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tutorials for rhapsody v.0.9.7
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‎README.md

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Collection of Jupyter notebooks containing:
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* tutorials for basic and advanced usage of Rhapsody,
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* data and instructions to reproduce results from the main publication.
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Author: Luca Ponzoni, [email protected]

‎tutorials/0-Getting_started/0-Installation_and_basic_usage.ipynb

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"name": "stderr",
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"output_type": "stream",
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"text": [
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"@> You are running Rhapsody v0.9.4\n",
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"@> You are running Rhapsody v0.9.7\n",
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"\n",
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"@> Pre-existing working directory detected: /home/luca/rhapsody\n",
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"@> Pre-existing classifiers found: /home/luca/rhapsody/default_classifiers-sklearn_v0.21.3\n",
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"@> Pre-existing EVmutation metrics found.\n",
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"output_type": "stream",
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"text": [
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"@> Logging into file: rhapsody-log.txt\n",
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"@> Logging started at 2019-11-14 12:21:55.107691\n",
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"@> Logging started at 2019-12-13 14:29:57.750729\n",
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"@> Imported feature set:\n",
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"@> 'wt_PSIC'* \n",
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"@> 'Delta_PSIC'* \n",
@@ -116,20 +117,20 @@
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"@> 'BLOSUM'* \n",
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"@> (* auxiliary feature set)\n",
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"@> Submitting query to PolyPhen-2...\n",
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"@> Query to PolyPhen-2 started in 19.5s.\n",
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"@> Query to PolyPhen-2 started in 0.5s.\n",
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"@> PolyPhen-2 is running...\n",
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"@> Query to PolyPhen-2 completed in 0.1s.\n",
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"@> Query to PolyPhen-2 completed in 19.6s.\n",
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"@> PolyPhen-2's output parsed.\n",
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"@> Sequence-conservation features have been retrieved from PolyPhen-2's output.\n",
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"@> Mapping SAVs to PDB structures...\n",
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"Mapping SAV 'O00238 31 R H' to PDB: 0%| | 0/5 [00:00<?]@> Pickle 'UniprotMap-O00238.pkl' recovered.\n",
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"Mapping SAV 'O00294 496 A T' to PDB: 0%| | 0/5 [00:00<?]@> Pickle 'UniprotMap-O00238.pkl' saved.\n",
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"@> Pickle 'UniprotMap-O00294.pkl' recovered.\n",
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"Mapping SAV 'P01112 58 T R' to PDB: 0%| | 0/5 [00:00<?] @> Pickle 'UniprotMap-O00294.pkl' saved.\n",
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"Mapping SAV 'P01112 58 T R' to PDB: 40%|████ | 2/5 [00:00<00:00] @> Pickle 'UniprotMap-O00294.pkl' saved.\n",
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"@> Pickle 'UniprotMap-P01112.pkl' recovered.\n",
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"Mapping SAV 'P01112 170 K I' to PDB: 100%|██████████| 5/5 [00:00<00:00]\n",
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"@> Pickle 'UniprotMap-P01112.pkl' saved.\n",
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"@> 4 out of 5 SAVs have been mapped to PDB in 0.1s.\n",
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"@> 4 out of 5 SAVs have been mapped to PDB in 0.7s.\n",
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"@> Computing structural and dynamical features from PDB structures...\n",
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"Analizing mutation site 1AA9:A 170: 0%| | 0/5 [00:00<?]@> Pickle 'PDBfeatures-1AA9.pkl' recovered.\n",
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"Analizing mutation site 2FIM:A 443: 0%| | 0/5 [00:00<?]@> Pickle 'PDBfeatures-1AA9.pkl' saved.\n",
@@ -149,13 +150,13 @@
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"@> Pickle 'UniprotMap-P01112.pkl' saved.\n",
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"Mapping SAV 'P01112 170 K I' to Pfam: 100%|██████████| 5/5 [00:00<00:00]\n",
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"@> SAVs have been mapped on Pfam domains and sequence properties have been computed in 0.1s.\n",
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"@> Random Forest classifier imported in 0.3s.\n",
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"@> 3 predictions computed in 0.5s.\n",
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"@> Random Forest classifier imported in 0.4s.\n",
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"@> 3 predictions computed in 0.4s.\n",
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"@> Random Forest classifier imported in 0.4s.\n",
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"@> 4 predictions computed in 0.3s.\n",
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"@> 4 predictions computed in 0.4s.\n",
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"@> Recovering EVmutation data...\n",
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"@> EVmutation scores recovered in 0.1s.\n",
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"@> Logging stopped at 2019-11-14 12:22:20.525105\n",
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"@> EVmutation scores recovered in 0.0s.\n",
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"@> Logging stopped at 2019-12-13 14:30:29.761256\n",
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"@> Closing logfile: rhapsody-log.txt\n"
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]
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}
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"pph2-completed.txt rhapsody-log.txt\n",
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"pph2-full.txt\t rhapsody-pickle.pkl\n",
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"pph2-log.txt\t rhapsody-predictions-full_vs_reduced.txt\n",
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"pph2-short.txt\t rhapsody-predictions.txt\n",
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"pph2-snps.txt\t rhapsody-SAVs.txt\n",
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"pph2-started.txt rhapsody-Uniprot2PDB.txt\n",
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"rhapsody-features.txt\n"
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"pph2-completed.txt rhapsody-log.txt\r\n",
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"pph2-full.txt\t rhapsody-log.txt.1\r\n",
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"pph2-log.txt\t rhapsody-pickle.pkl\r\n",
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"pph2-short.txt\t rhapsody-predictions-full_vs_reduced.txt\r\n",
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"pph2-snps.txt\t rhapsody-predictions.txt\r\n",
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"pph2-started.txt rhapsody-SAVs.txt\r\n",
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"rhapsody-features.txt rhapsody-Uniprot2PDB.txt\r\n"
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]
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}
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],
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{
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"data": {
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"text/plain": [
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"array([('O00294 496 A T', 'known_neu', 0.106 , 0.04059326, 'neutral', 0.351, 'neutral', -3.1479, 'neutral'),\n",
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"array([('O00294 496 A T', 'known_neu', 0.10733333, 0.04343577, 'neutral', 0.351, 'neutral', -3.1479, 'neutral'),\n",
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" ('O00238 31 R H', 'new', nan, nan, '?', 0.219, 'neutral', -2.4718, 'neutral'),\n",
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" ('P01112 58 T R', 'new', 0.9493333 , 0.8930122 , 'deleterious', 1. , 'deleterious', -9.7604, 'deleterious'),\n",
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" ('P01112 30 D E', 'new', 0.10733333, 0.04122762, 'neutral', 0.001, 'neutral', 0.2196, 'neutral'),\n",
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" ('P01112 170 K I', 'new', 0.424 , 0.25303605, 'neutral', 0. , 'neutral', nan, '?')],\n",
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" ('P01112 58 T R', 'new', 0.952 , 0.8950683 , 'deleterious', 1. , 'deleterious', -9.7604, 'deleterious'),\n",
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" ('P01112 30 D E', 'new', 0.122 , 0.0495388 , 'neutral', 0.001, 'neutral', 0.2196, 'neutral'),\n",
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" ('P01112 170 K I', 'new', 0.43533334, 0.25916612, 'neutral', 0. , 'neutral', nan, '?')],\n",
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" dtype=[('SAV coords', '<U50'), ('training info', '<U12'), ('score', '<f4'), ('path. prob.', '<f4'), ('path. class', '<U12'), ('PolyPhen-2 score', '<f4'), ('PolyPhen-2 path. class', '<U12'), ('EVmutation score', '<f4'), ('EVmutation path. class', '<U12')])"
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]
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},

‎tutorials/0-Getting_started/1-How_to_train_custom_classifiers.ipynb

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"output_type": "stream",
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"text": [
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"@> 3918 out of 20361 cases ignored with missing features.\n",
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"@> CV iteration # 1: AUROC = 0.871 AUPRC = 0.932 OOB score = 0.820\n",
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"@> CV iteration # 2: AUROC = 0.874 AUPRC = 0.934 OOB score = 0.818\n",
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"@> CV iteration # 3: AUROC = 0.866 AUPRC = 0.925 OOB score = 0.821\n",
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"@> CV iteration # 4: AUROC = 0.878 AUPRC = 0.934 OOB score = 0.819\n",
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"@> CV iteration # 1: AUROC = 0.871 AUPRC = 0.931 OOB score = 0.820\n",
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"@> CV iteration # 2: AUROC = 0.875 AUPRC = 0.934 OOB score = 0.820\n",
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"@> CV iteration # 3: AUROC = 0.867 AUPRC = 0.926 OOB score = 0.820\n",
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"@> CV iteration # 4: AUROC = 0.878 AUPRC = 0.934 OOB score = 0.818\n",
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"@> CV iteration # 5: AUROC = 0.872 AUPRC = 0.935 OOB score = 0.821\n",
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"@> CV iteration # 6: AUROC = 0.877 AUPRC = 0.937 OOB score = 0.820\n",
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"@> CV iteration # 7: AUROC = 0.871 AUPRC = 0.931 OOB score = 0.820\n",
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"@> CV iteration # 8: AUROC = 0.871 AUPRC = 0.933 OOB score = 0.821\n",
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"@> CV iteration # 9: AUROC = 0.862 AUPRC = 0.923 OOB score = 0.820\n",
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"@> CV iteration #10: AUROC = 0.879 AUPRC = 0.934 OOB score = 0.819\n",
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"@> CV iteration # 6: AUROC = 0.875 AUPRC = 0.935 OOB score = 0.820\n",
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"@> CV iteration # 7: AUROC = 0.871 AUPRC = 0.931 OOB score = 0.819\n",
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"@> CV iteration # 8: AUROC = 0.873 AUPRC = 0.934 OOB score = 0.821\n",
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"@> CV iteration # 9: AUROC = 0.861 AUPRC = 0.922 OOB score = 0.820\n",
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"@> CV iteration #10: AUROC = 0.879 AUPRC = 0.935 OOB score = 0.818\n",
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"@> ------------------------------------------------------------\n",
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"@> Cross-validation summary:\n",
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"@> training dataset size: 16443\n",
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"@> fraction of positives: 0.690\n",
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"@> mean AUROC: 0.872 +/- 0.005\n",
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"@> mean AUPRC: 0.932 +/- 0.004\n",
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"@> mean OOB score: 0.820 +/- 0.001\n",
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"@> optimal cutoff*: 0.711 +/- 0.034\n",
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"@> optimal cutoff*: 0.709 +/- 0.036\n",
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"@> (* argmax of Youden's index)\n",
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"@> feature importances:\n",
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"@> wt_PSIC: 0.143\n",
285-
"@> Delta_PSIC: 0.189\n",
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"@> Delta_PSIC: 0.188\n",
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"@> SASA: 0.068\n",
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"@> ANM_MSF-chain: 0.074\n",
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"@> ANM_effectiveness-chain: 0.078\n",
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"@> ROC plot saved to ROC.png\n",
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"@> ------------------------------------------------------------\n",
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"@> Classifier training summary:\n",
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"@> mean OOB score: 0.821\n",
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"@> mean OOB score: 0.820\n",
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"@> feature importances:\n",
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"@> wt_PSIC: 0.140\n",
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"@> Delta_PSIC: 0.191\n",
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"@> SASA: 0.068\n",
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"@> wt_PSIC: 0.144\n",
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"@> Delta_PSIC: 0.188\n",
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"@> SASA: 0.069\n",
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"@> ANM_MSF-chain: 0.074\n",
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"@> ANM_effectiveness-chain: 0.078\n",
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"@> ANM_sensitivity-chain: 0.071\n",
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"@> stiffness-chain: 0.080\n",
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"@> entropy: 0.098\n",
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"@> ranked_MI: 0.068\n",
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"@> BLOSUM: 0.048\n",
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"@> BLOSUM: 0.047\n",
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"@> new_feature: 0.084\n",
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"@> ------------------------------------------------------------\n",
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"@> Feat. importance plot saved to feat_importances.png\n"
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"We cannot simply use the main interface `rhapsody()`, because the new feature cannot be computed automatically by Rhapsody:"
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]
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},
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{
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"cell_type": "raw",
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"metadata": {},
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"source": [
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"# This will cause an error\n",
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"rh = rd.rhapsody(test_SAVs, main_classifier='custom_classifier.pkl')"
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"We cannot simply use the main interface `rhapsody()`, because the new feature cannot be computed automatically by Rhapsody:\n",
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"```\n",
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"# This would cause an error\n",
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"rh = rd.rhapsody(test_SAVs, main_classifier='custom_classifier.pkl')\n",
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"```"
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{
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"output_type": "stream",
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"text": [
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"@> Submitting query to PolyPhen-2...\n",
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"@> Query to PolyPhen-2 started in 9.9s.\n",
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"@> Query to PolyPhen-2 started in 1.7s.\n",
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"@> PolyPhen-2 is running...\n",
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"@> Query to PolyPhen-2 completed in 9.7s.\n",
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"@> Query to PolyPhen-2 completed in 20.0s.\n",
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"@> PolyPhen-2's output parsed.\n"
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}
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"text": [
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"@> Sequence-conservation features have been retrieved from PolyPhen-2's output.\n",
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"@> Mapping SAVs to PDB structures...\n",
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"Mapping SAV 'O00238 31 R H' to PDB: 0%| | 0/5 [00:00<?]@> WARNING Unable to recover pickle: Pickle UniprotMap-O00238.pkl was too old and was ignored.\n",
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"@> PDB file is found in the local folder (/home/luca/.../3mdy.pdb.gz).\n",
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"@> 858 atoms and 1 coordinate set(s) were parsed in 0.06s.\n",
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"Mapping SAV 'O00294 496 A T' to PDB: 20%|██ | 1/5 [00:01<00:05]@> Pickle 'UniprotMap-O00238.pkl' saved.\n",
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"@> WARNING Unable to recover pickle: Pickle UniprotMap-O00294.pkl was too old and was ignored.\n",
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"@> PDB file is found in the local folder (/home/luca/.../2fim.pdb.gz).\n",
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"@> 456 atoms and 1 coordinate set(s) were parsed in 0.06s.\n",
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"@> PDB file is found in the local folder (/home/luca/.../3c5n.pdb.gz).\n",
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"@> 454 atoms and 1 coordinate set(s) were parsed in 0.17s.\n",
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"@> Chain A in 2FIM was aligned in 0.1s.\n",
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"Mapping SAV 'P01112 58 T R' to PDB: 40%|████ | 2/5 [00:02<00:03] @> Pickle 'UniprotMap-O00294.pkl' saved.\n",
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"Mapping SAV 'O00238 31 R H' to PDB: 0%| | 0/5 [00:00<?]@> Pickle 'UniprotMap-O00238.pkl' recovered.\n",
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"Mapping SAV 'O00294 496 A T' to PDB: 20%|██ | 1/5 [00:00<00:00]@> Pickle 'UniprotMap-O00238.pkl' saved.\n",
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"@> Pickle 'UniprotMap-O00294.pkl' recovered.\n",
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"Mapping SAV 'P01112 58 T R' to PDB: 40%|████ | 2/5 [00:00<00:00] @> Pickle 'UniprotMap-O00294.pkl' saved.\n",
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"@> Pickle 'UniprotMap-P01112.pkl' recovered.\n",
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"Mapping SAV 'P01112 170 K I' to PDB: 100%|██████████| 5/5 [00:02<00:00]\n",
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"@> Pickle 'UniprotMap-P01112.pkl' saved.\n",
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"@> 4 out of 5 SAVs have been mapped to PDB in 2.6s.\n",
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"@> 4 out of 5 SAVs have been mapped to PDB in 2.3s.\n",
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"@> Computing structural and dynamical features from PDB structures...\n",
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"Analizing mutation site 1AA9:A 170: 0%| | 0/5 [00:00<?]@> Pickle 'PDBfeatures-1AA9.pkl' recovered.\n",
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"Analizing mutation site 2FIM:A 443: 0%| | 0/5 [00:00<?]@> Pickle 'PDBfeatures-1AA9.pkl' saved.\n",
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"@> WARNING Unable to recover pickle: Pickle was too old and was ignored.\n",
496-
"@> PDB file is found in the local folder (/home/luca/.../2fim.pdb.gz).\n",
497-
"@> 3841 atoms and 1 coordinate set(s) were parsed in 0.06s.\n",
498-
"@> Running DSSP...\n",
499-
"@> DSSP finished in 1.4s.\n",
500-
"@> Kirchhoff was built in 0.01s.\n",
501-
"@> 223 modes were calculated in 0.61s.\n",
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"@> Hessian was built in 0.18s.\n",
503-
"@> 666 modes were calculated in 0.11s.\n",
504-
"@> Calculating covariance matrix\n",
505-
"@> Covariance matrix calculated in 0.0s.\n",
506-
"@> Calculating perturbation response\n",
507-
"@> Perturbation response matrix calculated in 0.0s.\n",
508-
"@> Perturbation response scanning completed in 0.1s.\n",
509-
"@> Calculating stiffness matrix.\n",
510-
"@> Stiffness matrix calculated in 0.24s.\n",
511-
"@> The range of effective force constant is: 4.581280954242648 to 26.124107763482908.\n",
512-
"Analizing mutation site 4Q21:A 58: 60%|██████ | 3/5 [00:03<00:02] @> Pickle 'PDBfeatures-2FIM.pkl' saved.\n",
484+
"@> Pickle 'PDBfeatures-2FIM.pkl' recovered.\n",
485+
"Analizing mutation site 4Q21:A 58: 0%| | 0/5 [00:00<?] @> Pickle 'PDBfeatures-2FIM.pkl' saved.\n",
513486
"@> Pickle 'PDBfeatures-4Q21.pkl' recovered.\n",
514-
"Analizing mutation site 4Q21:A 30: 60%|██████ | 3/5 [00:03<00:02]@> Pickle 'PDBfeatures-4Q21.pkl' saved.\n",
515-
"Analizing mutation site 4Q21:A 30: 100%|██████████| 5/5 [00:03<00:00]\n",
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"@> PDB features have been computed in 3.1s.\n",
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"Analizing mutation site 4Q21:A 30: 0%| | 0/5 [00:00<?]@> Pickle 'PDBfeatures-4Q21.pkl' saved.\n",
488+
"Analizing mutation site 4Q21:A 30: 100%|██████████| 5/5 [00:00<00:00]\n",
489+
"@> PDB features have been computed in 0.0s.\n",
517490
"@> Computing sequence properties from Pfam domains...\n",
518491
"Mapping SAV 'O00238 31 R H' to Pfam: 0%| | 0/5 [00:00<?]@> Pickle 'UniprotMap-O00238.pkl' recovered.\n",
519-
"@> Retrieving Pfam search results: https://pfam.xfam.org/protein/O00238?output=xml\n",
520-
"@> Pfam search completed in 1.44s.\n",
521-
"@> Query 'O00238' matched 3 Pfam families.\n",
522-
"@> Processing PF01064...\n",
523-
"@> Pfam MSA for PF01064 is written as PF01064_full.sth.\n",
524-
"@> 1768 sequence(s) with 359 residues were parsed in 0.03s.\n",
525-
"@> Number of columns in MSA reduced to 77.\n",
526-
"@> Row occupancy refinement reduced number of rows from 1768 to 1728 in 0.01s.\n",
527-
"@> Sequence identity refinement reduced number of rows from 1728 to 668 in 0.16s.\n",
528-
"@> Mutual information matrix was calculated in 0.02s.\n",
529-
"Mapping SAV 'O00294 496 A T' to Pfam: 20%|██ | 1/5 [00:05<00:23]@> Pickle 'UniprotMap-O00238.pkl' saved.\n",
492+
"Mapping SAV 'O00294 496 A T' to Pfam: 0%| | 0/5 [00:00<?]@> Pickle 'UniprotMap-O00238.pkl' saved.\n",
530493
"@> Pickle 'UniprotMap-O00294.pkl' recovered.\n",
531-
"@> Retrieving Pfam search results: https://pfam.xfam.org/protein/O00294?output=xml\n",
532-
"@> Pfam search completed in 1.07s.\n",
533-
"@> Query 'O00294' matched 1 Pfam families.\n",
534-
"@> Processing PF01167...\n",
535-
"@> Pfam MSA for PF01167 is written as PF01167_full.sth.\n",
536-
"@> 2789 sequence(s) with 1659 residues were parsed in 0.02s.\n",
537-
"@> Number of columns in MSA reduced to 241.\n",
538-
"@> Row occupancy refinement reduced number of rows from 2789 to 2108 in 0.00s.\n",
539-
"@> Sequence identity refinement reduced number of rows from 2108 to 1102 in 1.07s.\n",
540-
"@> Mutual information matrix was calculated in 0.24s.\n",
541-
"Mapping SAV 'P01112 58 T R' to Pfam: 40%|████ | 2/5 [00:14<00:20] @> Pickle 'UniprotMap-O00294.pkl' saved.\n",
494+
"Mapping SAV 'P01112 58 T R' to Pfam: 0%| | 0/5 [00:00<?] @> Pickle 'UniprotMap-O00294.pkl' saved.\n",
542495
"@> Pickle 'UniprotMap-P01112.pkl' recovered.\n",
543-
"Mapping SAV 'P01112 170 K I' to Pfam: 40%|████ | 2/5 [00:14<00:20]@> WARNING Unable to compute Pfam features: No Pfam domain for resid 170.\n",
496+
"Mapping SAV 'P01112 170 K I' to Pfam: 60%|██████ | 3/5 [00:00<00:00]@> WARNING Unable to compute Pfam features: No Pfam domain for resid 170.\n",
544497
"@> Pickle 'UniprotMap-P01112.pkl' saved.\n",
545-
"Mapping SAV 'P01112 170 K I' to Pfam: 100%|██████████| 5/5 [00:14<00:00]\n",
546-
"@> SAVs have been mapped on Pfam domains and sequence properties have been computed in 15.0s.\n",
547-
"@> Random Forest classifier imported in 12.6s.\n",
548-
"@> 3 predictions computed in 0.8s.\n",
498+
"Mapping SAV 'P01112 170 K I' to Pfam: 100%|██████████| 5/5 [00:00<00:00]\n",
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"@> SAVs have been mapped on Pfam domains and sequence properties have been computed in 0.4s.\n",
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"@> Random Forest classifier imported in 22.6s.\n",
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"@> 3 predictions computed in 0.5s.\n",
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"@> Recovering EVmutation data...\n",
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"@> EVmutation scores recovered in 0.1s.\n"
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"@> EVmutation scores recovered in 0.5s.\n"
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]
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},
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{
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"data": {
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"text/plain": [
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"array([('O00294 496 A T', 'known_neu', 0.07533333, 0.02985149, 'neutral', 0.351, 'neutral', -3.1479, 'neutral'),\n",
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"array([('O00294 496 A T', 'known_neu', 0.086 , 0.03065213, 'neutral', 0.351, 'neutral', -3.1479, 'neutral'),\n",
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" ('O00238 31 R H', 'new', nan, nan, '?', 0.219, 'neutral', -2.4718, 'neutral'),\n",
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" ('P01112 58 T R', 'new', 0.9486667 , 0.9037717 , 'deleterious', 1. , 'deleterious', -9.7604, 'deleterious'),\n",
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" ('P01112 30 D E', 'new', 0.126 , 0.04657676, 'neutral', 0.001, 'neutral', 0.2196, 'neutral'),\n",
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" ('P01112 58 T R', 'new', 0.956 , 0.913615 , 'deleterious', 1. , 'deleterious', -9.7604, 'deleterious'),\n",
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" ('P01112 30 D E', 'new', 0.12666667, 0.044859 , 'neutral', 0.001, 'neutral', 0.2196, 'neutral'),\n",
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" ('P01112 170 K I', 'new', nan, nan, '?', 0. , 'neutral', nan, '?')],\n",
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" dtype=[('SAV coords', '<U50'), ('training info', '<U12'), ('score', '<f4'), ('path. prob.', '<f4'), ('path. class', '<U12'), ('PolyPhen-2 score', '<f4'), ('PolyPhen-2 path. class', '<U12'), ('EVmutation score', '<f4'), ('EVmutation path. class', '<U12')])"
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.7.5"
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"version": "3.7.4"
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"nbformat": 4,

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