{ "format": "oscr-script-manifest/1", "repository": "github.com/matsengrp/epam", "url": "https://github.com/matsengrp/epam", "host": "github.com", "commit": "d8bd3666d93bf2f8e8c2f2b441a64a158cc99c26", "license": "MIT", "license_confirmed_by": "license file LICENSE", "redistribution": "yes", "files": [ { "path": "LICENSE", "sha256": "87a77f9cf93a0a081d45d06b37a15a14a116453773ea1644b2eafac157eff40e", "language": "License", "lines": 21, "truncated": false, "block": 14, "row": 16909 }, { "path": "README.md", "sha256": "1246899eb9131bb1c18f931cd3bd17a73c211c858f9e58f6ed30840f2d8449c1", "language": "Text", "lines": 45, "truncated": false, "block": 16, "row": 7181 }, { "path": "epam/annotate_pcps.py", "sha256": "13e6b7868ee95c4199e2b025b042acb0e7ed903978b8f0a055e2f21777a8749b", "language": "Python", "lines": 147, "truncated": false, "block": 15, "row": 16992 }, { "path": "epam/cli.py", "sha256": "e087ee7ecae8dcbf3da54b2cee2d6ec244b86208e2557a68411e07215d337734", "language": "Python", "lines": 186, "truncated": false, "block": 15, "row": 19496 }, { "path": "epam/df_for_plots.py", "sha256": "c5cc40dc9bcc1a2f5c82adafad9921b85a9d0d182984334b75ceaefd9b679095", "language": "Python", "lines": 336, "truncated": false, "block": 15, "row": 23313 }, { "path": "epam/esm_precompute.py", "sha256": "4fe087bf0cac42e514dc7cb8c7bff16753bd79ab67d35f6150034b7e3d4419b5", "language": "Python", "lines": 326, "truncated": false, "block": 15, "row": 23237 }, { "path": "epam/evaluation.py", "sha256": "9d1f86ee4e85a6516295928ee3c46a7e2c347880ec694eaa734b528be93eb095", "language": "Python", "lines": 525, "truncated": false, "block": 15, "row": 24812 }, { "path": "epam/gcreplay_models.py", "sha256": "fe8c804160a937e3a9ecdf0478e6d22c27ba883dba70f76c0171240875a86589", "language": "Python", "lines": 368, "truncated": false, "block": 15, "row": 23484 }, { "path": "epam/models.py", "sha256": "13982a888512c70440fe6c1dc388d29937de6c0dcaddba14b2a1b18661c33893", "language": "Python", "lines": 1223, "truncated": false, "block": 16, "row": 1107 }, { "path": "epam/mutsel_simulation.py", "sha256": "2c25e1bb313d0dcade3ce5cd86f975805076815886d05fbe5c3e45f2b432e527", "language": "Python", "lines": 142, "truncated": false, "block": 15, "row": 17550 }, { "path": "epam/oe_plot.py", "sha256": "91aeda2d492a3e853ac748678506bf108765244693a889175fb3feec91f24d05", "language": "Python", "lines": 1361, "truncated": false, "block": 16, "row": 1165 }, { "path": "epam/utils.py", "sha256": "357aed86674aaab36a79e5e0c19ca138413e7074f321ead578c9c46bba4a7bf2", "language": "Python", "lines": 109, "truncated": false, "block": 15, "row": 13381 }, { "path": "notebooks/conserved_quantile.py", "sha256": "d7de3f0134b7b8f7e9ce5ccbfd37d306b785434544f325be14747313efff8785", "language": "Python", "lines": 54, "truncated": false, "block": 15, "row": 10021 }, { "path": "notebooks/eval_per_mut_count.py", "sha256": "3ce333dd6c4ba2b71e8bfe09e66e29021eb73a42e364d5ab978bf2b92960f5f7", "language": "Python", "lines": 140, "truncated": false, "block": 15, "row": 16098 }, { "path": "notebooks/gcreplay_dms_esm.Rmd", "sha256": "be3c6dbe43f4a4f9d8ec634085194937be37abef8b9aa378b42637970a846390", "language": "R", "lines": 950, "truncated": false, "block": 16, "row": 4138 }, { "path": "notebooks/gcreplay_esm.py", "sha256": "eb65b3e6605c2714cdd7b8f42588b890c2720639936ab0f76292095d1f292f79", "language": "Python", "lines": 85, "truncated": false, "block": 15, "row": 13632 }, { "path": "notebooks/plot_ablang_comp.py", "sha256": "e37160e9abea7db4befdbf0753d604793f60db00c3c5661da553dd07a895cea5", "language": "Python", "lines": 92, "truncated": false, "block": 15, "row": 12932 }, { "path": "notebooks/plot_conscount_cfsize.py", "sha256": "219922365ffb01666060007838e4184b28694a9f116e71e80f335e160adfe398", "language": "Python", "lines": 83, "truncated": false, "block": 15, "row": 11852 }, { "path": "notebooks/plot_conserved.py", "sha256": "08ec76ed229594e99c494363272ca77447350d1a3a08d425c9ce05bb47e4e445", "language": "Python", "lines": 138, "truncated": false, "block": 15, "row": 16086 }, { "path": "notebooks/plot_cspperp.py", "sha256": "2a820b9c8333236cac7c46cf05fe5ce1d666265da42725da40345b26791aa344", "language": "Python", "lines": 60, "truncated": false, "block": 15, "row": 10353 }, { "path": "notebooks/plot_esm_ensemble.py", "sha256": "9e6d76fd5af197530dc913ff0b8c7af345976065c754e97a53792449caf3aad7", "language": "Python", "lines": 170, "truncated": false, "block": 15, "row": 16787 }, { "path": "notebooks/plot_gcreplay_cspperp.py", "sha256": "915ed459479cad42d98c1515f7c699e78162398453debca2002a3f8dfaf3997b", "language": "Python", "lines": 64, "truncated": false, "block": 15, "row": 11191 }, { "path": "notebooks/plot_gcreplay_model_oe_all.py", "sha256": "f3c760fc088fdc9cd504373a8a79d14e0b7ba13247b2f61af8dd846abf2987fe", "language": "Python", "lines": 201, "truncated": false, "block": 15, "row": 19889 }, { "path": "notebooks/plot_gcreplay_model_oe_all_supp.py", "sha256": "63dc9e433c8e0923aaef8745d530566a2d6d200e7b5676594d10c13de033ec0c", "language": "Python", "lines": 191, "truncated": false, "block": 15, "row": 19123 }, { "path": "notebooks/plot_gcreplay_mutability_metrics.py", "sha256": "f49e2762ab6fbc3fcc48f2e8b5817d56f8ff3c17ebc174eac6a9b25b68085972", "language": "Python", "lines": 62, "truncated": false, "block": 15, "row": 10688 }, { "path": "notebooks/plot_gcreplay_mutability_subacc_cspperp.py", "sha256": "67bf78f0bf05cc5504b54e344270029b5982b8684b27994d677a1d6ebbbc6e33", "language": "Python", "lines": 162, "truncated": false, "block": 15, "row": 18618 }, { "path": "notebooks/plot_gcreplay_overlap.py", "sha256": "4b2d064ac7b20e96c57a5137c3f80b36f3175c48242d81ff129e2ff3d85dbeb2", "language": "Python", "lines": 63, "truncated": false, "block": 15, "row": 11060 }, { "path": "notebooks/plot_gcreplay_rprec.py", "sha256": "ab1c3c12a62da9c8b0efedc4b037b7d53a2037dac190bc6878ced9f061eea2fc", "language": "Python", "lines": 63, "truncated": false, "block": 15, "row": 11062 }, { "path": "notebooks/plot_gcreplay_subacc.py", "sha256": "a7ae1ff343eee7e629a13bb9b9a6661cae234e160a35dcdafcf15546fde661f1", "language": "Python", "lines": 64, "truncated": false, "block": 15, "row": 11242 }, { "path": "notebooks/plot_model_oe_all.py", "sha256": "f55a1f27623f620758028698ff8ee687e297171d21e6db4b619f2242e144f4c0", "language": "Python", "lines": 214, "truncated": false, "block": 15, "row": 20372 }, { "path": "notebooks/plot_model_oe_all_nsubs.py", "sha256": "d37096adfcfdd45390bf90429b0a66c832c38a14e26f6abbc24a99c9c70e662d", "language": "Python", "lines": 234, "truncated": false, "block": 15, "row": 22022 }, { "path": "notebooks/plot_model_oe_all_supp.py", "sha256": "557b733c3871fe87352c809e94353f27a51a180cc77f91a951b18df05a1d89c6", "language": "Python", "lines": 208, "truncated": false, "block": 15, "row": 19837 }, { "path": "notebooks/plot_model_tau.py", "sha256": "921b378a1157e68df5b3970efc2e2a4bd4dfb26432f8a08f56a05bca544a3de0", "language": "Python", "lines": 193, "truncated": false, "block": 15, "row": 19919 }, { "path": "notebooks/plot_mutability_metrics.py", "sha256": "d4abebd0c5b96f122342bd6850308b273198e5e2d1f718222fc2882b3f4deb45", "language": "Python", "lines": 58, "truncated": false, "block": 15, "row": 10029 }, { "path": "notebooks/plot_nsubs.py", "sha256": "8937ab5f157a5faae6927dcecbced09fe0601f7a8c64faf7e52935ce299cdd8e", "language": "Python", "lines": 70, "truncated": false, "block": 15, "row": 10773 }, { "path": "notebooks/plot_nt_model_tau_mut.py", "sha256": "8af0614fb8fac58ddfed23ec4a6ddbe757b8511e43a8050cca2dceab96673847", "language": "Python", "lines": 156, "truncated": false, "block": 15, "row": 18004 }, { "path": "notebooks/plot_oe_and_mutability.py", "sha256": "6f84c2ac4971356f2dae707e1cda3033cc8274b6ca160bfe8407700a63f62173", "language": "Python", "lines": 147, "truncated": false, "block": 15, "row": 16834 }, { "path": "notebooks/plot_overlap.py", "sha256": "c3a6e8ecf75bc798349af2f22e82d1c2e78f9a6bfb932a138a0db74c5c59c5c8", "language": "Python", "lines": 63, "truncated": false, "block": 15, "row": 10741 }, { "path": "notebooks/plot_overlap_and_rprec.py", "sha256": "cc2c3a56f574c14299c76765d94df1dd4004a4747b9a11e499b685321bbfaa57", "language": "Python", "lines": 108, "truncated": false, "block": 15, "row": 14862 }, { "path": "notebooks/plot_performance_per_mut_count.py", "sha256": "069103bc43175cac629ac25baa44892f7f9d5890dfceb207c805a850f88752ea", "language": "Python", "lines": 108, "truncated": false, "block": 15, "row": 13372 }, { "path": "notebooks/plot_performance_per_mut_count_4plots.py", "sha256": "373990879e3f16fd6a3adca425407174046a0398928bf7632e03dd435993e0a1", "language": "Python", "lines": 140, "truncated": false, "block": 15, "row": 16065 }, { "path": "notebooks/plot_performance_per_mut_count_anc_leaf.py", "sha256": "4df3e3d29f8f331d62e87850835df177ca921f725b76e82d6a2acb9706480967", "language": "Python", "lines": 217, "truncated": false, "block": 15, "row": 20023 }, { "path": "notebooks/plot_rprec.py", "sha256": "961e280b88e1019eb56726bce57b29a896338a91b8cbfc4ef99f5baac0b4b898", "language": "Python", "lines": 61, "truncated": false, "block": 15, "row": 10587 }, { "path": "notebooks/plot_schematic_oe.py", "sha256": "7a9da6fe74dff68284255452d2a407a5fd89fe67c54d5f3b8187afd130ffbd17", "language": "Python", "lines": 66, "truncated": false, "block": 15, "row": 11188 }, { "path": "notebooks/plot_sites_oe.py", "sha256": "f99a8b1e54f7649f02b9fedce3ba6ea5dcf813392ffc81b2fe340c8ba589f805", "language": "Python", "lines": 101, "truncated": false, "block": 15, "row": 13580 }, { "path": "notebooks/plot_subacc.py", "sha256": "0e7b3d5c1c283debb95885b9926a33e065b001a27340bc5beb177c09fc80d3ed", "language": "Python", "lines": 61, "truncated": false, "block": 15, "row": 10445 }, { "path": "notebooks/plot_subacc_and_cspperp.py", "sha256": "3b90ddaeae899d0423b5a3f59654a2175a9a6f0c05bd7568870b91d281b06f04", "language": "Python", "lines": 110, "truncated": false, "block": 15, "row": 14878 }, { "path": "notebooks/plot_subacc_cfsize.py", "sha256": "669d4d1e0839f25b27b78ebe79878094d540572327c14831b176771079e90bc5", "language": "Python", "lines": 80, "truncated": false, "block": 15, "row": 11270 }, { "path": "notebooks/plot_subacc_conscount.py", "sha256": "1eb99c4c88e619c7b4a373e6a211358f9f945f8e0c2ae8ff662a8845a4519690", "language": "Python", "lines": 80, "truncated": false, "block": 15, "row": 11245 }, { "path": "notebooks/plot_subacc_nsubs.py", "sha256": "66c501c907b30f9df505635a494d73fdde5c606886d6fe7e44f1b87da8e3ce70", "language": "Python", "lines": 69, "truncated": false, "block": 15, "row": 11741 }, { "path": "notebooks/write_branch_length_csv.py", "sha256": "9f21180b4fbc5c3047f10c16be4cc27d81e220962e593bbdbb163ae087c88a68", "language": "Python", "lines": 60, "truncated": false, "block": 15, "row": 10735 }, { "path": "notebooks/write_conscount.py", "sha256": "ffd6cb96840cc70d91bf761b18c8c24b689fc655b104af150da37c6028a85306", "language": "Python", "lines": 46, "truncated": false, "block": 15, "row": 8302 }, { "path": "notebooks/write_conscount_cfsize.py", "sha256": "d666c02b16f20c365652b1eb09dbf1f24e29b7a04c7bbf1e98ef297c5e977166", "language": "Python", "lines": 57, "truncated": false, "block": 15, "row": 10396 }, { "path": "notebooks/write_conserved_csv.py", "sha256": "fec43ea5b63dd8eb539eb39cbd09655051659ebcac5ac326e87f40124293ecfd", "language": "Python", "lines": 59, "truncated": false, "block": 15, "row": 10261 }, { "path": "notebooks/write_cspperp_csv.py", "sha256": "5f75ec2dc0a9077679b7cc3aabcda7b6794b912175ae022db2458f559552f3d5", "language": "Python", "lines": 114, "truncated": false, "block": 15, "row": 15012 }, { "path": "notebooks/write_dfs_for_plots.py", "sha256": "f3e24023daf782e1432da73a46ec8f3cc3032016341f64f5ec4d21d64ec024d2", "language": "Python", "lines": 88, "truncated": false, "block": 15, "row": 13600 }, { "path": "notebooks/write_dfs_for_plots_anc_leaf.py", "sha256": "7c4ef324ed4540533e775f4939df0a2c8364bd3e4cbeb5f759764523d4637e34", "language": "Python", "lines": 84, "truncated": false, "block": 15, "row": 13942 }, { "path": "notebooks/write_dfs_for_plots_esm_ensemble.py", "sha256": "59eeee0760c8165752c1d1f9f8290f4e29456c59e59e9bafeb80f588100b172c", "language": "Python", "lines": 59, "truncated": false, "block": 15, "row": 10365 }, { "path": "notebooks/write_gcreplay_cspperp_csv.py", "sha256": "dc7c7741734cddcd2f2d00af2dbfe081faf79fb7f8f57d24d749de1dfe3eff75", "language": "Python", "lines": 146, "truncated": false, "block": 15, "row": 17206 }, { "path": "notebooks/write_gcreplay_dfs_for_plots.py", "sha256": "40e6ec7f60378215d25cecdb0b90ff4223455641ea34566cd37e1647434282f4", "language": "Python", "lines": 51, "truncated": false, "block": 15, "row": 10752 }, { "path": "notebooks/write_gcreplay_overlap_csv.py", "sha256": "5808f9ba3bfef469e1a73e930f0b792710280d64fd1f0f8f90f7b980afab3526", "language": "Python", "lines": 114, "truncated": false, "block": 15, "row": 16044 }, { "path": "notebooks/write_gcreplay_rprec_csv.py", "sha256": "7876e46bdcb2b83a9481cf8a822af352eeba8dc0a14f04c3e8db249a055c9fc9", "language": "Python", "lines": 133, "truncated": false, "block": 15, "row": 18110 }, { "path": "notebooks/write_gcreplay_subacc_csv.py", "sha256": "e36c23c286753a4a58d22f99da03675ad67a17d50222ead0f382f4f939f558e9", "language": "Python", "lines": 141, "truncated": false, "block": 15, "row": 17389 }, { "path": "notebooks/write_overlap_csv.py", "sha256": "bdfa652c14ff4999fb12f61ebb9961d599633e02f252e7f0cd0b8b78374dd374", "language": "Python", "lines": 77, "truncated": false, "block": 15, "row": 12496 }, { "path": "notebooks/write_rprec_csv.py", "sha256": "80238c637e332c9faa2dd7df11318559a1b58b438c73c459eefab0541b1ed27a", "language": "Python", "lines": 89, "truncated": false, "block": 15, "row": 13658 }, { "path": "notebooks/write_subacc_cfsize.py", "sha256": "4f5d96761d843fb1c599edd715b0cf53bcbb9df766376d5ce9e4b736f00ac03c", "language": "Python", "lines": 141, "truncated": false, "block": 15, "row": 17598 }, { "path": "notebooks/write_subacc_conscount.py", "sha256": "ab09a9019065c08c4497b1278263e720870ee7507f1c6563c87810971d4e2be3", "language": "Python", "lines": 140, "truncated": false, "block": 15, "row": 17492 }, { "path": "notebooks/write_subacc_csv.py", "sha256": "e792afe2a05bd4a1bd01a4abaf79e95263162fc37876a7e9a5bccac3cdfcf799", "language": "Python", "lines": 109, "truncated": false, "block": 15, "row": 15083 }, { "path": "notebooks/write_subacc_nsubs.py", "sha256": "892b9cf17b63769f22fcd1b4c216c8c09ed2d620faf65d9ebf8220a79882e41d", "language": "Python", "lines": 122, "truncated": false, "block": 15, "row": 16509 }, { "path": "scripts/run_anarci_epam_naive_v2.sh", "sha256": "e8a1f7202ac9f4abb677f04d9e6344b23773c6bbdb7d6b6bdd2533f214b51af4", "language": "Shell", "lines": 16, "truncated": false, "block": 16, "row": 5937 }, { "path": "scripts/split_pcp_files.py", "sha256": "b192ed85b4e81ea966cfb4bbef0327b70420294b1125c68ad6e69778b89c2f88", "language": "Python", "lines": 50, "truncated": false, "block": 15, "row": 10485 }, { "path": "scripts/summarize_pcps.py", "sha256": "88546b7f852847885bb9803da3e2e32b4830adee43d129d3f6bf9b1d184b2c94", "language": "Python", "lines": 78, "truncated": false, "block": 15, "row": 12313 }, { "path": "setup.py", "sha256": "f1ea534e28a5cc768909c5333e61a54ec357828b4cfff5650e195d5793654573", "language": "Python", "lines": 34, "truncated": false, "block": 15, "row": 8189 }, { "path": "tests/test_encode_decode.py", "sha256": "0185443b5e8b8afc2a717cdb7b60ff7f33d1c995e80352b7de69462592fe6b52", "language": "Python", "lines": 17, "truncated": false, "block": 15, "row": 6885 }, { "path": "tests/test_evaluation.py", "sha256": "e92e80878259de538898b1418f53965033f9e3e12fba7e49981b532cae8d7fa4", "language": "Python", "lines": 172, "truncated": false, "block": 15, "row": 16971 }, { "path": "tests/test_models.py", "sha256": "78e8deb31687d1228c9e7dc6a686b7abe51639a96d0956f75aa72807dcc5837c", "language": "Python", "lines": 176, "truncated": false, "block": 15, "row": 19317 } ] }