src/pufprobe/context/phyloprofile.py
src/pufprobe/context/pipeline.py
src/pufprobe/embed/__init__.py
src/pufprobe/embed/esm.py
src/pufprobe/embed/fallback.py
src/pufprobe/embed/pipeline.py
src/pufprobe/fold/__init__.py
src/pufprobe/fold/esmfold.py
src/pufprobe/fold/pipeline.py
src/pufprobe/geneqc/__init__.py
src/pufprobe/geneqc/classifier.py
src/pufprobe/prepare/__init__.py
src/pufprobe/prepare/gbk.py
src/pufprobe/prepare/gff.py
src/pufprobe/prepare/pipeline.py
src/pufprobe/rank/__init__.py
src/pufprobe/rank/calibrate.py
src/pufprobe/rank/fuse.py
src/pufprobe/rank/pipeline.py
src/pufprobe/rank/priority.py
src/pufprobe/report/__init__.py
src/pufprobe/report/html_report.py
src/pufprobe/report/pipeline.py
src/pufprobe/search/__init__.py
src/pufprobe/search/foldseek.py
src/pufprobe/search/hhblits.py
src/pufprobe/search/idmapping.py
src/pufprobe/search/mmseqs_search.py
src/pufprobe/search/pipeline.py
src/pufprobe/search/sifts.py
tests/test_clustering.py
tests/test_context.py
tests/test_embed.py
tests/test_fold.py
tests/test_geneqc.py
tests/test_hypothetical_faa.py
tests/test_idmapping.py
tests/test_ontology.py
tests/test_ontology_names.py
tests/test_prepare.py
tests/test_rank.py
tests/test_real_formats.py
tests/test_report_annotate.py
tests/test_search.py
tests/test_smoke.py