Datasetpublic
OpenScientificCodeRegistry/Database

Open Scientific Code Registry (OSCR): the authors' scripts The code published by the authors of open-access neuroscience papers, as found and verified by Open Scientific Code Registry (OSCR). Each file is here exactly as it is at the source, at the verified commit, under the license of its repository. 421,275 unique files (3,782 MB of text) from 8,849 repositories, in 24 Parquet block(s). Only files whose repository's license allows redistribution, confirmed by the repository's… See the full description on the dataset page: https://huggingface.co/datasets/OpenScientificCodeRegistry/Database.
sourceHugging Faceotherupdated 2d agoView on Hugging Face
0likes5.6kdownloads
rootmanifests3dgithub.com__inab__trimal.json
github.com__inab__trimal.json327 linesDownload Raw Back to 3d
1{2 "format": "oscr-script-manifest/1",3 "repository": "github.com/inab/trimal",4 "url": "https://github.com/inab/trimal",5 "host": "github.com",6 "commit": "5b5f730430843d39c579acdf8094969780c3c23e",7 "license": "GPL-3.0",8 "license_confirmed_by": "license file LICENSE",9 "redistribution": "yes",10 "files": [11  {12   "path": "LICENSE",13   "sha256": "8ceb4b9ee5adedde47b31e975c1d90c73ad27b6b165a1dcd80c7c545eb65b903",14   "language": "License",15   "lines": 674,16   "truncated": false,17   "block": 1,18   "row": 223419  },20  {21   "path": "README.md",22   "sha256": "083d1a6ab78ccc0d0ffa7647aae0129f8aca6d3dcb56c43874f42e0f7202d30e",23   "language": "Text",24   "lines": 19,25   "truncated": false,26   "block": 16,27   "row": 720828  },29  {30   "path": "docs/source/conf.py",31   "sha256": "45fb71d6de383b44a9c2f6c1261c7837302e5e7ac42b48a69e66ae66564a82b5",32   "language": "Python",33   "lines": 40,34   "truncated": false,35   "block": 15,36   "row": 891537  },38  {39   "path": "scripts/check_codon_alignments.py",40   "sha256": "0311d65213ce21bb78a2f84152e77c90b06c80c61e0eb93f26609fca07688aa5",41   "language": "Python",42   "lines": 107,43   "truncated": false,44   "block": 15,45   "row": 1578846  },47  {48   "path": "scripts/compare_trimmed_msas.sh",49   "sha256": "26f187cf6a365fd383200954db1205945b473c88c25a5cacf82d4434e6a0dc67",50   "language": "Shell",51   "lines": 11,52   "truncated": false,53   "block": 16,54   "row": 488755  },56  {57   "path": "scripts/generateRandomAlignmentsUsingAsSeedRealAlignments.py",58   "sha256": "39410822e5f6868519dfd1bdc420de60336327cf531140d572b28fa5d511a5c3",59   "language": "Python",60   "lines": 143,61   "truncated": false,62   "block": 15,63   "row": 1700264  },65  {66   "path": "scripts/generate_trimmed_msas.sh",67   "sha256": "43f78c69102fbd4273229529713e7e772b34809cd6bac7a98b8d336c4264843b",68   "language": "Shell",69   "lines": 512,70   "truncated": false,71   "block": 16,72   "row": 674073  },74  {75   "path": "scripts/get_sequence_representative_from_alignment.py",76   "sha256": "7ba4250016b37fb745c09c313bb1ef38870d16ef79dda148716d5fc5c6c77a7f",77   "language": "Python",78   "lines": 95,79   "truncated": false,80   "block": 15,81   "row": 1506282  },83  {84   "path": "scripts/get_sequences_gaps_ratio.py",85   "sha256": "ce69d06ecfebd422621d1fe4705338c6a493ef1763c16f38dbaad70a06dc1615",86   "language": "Python",87   "lines": 78,88   "truncated": false,89   "block": 15,90   "row": 1310191  },92  {93   "path": "scripts/remove_shorter_sequences.py",94   "sha256": "79457987bad2b85a57061dc2dcc241b6a2350d3a2a2f6c340d915347f1c68b9c",95   "language": "Python",96   "lines": 73,97   "truncated": false,98   "block": 15,99   "row": 12980100  },101  {102   "path": "scripts/selective_trimming_for_dNdS_analyses.based_neighbours.py",103   "sha256": "c7bead6adaa6cb48f1eb7b7b21e6a8e2ad16693c54c7ab2a86f0dd9a8a0613b4",104   "language": "Python",105   "lines": 273,106   "truncated": false,107   "block": 15,108   "row": 21530109  },110  {111   "path": "scripts/set_manual_boundaries.py",112   "sha256": "c5b2747d7dcbf026a5ae316bbf77d4a729832f5281a2ad17093628e847c4c473",113   "language": "Python",114   "lines": 198,115   "truncated": false,116   "block": 15,117   "row": 19765118  },119  {120   "path": "source/alignment.cpp",121   "sha256": "655a8cfa456844dfcca5e3c6934067643b312071466eb33489eeaf65e651b27c",122   "language": "C++",123   "lines": 3389,124   "truncated": false,125   "block": 14,126   "row": 3512127  },128  {129   "path": "source/alignment.h",130   "sha256": "c3f1af373de4ff7eb6e4909dfe1422520306d487b28cd00fd7ccf51aeefebd9e",131   "language": "C/C++",132   "lines": 548,133   "truncated": false,134   "block": 14,135   "row": 6533136  },137  {138   "path": "source/autAlignment.cpp",139   "sha256": "9bc8e65555f7e8090ef6dc498b19241f51054230649dbdcd9d7afebcdeb1cb8a",140   "language": "C++",141   "lines": 450,142   "truncated": false,143   "block": 14,144   "row": 3055145  },146  {147   "path": "source/compareFiles.cpp",148   "sha256": "34c9f0a2a2050e43c968118787153ceb3991fbd031bea9a6bc07c7e07abbaa23",149   "language": "C++",150   "lines": 520,151   "truncated": false,152   "block": 14,153   "row": 3194154  },155  {156   "path": "source/compareFiles.h",157   "sha256": "30802a1a0ec010137c1ac45cc2234bba2402d4fc88c1472f80fc7a2e8347d52b",158   "language": "C/C++",159   "lines": 53,160   "truncated": false,161   "block": 14,162   "row": 4237163  },164  {165   "path": "source/defines.h",166   "sha256": "036f89c856e6e2edc761cd2087cf79c1fc3851f1fb50b982eb19d5a661d4436a",167   "language": "C/C++",168   "lines": 56,169   "truncated": false,170   "block": 14,171   "row": 4340172  },173  {174   "path": "source/main.cpp",175   "sha256": "330c38155df1c21603768ce3951a6e216426397e44e345c14b1bf4d7ed0cec2f",176   "language": "C++",177   "lines": 1975,178   "truncated": false,179   "block": 14,180   "row": 3490181  },182  {183   "path": "source/readAl.cpp",184   "sha256": "d6d7b45e9d4da2d039e98709f661ede6186fecb86541821ca0a188e4e171dd0e",185   "language": "C++",186   "lines": 385,187   "truncated": false,188   "block": 14,189   "row": 2969190  },191  {192   "path": "source/rwAlignment.cpp",193   "sha256": "a78eb604d92e0fac1c7cf70eedd215f5207fbc870cdfc107c449b0b942ea14bf",194   "language": "C++",195   "lines": 2255,196   "truncated": false,197   "block": 14,198   "row": 3471199  },200  {201   "path": "source/sequencesMatrix.cpp",202   "sha256": "63ba4ed6f739cfbb3cb62441cc15b390482f3c47ae752ba56d3392730f98cb5c",203   "language": "C++",204   "lines": 211,205   "truncated": false,206   "block": 14,207   "row": 2310208  },209  {210   "path": "source/sequencesMatrix.h",211   "sha256": "4bf2d5d6a427d10a7a74e95e26575ce55ba1c0b1576fcf487f27df88533f4be9",212   "language": "C/C++",213   "lines": 119,214   "truncated": false,215   "block": 14,216   "row": 4894217  },218  {219   "path": "source/similarityMatrix.cpp",220   "sha256": "e5ace5c3c3e960e073baa5ddfa85729a47bad92f61e579f89969e861b211217f",221   "language": "C++",222   "lines": 465,223   "truncated": false,224   "block": 14,225   "row": 2965226  },227  {228   "path": "source/similarityMatrix.h",229   "sha256": "86a783089e1f1fa649f740fe20e864c87af2dcfc54608f43df498263598a5564",230   "language": "C/C++",231   "lines": 72,232   "truncated": false,233   "block": 14,234   "row": 4335235  },236  {237   "path": "source/statAl.cpp",238   "sha256": "1647f0b534ff283e35e8e8f3732c9489441b90c0680e91c4553f1ac3c8043682",239   "language": "C++",240   "lines": 576,241   "truncated": false,242   "block": 14,243   "row": 3213244  },245  {246   "path": "source/statisticsConservation.cpp",247   "sha256": "eb8fd7dc13f7b44d75757740b74aa7528c4b63f7932d6ce767378f86fa3c4822",248   "language": "C++",249   "lines": 430,250   "truncated": false,251   "block": 14,252   "row": 3189253  },254  {255   "path": "source/statisticsConservation.h",256   "sha256": "8e81bcd7278cbaa70d46334621ab024b96607ec93944f4d98a3b89d105270575",257   "language": "C/C++",258   "lines": 114,259   "truncated": false,260   "block": 14,261   "row": 5016262  },263  {264   "path": "source/statisticsFiles.cpp",265   "sha256": "d76a892ff6152ac14fcf5b5a90addbb899e8375bf3428e9899f8110b4c199e06",266   "language": "C++",267   "lines": 58,268   "truncated": false,269   "block": 14,270   "row": 1483271  },272  {273   "path": "source/statisticsFiles.h",274   "sha256": "6d673ebe2fd30e1ebb295d11ab5225378fc0e6931e43358d428b94d841818ccc",275   "language": "C/C++",276   "lines": 50,277   "truncated": false,278   "block": 14,279   "row": 4157280  },281  {282   "path": "source/statisticsGaps.cpp",283   "sha256": "9dfeee68a7176490d13786ba3b8d6b58feb6fc2c5b0ef1ec3a4ce9ac56fcb62e",284   "language": "C++",285   "lines": 466,286   "truncated": false,287   "block": 14,288   "row": 3202289  },290  {291   "path": "source/statisticsGaps.h",292   "sha256": "b1740c11252d496681455135291fdbc56eb0f2b6c5a5bf54f0ad3fd7675c2fd9",293   "language": "C/C++",294   "lines": 89,295   "truncated": false,296   "block": 14,297   "row": 4748298  },299  {300   "path": "source/utils.cpp",301   "sha256": "ab32780a42262e345b56ecc7b58b013222867c2c411ea1982f2323f1cf14f052",302   "language": "C++",303   "lines": 852,304   "truncated": false,305   "block": 14,306   "row": 3253307  },308  {309   "path": "source/utils.h",310   "sha256": "2549ebc46b70dd723c556301028691a12c14b414c83e558f2d5245d0fac1e868",311   "language": "C/C++",312   "lines": 209,313   "truncated": false,314   "block": 14,315   "row": 5574316  },317  {318   "path": "source/values.h",319   "sha256": "63b49fcee9c48089a196f22511d6dd6e0e04fedb5f646ff67be78911505896d3",320   "language": "C/C++",321   "lines": 121,322   "truncated": false,323   "block": 14,324   "row": 5575325  }326 ]327}