{
 "format": "oscr-script-manifest/1",
 "repository": "github.com/ljw20180420/cop",
 "url": "https://github.com/ljw20180420/COP",
 "host": "github.com",
 "commit": "353997b21fa1b80fc71654e48a3c406c70572702",
 "license": "MIT",
 "license_confirmed_by": "license file LICENSE.md",
 "redistribution": "yes",
 "files": [
  {
   "path": "AI/dataset.py",
   "sha256": "6115e36198a8fe1a309f63abacc4f2860d7fae47fd7e85530da49a992cec87f9",
   "language": "Python",
   "lines": 31,
   "truncated": false,
   "block": 6,
   "row": 24047
  },
  {
   "path": "AI/dataset/extra/scripts/transform_protein_feature.py",
   "sha256": "db6cb6d10cd45ec7f9832061d253042274e36e306e088216c0e4c53fe1fa79fc",
   "language": "Python",
   "lines": 77,
   "truncated": false,
   "block": 6,
   "row": 35154
  },
  {
   "path": "AI/dataset/run.sh",
   "sha256": "0fc98c91e68a5c2c0eb361cfa36cd41de871047c34a1c07f7448d9884b87c61b",
   "language": "Shell",
   "lines": 382,
   "truncated": false,
   "block": 8,
   "row": 9304
  },
  {
   "path": "AI/dataset/scripts/assess_SRR.py",
   "sha256": "e9d45b67c491297ddbb7093212561a6134d87691e6fe7720d73e53dfb5c447cf",
   "language": "Python",
   "lines": 34,
   "truncated": false,
   "block": 6,
   "row": 26488
  },
  {
   "path": "AI/dataset/scripts/assess_peak_width.py",
   "sha256": "9f5cb564837b061d47e7d6fdbb2fa1b4ef941ee39292d129d5c4cf350703a848",
   "language": "Python",
   "lines": 19,
   "truncated": false,
   "block": 6,
   "row": 22871
  },
  {
   "path": "AI/dataset/scripts/balance_data.py",
   "sha256": "32d18d3837be6c6b563ad7355bf31551c86438eb8c8e9fcbba5137d68b6b72ca",
   "language": "Python",
   "lines": 43,
   "truncated": false,
   "block": 6,
   "row": 29151
  },
  {
   "path": "AI/dataset/scripts/download_alphafoldDB_mmcif.py",
   "sha256": "890c8f31814c71a770947030c664e8cb7438e44e42683131324cc7e9aa61f8e2",
   "language": "Python",
   "lines": 44,
   "truncated": false,
   "block": 6,
   "row": 28388
  },
  {
   "path": "AI/dataset/scripts/download_uniprot_C2H2_protein_table.py",
   "sha256": "618dbf5f22154a907566fcac950919595ac6217912e8e780bfde15053d0e99f5",
   "language": "Python",
   "lines": 45,
   "truncated": false,
   "block": 6,
   "row": 27785
  },
  {
   "path": "AI/dataset/scripts/generate_unittest_data.py",
   "sha256": "ac7ef7f12a6848c0838fd6f363ea3d8a48c88d11c455fca667b15b32b52b1752",
   "language": "Python",
   "lines": 15,
   "truncated": false,
   "block": 6,
   "row": 22350
  },
  {
   "path": "AI/dataset/scripts/get_pCBS.py",
   "sha256": "7b2d06061161976bd163af137726310674b672a363f83917287bee2aa653894a",
   "language": "Python",
   "lines": 63,
   "truncated": false,
   "block": 6,
   "row": 32165
  },
  {
   "path": "AI/dataset/scripts/parse_protein_feature.py",
   "sha256": "bc6b0cbd7e867ab2f4be2b3324aee7a62d139d2151680da8a2658de9abedbbac",
   "language": "Python",
   "lines": 60,
   "truncated": false,
   "block": 6,
   "row": 29092
  },
  {
   "path": "AI/dataset/scripts/sample_data.py",
   "sha256": "d77d628777d3c3d98b264de2e6034146f5f4566b483805e3c456de532bd95349",
   "language": "Python",
   "lines": 23,
   "truncated": false,
   "block": 6,
   "row": 23391
  },
  {
   "path": "AI/dataset/scripts/select_SRR.py",
   "sha256": "2f18550daa81b1c2bf72a85d887232b006a46fc8e267af7d2b1b828e39973cf0",
   "language": "Python",
   "lines": 22,
   "truncated": false,
   "block": 6,
   "row": 23759
  },
  {
   "path": "AI/dataset/scripts/select_seed.py",
   "sha256": "bf95ab4f4d381097e4ede55cac1f0dd2781ce42d8989dd76294c0f7ed792ded1",
   "language": "Python",
   "lines": 27,
   "truncated": false,
   "block": 6,
   "row": 23638
  },
  {
   "path": "AI/dataset/scripts/split_data.py",
   "sha256": "71d7a6f14418c7bf263e4d0ba6084c3deefa1972ffc453f9c7ad8afe80aa99f4",
   "language": "Python",
   "lines": 22,
   "truncated": false,
   "block": 6,
   "row": 23852
  },
  {
   "path": "AI/gradio_fn.py",
   "sha256": "5165c6454208c17694dd2343849b55a6dfdddeef6e0065a3db7a78a0d7357fc8",
   "language": "Python",
   "lines": 58,
   "truncated": false,
   "block": 6,
   "row": 33129
  },
  {
   "path": "AI/inference.py",
   "sha256": "1abeddb62fc0b3ec20fbe49f6279d8803214d42ea7a571159e37d5de4e524821",
   "language": "Python",
   "lines": 44,
   "truncated": false,
   "block": 6,
   "row": 28185
  },
  {
   "path": "AI/metric.py",
   "sha256": "0063e590b56340fa62c2ecb687af24dc34ba998c145f90379dd252242eba404a",
   "language": "Python",
   "lines": 326,
   "truncated": false,
   "block": 7,
   "row": 2351
  },
  {
   "path": "AI/metric/accuracy.py",
   "sha256": "13c80a4b9777ae25ced377fc1fb74be243653fe233ddc711388c34918f5f63e4",
   "language": "Python",
   "lines": 106,
   "truncated": false,
   "block": 6,
   "row": 39340
  },
  {
   "path": "AI/metric/brier_score.py",
   "sha256": "6cf92c48aa7f956272e25732e3956bd3a6d863b06ddc4e25672b0992fff80e4c",
   "language": "Python",
   "lines": 134,
   "truncated": false,
   "block": 6,
   "row": 41337
  },
  {
   "path": "AI/metric/confusion_matrix.py",
   "sha256": "30d60b0809eaba3f2f7ef68f14749a904aa7d91ef0c0012fd18b710b1de47459",
   "language": "Python",
   "lines": 88,
   "truncated": false,
   "block": 6,
   "row": 37910
  },
  {
   "path": "AI/metric/f1.py",
   "sha256": "dbe4c6e47b60910b5e091952f528fb6efdf52fc90d65056a34ae96a2fc8e2ee0",
   "language": "Python",
   "lines": 130,
   "truncated": false,
   "block": 6,
   "row": 44631
  },
  {
   "path": "AI/metric/matthews_correlation.py",
   "sha256": "4d066d1a695034fc2765339ca2fe6acf64d8c6a0966ff7c1303f614694c6ef5b",
   "language": "Python",
   "lines": 140,
   "truncated": false,
   "block": 6,
   "row": 44336
  },
  {
   "path": "AI/metric/precision.py",
   "sha256": "2937eca901b5798f1d9046b874ce4afa117faeb1ea481a7735cf64b03f72813f",
   "language": "Python",
   "lines": 145,
   "truncated": false,
   "block": 7,
   "row": 191
  },
  {
   "path": "AI/metric/recall.py",
   "sha256": "e6dc65e223b2273797e7f4fe19957400c51725a02ef4e1921cee643191522ec6",
   "language": "Python",
   "lines": 135,
   "truncated": false,
   "block": 6,
   "row": 45529
  },
  {
   "path": "AI/metric/roc_auc.py",
   "sha256": "27e8c3af5e2944f5ea955d2bf848c7bf0438b7461a2d84d6ccab3e90f4d67ee8",
   "language": "Python",
   "lines": 191,
   "truncated": false,
   "block": 7,
   "row": 2419
  },
  {
   "path": "AI/preprocess/COP/encoder.py",
   "sha256": "c313a33d999c5fd83a4c132eac458e867645b6ea61d7ea5ddebebf787f13ec56",
   "language": "Python",
   "lines": 413,
   "truncated": false,
   "block": 7,
   "row": 6336
  },
  {
   "path": "AI/preprocess/COP/model.py",
   "sha256": "b17e250edd3a7b8c11e276f7148a87f89448b4e1d33d861167b3c61e474b954f",
   "language": "Python",
   "lines": 235,
   "truncated": false,
   "block": 6,
   "row": 45533
  },
  {
   "path": "AI/preprocess/DeepZF/data_collator.py",
   "sha256": "a4a2bb0aa83a4a201aad80579bb1e76539315ac395a86aec2c68ecb7bc6773b5",
   "language": "Python",
   "lines": 74,
   "truncated": false,
   "block": 6,
   "row": 32968
  },
  {
   "path": "AI/preprocess/DeepZF/model.py",
   "sha256": "350d62978e33da84efd0f73d2a8e779a6e254bd249c6d706f9ff652839bac351",
   "language": "Python",
   "lines": 337,
   "truncated": false,
   "block": 7,
   "row": 4396
  },
  {
   "path": "AI/preprocess/LightGBM/model.py",
   "sha256": "5b07b0fccf0d01c989d945c7c3f00cb048706a31a7b9816d24b1811f07992618",
   "language": "Python",
   "lines": 205,
   "truncated": false,
   "block": 6,
   "row": 44565
  },
  {
   "path": "AI/preprocess/Scikit/model.py",
   "sha256": "1dd8647e9c74aa38cb0179e4d842dfce2a7460c30854d5213a0bf80bbd631281",
   "language": "Python",
   "lines": 346,
   "truncated": false,
   "block": 7,
   "row": 3965
  },
  {
   "path": "AI/preprocess/XGBoost/model.py",
   "sha256": "6f4b99e526759ccc7a5cd8a40afc4965973d67a0a0a5e7faf0bfbc49d2ce45fc",
   "language": "Python",
   "lines": 306,
   "truncated": false,
   "block": 7,
   "row": 3164
  },
  {
   "path": "AI/preprocess/data_collator.py",
   "sha256": "20bcc1aae2f33b692a50c36435e3b1b1232abab3faf44ea930facbd7fa6cf9ac",
   "language": "Python",
   "lines": 139,
   "truncated": false,
   "block": 6,
   "row": 40963
  },
  {
   "path": "AI/preprocess/model.py",
   "sha256": "9dcf1832791a3f53827351ec967ce451a1c4c706fdd1f03a75d7038bc78398cc",
   "language": "Python",
   "lines": 71,
   "truncated": false,
   "block": 6,
   "row": 31514
  },
  {
   "path": "DeepZF/BindZFPredictor.ipynb",
   "sha256": "8b0db9844707294a0127100d9f331476450f18845d1cfb0173e1740e1ed4c51f",
   "language": "Jupyter",
   "lines": 30,
   "truncated": false,
   "block": 5,
   "row": 16058
  },
  {
   "path": "DeepZF/BindZF_predictor/code/create_zf_pred_df_and_cal_auc.py",
   "sha256": "57b4a6fbb881601fef050368339c9a3010d632a3901ea213b1129a8f09a9d95d",
   "language": "Python",
   "lines": 54,
   "truncated": false,
   "block": 6,
   "row": 31716
  },
  {
   "path": "DeepZF/BindZF_predictor/code/finetuning.py",
   "sha256": "83af420534f07c5728f03c2287241d9bbaa99c57208944d7e565aa1694848520",
   "language": "Python",
   "lines": 249,
   "truncated": false,
   "block": 7,
   "row": 3460
  },
  {
   "path": "DeepZF/BindZF_predictor/code/main_bindzfpredictor_predict.py",
   "sha256": "9708803f229b3f2686f997ed38bf896dc2bd86d381661e52eafb2f4f9586f491",
   "language": "Python",
   "lines": 140,
   "truncated": false,
   "block": 6,
   "row": 38316
  },
  {
   "path": "DeepZF/BindZF_predictor/code/main_loo_bindzfpredictor.py",
   "sha256": "6ea5f59a40cf67278c709bdbac8492126793baa4f211578e3b4b6c1697dbdfd8",
   "language": "Python",
   "lines": 94,
   "truncated": false,
   "block": 6,
   "row": 39236
  },
  {
   "path": "DeepZF/PWMpredictor.ipynb",
   "sha256": "950ec345d5a0435d2e9c401400efa4b5f95219386e2e14e310670d01d3d7a790",
   "language": "Jupyter",
   "lines": 31,
   "truncated": false,
   "block": 5,
   "row": 16040
  },
  {
   "path": "DeepZF/PWMpredictor/code/create_b1h_input_and_label_data.py",
   "sha256": "db882be91b74b9e87766478f97a19e44f118b962af6ea278dc46aef06c108d36",
   "language": "Python",
   "lines": 83,
   "truncated": false,
   "block": 6,
   "row": 36839
  },
  {
   "path": "DeepZF/PWMpredictor/code/create_c_rc_input_and_label.py",
   "sha256": "4ed8ec491cdaa798e408de7597ca1836d2f921d33b3cb8ecbb610f6ef9a2ed7b",
   "language": "Python",
   "lines": 39,
   "truncated": false,
   "block": 6,
   "row": 30994
  },
  {
   "path": "DeepZF/PWMpredictor/code/functions.py",
   "sha256": "a5508ae86e5c3da5badcb913d1d5b95af083393ecdc4053176814903aacbf0e0",
   "language": "Python",
   "lines": 321,
   "truncated": false,
   "block": 7,
   "row": 3415
  },
  {
   "path": "DeepZF/PWMpredictor/code/main_PWMpredictor.py",
   "sha256": "30306fb445543d782422d2986a59ab2804a00d5de52878f8e144fdfd1e814b6d",
   "language": "Python",
   "lines": 83,
   "truncated": false,
   "block": 6,
   "row": 38025
  },
  {
   "path": "DeepZF/PWMpredictor/code/main_loo_PWMpredictor.py",
   "sha256": "3f122aaa1a69eaf94b333104160c4b9f984cc1d29073edebf0b3cb3c2f9fb21e",
   "language": "Python",
   "lines": 71,
   "truncated": false,
   "block": 6,
   "row": 35851
  },
  {
   "path": "DeepZF/PWMpredictor/code/models_PWMpredictor.py",
   "sha256": "72cf39a4c45e5f294452e7b9f7533c05cbe2c28a310bc14f5849d4800cbafc51",
   "language": "Python",
   "lines": 16,
   "truncated": false,
   "block": 6,
   "row": 23320
  },
  {
   "path": "DeepZF/PWMpredictor/code/models_loo_PWMpredictor.py",
   "sha256": "bf9d58508e9ac83dbf897ed0bf9e832328165b1270d136f92b99b362bd54523e",
   "language": "Python",
   "lines": 12,
   "truncated": false,
   "block": 6,
   "row": 22570
  },
  {
   "path": "DeepZF/PWMpredictor/code/utiles_loo_PWMpredictor.py",
   "sha256": "7fbd35bb5f3a2aaf65075bbb1d398d5c60c9703b79c56da24781e0c4f322b590",
   "language": "Python",
   "lines": 19,
   "truncated": false,
   "block": 6,
   "row": 23000
  },
  {
   "path": "DeepZF/PWMpredictor/code/utiles_models_PWMpredictor.py",
   "sha256": "5ea1f9e53028367ee261eacd1e5272498fde8c7cc462eaa8129167f202d1834a",
   "language": "Python",
   "lines": 152,
   "truncated": false,
   "block": 6,
   "row": 41546
  },
  {
   "path": "DeepZF/PWMpredictor/code/utiles_models_loo_PWMpredictor.py",
   "sha256": "5d736e9e5ea835d5765a79eae033b25009022c7559e81a17c67f7196cda3a376",
   "language": "Python",
   "lines": 97,
   "truncated": false,
   "block": 6,
   "row": 38508
  },
  {
   "path": "DeepZF/PWMpredictor/result_analysis/create_mosbat_input_protein_bert.py",
   "sha256": "4e5cf97453476a1c28e1d92098b78c7a9bfc84cc9c774e5f5b2a4a51d59062c8",
   "language": "Python",
   "lines": 114,
   "truncated": false,
   "block": 6,
   "row": 38343
  },
  {
   "path": "DeepZF/PWMpredictor/result_analysis/eval_DeepZF.sh",
   "sha256": "ba16ca517a9e5b0b66fcbc64f135a54d9fedc424cbef590eb9aa24f3a4f5efef",
   "language": "Shell",
   "lines": 27,
   "truncated": false,
   "block": 8,
   "row": 7711
  },
  {
   "path": "DeepZF/PWMpredictor/result_analysis/eval_PWMpredictor.py",
   "sha256": "a818f724a3efa1318cb456008403344f296ac8af1b6b20c3d89bb0870d048a4a",
   "language": "Python",
   "lines": 51,
   "truncated": false,
   "block": 6,
   "row": 28148
  },
  {
   "path": "DeepZF/PWMpredictor/result_analysis/eval_mosbat.py",
   "sha256": "72115abdc8b49abf3a171dfc7ecdf5038146acb1a9a40624be9fe0226ddf7b5c",
   "language": "Python",
   "lines": 49,
   "truncated": false,
   "block": 6,
   "row": 30672
  },
  {
   "path": "DeepZF/PWMpredictor/result_analysis/pearson_cor_per_pos.py",
   "sha256": "3fd3853d528afaf1f4c435aec87dc85714a5be40d56e98dd7b72616939844f49",
   "language": "Python",
   "lines": 27,
   "truncated": false,
   "block": 6,
   "row": 27265
  },
  {
   "path": "LICENSE.md",
   "sha256": "4ff8c9db35f6de33743ab97fe9a2da020b1381447d6a3e8ba7ab8367e44d55f4",
   "language": "License",
   "lines": 9,
   "truncated": false,
   "block": 6,
   "row": 1462
  },
  {
   "path": "README.md",
   "sha256": "b879953b3d22ef13360468067c7c678a669de12b6c30c8e9269139249a33ab7f",
   "language": "Text",
   "lines": 72,
   "truncated": false,
   "block": 8,
   "row": 10200
  },
  {
   "path": "app_space.py",
   "sha256": "64286212f4177801e29594f979f0ea84a15f837f3482bb45fa12de2fae89eea7",
   "language": "Python",
   "lines": 12,
   "truncated": false,
   "block": 6,
   "row": 21617
  },
  {
   "path": "paper/benchmark.py",
   "sha256": "3a219316ae45a32f1bfc30b17e8e40f58f264014758bf2d5118edfbddafc8ae3",
   "language": "Python",
   "lines": 125,
   "truncated": false,
   "block": 6,
   "row": 38712
  },
  {
   "path": "paper/draw_pCBS.py",
   "sha256": "3ab382c887f11931b258a18da5606f8e61632507c6d2566631e58cebc40cc19e",
   "language": "Python",
   "lines": 50,
   "truncated": false,
   "block": 6,
   "row": 25854
  },
  {
   "path": "paper/extract_ctcf_binding_site.py",
   "sha256": "60b2e127a005ee95abd370fa4531ba09f3cf71fb7bb451afdd5ad421676562b2",
   "language": "Python",
   "lines": 50,
   "truncated": false,
   "block": 6,
   "row": 26567
  },
  {
   "path": "paper/pCBS.py",
   "sha256": "ed33af74df996ea28133ddc2f5d5d4ef0a45f31191b06f4166025aa5ad8f4bd7",
   "language": "Python",
   "lines": 111,
   "truncated": false,
   "block": 6,
   "row": 35746
  },
  {
   "path": "run.py",
   "sha256": "040b0c48a40aac40818d7bd60b379c34dec1f56d1a54520704fa51579608e070",
   "language": "Python",
   "lines": 72,
   "truncated": false,
   "block": 6,
   "row": 30461
  },
  {
   "path": "scripts/formal/app.sh",
   "sha256": "7ae9040ecc85c113c4b8b6f197a716e43ded0f6474f4992822fe553b23911d78",
   "language": "Shell",
   "lines": 10,
   "truncated": false,
   "block": 8,
   "row": 6633
  },
  {
   "path": "scripts/formal/hpo.sh",
   "sha256": "7d1634c14da7e12fc4fd3817623f4761addfb1dde4f21538f6553a8d85c386c3",
   "language": "Shell",
   "lines": 43,
   "truncated": false,
   "block": 8,
   "row": 7892
  },
  {
   "path": "scripts/formal/infer.sh",
   "sha256": "2993b9586b5da3c0a7737dbee5eb5fad7b059cf2ea28e02759af4a9fef524530",
   "language": "Shell",
   "lines": 45,
   "truncated": false,
   "block": 8,
   "row": 7914
  },
  {
   "path": "scripts/formal/space.py",
   "sha256": "9d04b65d7c72eec1f39cc77bf8bfb986ec21353efae8833030d905ce56c84f41",
   "language": "Python",
   "lines": 53,
   "truncated": false,
   "block": 6,
   "row": 27685
  },
  {
   "path": "scripts/formal/test.sh",
   "sha256": "04750def50ae9a242f9b609b935410c4b601f64061212ca6d2cc62226d49a4bb",
   "language": "Shell",
   "lines": 57,
   "truncated": false,
   "block": 8,
   "row": 8139
  },
  {
   "path": "scripts/formal/train.sh",
   "sha256": "fbffc2440ed1ddc0b87b78812d63d00d13dc75e0045924bf5a7d948d498f9aed",
   "language": "Shell",
   "lines": 103,
   "truncated": false,
   "block": 8,
   "row": 8909
  },
  {
   "path": "scripts/formal/upload.sh",
   "sha256": "066bb3c0f6965ab785fcbabce367b364739cc376403051f2c20cc176ef8a325e",
   "language": "Shell",
   "lines": 29,
   "truncated": false,
   "block": 8,
   "row": 7256
  },
  {
   "path": "scripts/formal/upload_dataset.sh",
   "sha256": "21d9bcf753ea9b728d0daf2e38aba2377a259a540796067727a01d5da8d5262f",
   "language": "Shell",
   "lines": 19,
   "truncated": false,
   "block": 8,
   "row": 7004
  },
  {
   "path": "scripts/unittest/hpo.sh",
   "sha256": "a8c359f41b911eff4b7cb2cf0327c44a3613aad89ee41e5ce0f19b82f65c8497",
   "language": "Shell",
   "lines": 41,
   "truncated": false,
   "block": 8,
   "row": 7837
  }
 ]
}