├── .gitignore ├── LICENSE ├── README.md ├── beta_release ├── __pycache__ │ ├── classifiers.cpython-310.pyc │ ├── distributed_utils.cpython-310.pyc │ ├── distributed_utils_v2.cpython-310.pyc │ ├── hmmscan_utils.cpython-310.pyc │ ├── ml_utils.cpython-310.pyc │ ├── ml_utils_batch.cpython-310.pyc │ ├── ml_utils_batched_old.cpython-310.pyc │ ├── parsers.cpython-310.pyc │ └── visualizations.cpython-310.pyc ├── bash_scripts │ ├── eval.sh │ ├── rebuild_profiles.sh │ ├── runner.sh │ ├── target_merged.sh │ ├── target_sharded.sh │ └── train_test.sh ├── examples │ └── Q59325.fasta ├── full_requirements.yml ├── info_files │ ├── maps.pkl │ ├── shard_seqs.pkl │ └── test_pids.pkl ├── logs │ ├── beta_test.err │ ├── beta_test.out │ ├── beta_train.err │ ├── beta_train.out │ ├── beta_trainfull.err │ └── beta_trainfull.out ├── py_scripts │ ├── classifiers.py │ ├── curate_phmmer_old.py │ ├── distributed_utils.py │ ├── distributed_utils_test.py │ ├── eval.py │ ├── full_data_curation.py │ ├── hmmscan_utils.py │ ├── ml_utils.py │ ├── parsers.py │ ├── psalm_test.py │ ├── psalm_test_multi.py │ ├── psalm_train_multi.py │ ├── psalm_viz_batch.py │ ├── target_precomputing.py │ ├── val_creator.py │ └── visualizations.py ├── requirements.yml ├── roc_data │ ├── ROC_final.ipynb │ ├── clan_rocs_100_100.pkl │ ├── clan_rocs_100_20.pkl │ ├── clan_rocs_100_50.pkl │ ├── clan_rocs_20_nu_20.pkl │ ├── clan_rocs_20_nu_50.pkl │ ├── clan_rocs_40_20.pkl │ ├── clan_rocs_40_50.pkl │ ├── clan_rocs_60_20.pkl │ ├── clan_rocs_60_50.pkl │ ├── clan_rocs_80_20.pkl │ ├── clan_rocs_80_50.pkl │ ├── fam_100.pkl │ ├── fam_20.pkl │ ├── fam_20_40e.pkl │ ├── fam_20_50e.pkl │ ├── fam_20_80e.pkl │ ├── fam_40.pkl │ ├── fam_40_60e.pkl │ ├── fam_40_80e.pkl │ ├── fam_60.pkl │ ├── fam_60_30e.pkl │ ├── fam_60_40e.pkl │ ├── fam_60_50e.pkl │ ├── fam_80.pkl │ ├── fam_rocs_100_100.pkl │ ├── fam_rocs_100_20.pkl │ ├── fam_rocs_100_50.pkl │ ├── fam_rocs_20_nu_20.pkl │ ├── fam_rocs_20_nu_50.pkl │ ├── fam_rocs_40_20.pkl │ ├── fam_rocs_40_50.pkl │ ├── fam_rocs_60_20.pkl │ ├── fam_rocs_60_50.pkl │ ├── fam_rocs_80_20.pkl │ └── fam_rocs_80_50.pkl └── wandb │ ├── debug-cli.asarkar.log │ ├── debug-cli.kumareshk.log │ ├── debug-internal.log │ ├── debug.log │ ├── latest-run │ ├── run-20240617_191122-541wvesv │ ├── files │ │ ├── conda-environment.yaml │ │ ├── config.yaml │ │ ├── output.log │ │ ├── requirements.txt │ │ ├── wandb-metadata.json │ │ └── wandb-summary.json │ ├── logs │ │ ├── debug-internal.log │ │ └── debug.log │ └── run-541wvesv.wandb │ ├── run-20240624_153500-txer5c80 │ ├── files │ │ ├── conda-environment.yaml │ │ ├── config.yaml │ │ ├── output.log │ │ ├── requirements.txt │ │ ├── wandb-metadata.json │ │ └── wandb-summary.json │ ├── logs │ │ ├── debug-internal.log │ │ └── debug.log │ └── run-txer5c80.wandb │ ├── run-20240624_153750-oztudpp2 │ ├── files │ │ ├── conda-environment.yaml │ │ ├── config.yaml │ │ ├── output.log │ │ ├── requirements.txt │ │ ├── wandb-metadata.json │ │ └── wandb-summary.json │ ├── logs │ │ ├── debug-internal.log │ │ └── debug.log │ └── run-oztudpp2.wandb │ ├── run-20240624_153954-5uxvtnv1 │ ├── files │ │ ├── conda-environment.yaml │ │ ├── config.yaml │ │ ├── output.log │ │ ├── requirements.txt │ │ ├── wandb-metadata.json │ │ └── wandb-summary.json │ ├── logs │ │ ├── debug-internal.log │ │ └── debug.log │ └── run-5uxvtnv1.wandb │ ├── run-20240624_154414-875gafq3 │ ├── files │ │ ├── conda-environment.yaml │ │ ├── config.yaml │ │ ├── output.log │ │ ├── requirements.txt │ │ ├── wandb-metadata.json │ │ └── wandb-summary.json │ ├── logs │ │ ├── debug-internal.log │ │ └── debug.log │ └── run-875gafq3.wandb │ ├── run-20240624_155100-nf1fb4v7 │ ├── files │ │ ├── conda-environment.yaml │ │ ├── config.yaml │ │ ├── output.log │ │ ├── requirements.txt │ │ └── wandb-metadata.json │ ├── logs │ │ ├── debug-internal.log │ │ └── debug.log │ └── run-nf1fb4v7.wandb │ ├── run-20240624_155944-u7lyh0h0 │ ├── files │ │ ├── conda-environment.yaml │ │ ├── config.yaml │ │ ├── output.log │ │ ├── requirements.txt │ │ ├── wandb-metadata.json │ │ └── wandb-summary.json │ ├── logs │ │ ├── debug-internal.log │ │ └── debug.log │ └── run-u7lyh0h0.wandb │ ├── run-20240624_165046-plsawk6x │ ├── files │ │ ├── conda-environment.yaml │ │ ├── config.yaml │ │ ├── output.log │ │ ├── requirements.txt │ │ ├── wandb-metadata.json │ │ └── wandb-summary.json │ ├── logs │ │ ├── debug-internal.log │ │ └── debug.log │ └── run-plsawk6x.wandb │ ├── run-20240624_165445-kwbnjke9 │ ├── files │ │ ├── conda-environment.yaml │ │ ├── config.yaml │ │ ├── output.log │ │ ├── requirements.txt │ │ ├── wandb-metadata.json │ │ └── wandb-summary.json │ ├── logs │ │ ├── debug-internal.log │ │ └── debug.log │ └── run-kwbnjke9.wandb │ ├── run-20240624_171627-r12xkroa │ ├── files │ │ ├── conda-environment.yaml │ │ ├── config.yaml │ │ ├── output.log │ │ ├── requirements.txt │ │ ├── wandb-metadata.json │ │ └── wandb-summary.json │ ├── logs │ │ ├── debug-internal.log │ │ └── debug.log │ └── run-r12xkroa.wandb │ ├── run-20240625_073656-c28fid7t │ ├── files │ │ ├── conda-environment.yaml │ │ ├── config.yaml │ │ ├── output.log │ │ ├── requirements.txt │ │ ├── wandb-metadata.json │ │ └── wandb-summary.json │ ├── logs │ │ ├── debug-internal.log │ │ └── debug.log │ └── run-c28fid7t.wandb │ ├── run-20240703_170252-e1r7skq4 │ ├── files │ │ ├── conda-environment.yaml │ │ ├── config.yaml │ │ ├── output.log │ │ ├── requirements.txt │ │ └── wandb-metadata.json │ ├── logs │ │ ├── debug-internal.log │ │ └── debug.log │ └── run-e1r7skq4.wandb │ ├── run-20240704_073450-34a3ka8m │ ├── files │ │ ├── conda-environment.yaml │ │ ├── config.yaml │ │ ├── output.log │ │ ├── requirements.txt │ │ └── wandb-metadata.json │ ├── logs │ │ ├── debug-internal.log │ │ └── debug.log │ └── run-34a3ka8m.wandb │ ├── run-20240704_080619-435avaak │ ├── files │ │ ├── conda-environment.yaml │ │ ├── config.yaml │ │ ├── output.log │ │ ├── requirements.txt │ │ └── wandb-metadata.json │ ├── logs │ │ ├── debug-internal.log │ │ └── debug.log │ └── run-435avaak.wandb │ ├── run-20240704_082135-5wil4e1o │ ├── files │ │ ├── conda-environment.yaml │ │ ├── config.yaml │ │ ├── output.log │ │ ├── requirements.txt │ │ ├── wandb-metadata.json │ │ └── wandb-summary.json │ ├── logs │ │ ├── debug-internal.log │ │ └── debug.log │ └── run-5wil4e1o.wandb │ ├── run-20240704_083636-ld2dl3vi │ ├── files │ │ ├── conda-environment.yaml │ │ ├── config.yaml │ │ ├── output.log │ │ ├── requirements.txt │ │ ├── wandb-metadata.json │ │ └── wandb-summary.json │ ├── logs │ │ ├── debug-internal.log │ │ └── debug.log │ └── run-ld2dl3vi.wandb │ ├── run-20240704_085358-dnkn0bj5 │ ├── files │ │ ├── conda-environment.yaml │ │ ├── config.yaml │ │ ├── output.log │ │ ├── requirements.txt │ │ ├── wandb-metadata.json │ │ └── wandb-summary.json │ ├── logs │ │ ├── debug-internal.log │ │ └── debug.log │ └── run-dnkn0bj5.wandb │ ├── run-20240704_094714-ywxh7md8 │ ├── files │ │ ├── conda-environment.yaml │ │ ├── config.yaml │ │ ├── output.log │ │ ├── requirements.txt │ │ ├── wandb-metadata.json │ │ └── wandb-summary.json │ ├── logs │ │ ├── debug-internal.log │ │ └── debug.log │ └── run-ywxh7md8.wandb │ ├── run-20240704_123021-1d78aoel │ ├── files │ │ ├── conda-environment.yaml │ │ ├── config.yaml │ │ ├── output.log │ │ ├── requirements.txt │ │ ├── wandb-metadata.json │ │ └── wandb-summary.json │ ├── logs │ │ ├── debug-internal.log │ │ └── debug.log │ └── run-1d78aoel.wandb │ └── run-20240709_123916-2dxm3vj4 │ ├── files │ ├── conda-environment.yaml │ ├── config.yaml │ ├── output.log │ ├── requirements.txt │ ├── wandb-metadata.json │ └── wandb-summary.json │ ├── logs │ ├── debug-internal.log │ └── debug.log │ └── run-2dxm3vj4.wandb └── protein_sequence_annotation ├── README.md ├── build └── lib │ └── psalm │ ├── __init__.py │ ├── psalm.py │ └── viz_utils.py ├── dist ├── protein-sequence-annotation-1.0.5.tar.gz ├── protein-sequence-annotation-1.0.6.tar.gz ├── protein-sequence-annotation-1.0.7.tar.gz ├── 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