Team Ai
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
rootmanifests25github.com__cschu__gff_quantifier.json
github.com__cschu__gff_quantifier.json498 linesDownload Raw Back to 25
1{2 "format": "oscr-script-manifest/1",3 "repository": "github.com/cschu/gff_quantifier",4 "url": "https://github.com/cschu/gff_quantifier",5 "host": "github.com",6 "commit": "9d5cfb3c37c4c0d3a876afd0296618d9c513f1f9",7 "license": "MIT",8 "license_confirmed_by": "license file LICENSE",9 "redistribution": "yes",10 "files": [11  {12   "path": "LICENSE",13   "sha256": "dc248f5d5767d0996a04d5c933f13aef32bb81706430d50bb2c58bfc0507072d",14   "language": "License",15   "lines": 21,16   "truncated": false,17   "block": 22,18   "row": 1407119  },20  {21   "path": "README.md",22   "sha256": "dd76dcac6c1b262df84b837e151a93a57d06ad85a11c83fa6bfbd78052140277",23   "language": "Text",24   "lines": 118,25   "truncated": false,26   "block": 24,27   "row": 84528  },29  {30   "path": "gffquant/__init__.py",31   "sha256": "71da71aad176c8431ff0c9405d1a29e9424e9e54d68b631588791ec29eef3182",32   "language": "Python",33   "lines": 52,34   "truncated": false,35   "block": 23,36   "row": 33037  },38  {39   "path": "gffquant/__main__.py",40   "sha256": "617e809630a8dab2d172fba4fe1fa6154f1f302c1ebfad3e3555518e1a81259b",41   "language": "Python",42   "lines": 167,43   "truncated": false,44   "block": 23,45   "row": 683746  },47  {48   "path": "gffquant/alignment/__init__.py",49   "sha256": "1b817c270502fa1d3be09d18193797dd6414c653ceea57fdf08aa42a72377074",50   "language": "Python",51   "lines": 58,52   "truncated": false,53   "block": 23,54   "row": 45755  },56  {57   "path": "gffquant/alignment/aln_group.py",58   "sha256": "7657036c6e0648c079da4f891b021805e16ebbe3930dfe9506d55755882504fc",59   "language": "Python",60   "lines": 105,61   "truncated": false,62   "block": 23,63   "row": 533164  },65  {66   "path": "gffquant/alignment/bamreader.py",67   "sha256": "9b715d156af849d15f626a536590c68501d6b51ea1cfa8d20a82cc46a2e7c5cf",68   "language": "Python",69   "lines": 462,70   "truncated": false,71   "block": 23,72   "row": 1210673  },74  {75   "path": "gffquant/alignment/cigarops.py",76   "sha256": "56bc06035e4cfd93076be6ddeb1da685938e9c4a78f07a54f5066616a4b4b17f",77   "language": "Python",78   "lines": 25,79   "truncated": false,80   "block": 22,81   "row": 2792582  },83  {84   "path": "gffquant/alignment/pysam_alignment_processor.py",85   "sha256": "8af508ccfa9803a4416f16a3bbe5ed5b22c6cad48dbf9ae344fe9f3d8e9eddb9",86   "language": "Python",87   "lines": 133,88   "truncated": false,89   "block": 23,90   "row": 550391  },92  {93   "path": "gffquant/alignment/reference_hit.py",94   "sha256": "eb56a769b45f62d6dec670819f408166cdebfe19b4fdc90bf9d0abaae18eba78",95   "language": "Python",96   "lines": 34,97   "truncated": false,98   "block": 22,99   "row": 28413100  },101  {102   "path": "gffquant/alignment/samflags.py",103   "sha256": "ae0ae5fc4bec7369142e7842a87fd78c1b634ac93e2482827f66705362aa95b6",104   "language": "Python",105   "lines": 24,106   "truncated": false,107   "block": 22,108   "row": 27433109  },110  {111   "path": "gffquant/annotation/__init__.py",112   "sha256": "0f0a13b39ba3d46d0b66ef17ae86ee8a6dc584a2d2243904da5297e7cd47c58b",113   "language": "Python",114   "lines": 8,115   "truncated": false,116   "block": 22,117   "row": 26274118  },119  {120   "path": "gffquant/annotation/count_annotator.py",121   "sha256": "8f4ebaaafe9774bb487b5accfef8feb037d12a86180d517f24f567ffeca83b4f",122   "language": "Python",123   "lines": 178,124   "truncated": false,125   "block": 23,126   "row": 8234127  },128  {129   "path": "gffquant/annotation/count_writer.py",130   "sha256": "8a8733607563c6e0a97bd247d327ed829272d217fcad0cdc436bd6b5ecb17d6b",131   "language": "Python",132   "lines": 139,133   "truncated": false,134   "block": 23,135   "row": 5749136  },137  {138   "path": "gffquant/annotation/genecount_annotator.py",139   "sha256": "b6e5d7b993b95474435e2a38d9804d4db83b41227e22794b5c345f588cd2aca7",140   "language": "Python",141   "lines": 87,142   "truncated": false,143   "block": 23,144   "row": 4612145  },146  {147   "path": "gffquant/annotation/regioncount_annotator.py",148   "sha256": "2626637e98e015779aafec2aa22bf0c61618ad14ca2527646aa4f9d6dca911be",149   "language": "Python",150   "lines": 81,151   "truncated": false,152   "block": 23,153   "row": 4250154  },155  {156   "path": "gffquant/bin/build_bed_database.py",157   "sha256": "db118ded0d51ff972cd8f1ef6fced94bb7656403aec5c35cd2b65b134c0ed45c",158   "language": "Python",159   "lines": 161,160   "truncated": false,161   "block": 23,162   "row": 6600163  },164  {165   "path": "gffquant/bin/build_custom_database.py",166   "sha256": "f96ab18573da32b638ab3832526d14d8285f3338834bf6faa1add4a4641cc9e9",167   "language": "Python",168   "lines": 71,169   "truncated": false,170   "block": 23,171   "row": 2019172  },173  {174   "path": "gffquant/bin/build_domain_database.py",175   "sha256": "0435964466fc4d1d865d7b360f8ddcc961d08bb5f55671df06ff85179a2b4748",176   "language": "Python",177   "lines": 162,178   "truncated": false,179   "block": 23,180   "row": 6718181  },182  {183   "path": "gffquant/bin/build_gene_database.py",184   "sha256": "e56f4149e526d365985e2ad5432a9cfe2633ac159aef1fdf650d85d65d604b40",185   "language": "Python",186   "lines": 61,187   "truncated": false,188   "block": 23,189   "row": 533190  },191  {192   "path": "gffquant/bin/collate_counts.py",193   "sha256": "d5fd5f9a59807ee87bb0af2e3e2ee3ef14d429a0449ea5af362d21a1a51d05d2",194   "language": "Python",195   "lines": 241,196   "truncated": false,197   "block": 23,198   "row": 10012199  },200  {201   "path": "gffquant/bin/collate_studies.py",202   "sha256": "1d58c3b49f7a2c36387fa3290a7c027c0b6674bc3ab0740ad394f83c36a97b7c",203   "language": "Python",204   "lines": 58,205   "truncated": false,206   "block": 23,207   "row": 1423208  },209  {210   "path": "gffquant/bin/db_collate.py",211   "sha256": "9c23621fed2dd1873b4a3c9d33ffb7f677526e952cab3f8ece5c60f382f15573",212   "language": "Python",213   "lines": 190,214   "truncated": false,215   "block": 23,216   "row": 6696217  },218  {219   "path": "gffquant/bin/split_table.py",220   "sha256": "dd71da87432770343690004a03360a67a2fcbf7a87cf349702a1a7406d6a6a1e",221   "language": "Python",222   "lines": 62,223   "truncated": false,224   "block": 23,225   "row": 1089226  },227  {228   "path": "gffquant/counters/__init__.py",229   "sha256": "10fce70e0bc074b3b10d52defb99deffaec5e2425b8bc42b0ac5f23c32a0b55b",230   "language": "Python",231   "lines": 8,232   "truncated": false,233   "block": 22,234   "row": 26053235  },236  {237   "path": "gffquant/counters/alignment_counter.py",238   "sha256": "da099251ca9484ca4304e6a6239312225fa4b1b20fb169558a93112225adc9a4",239   "language": "Python",240   "lines": 164,241   "truncated": false,242   "block": 23,243   "row": 7510244  },245  {246   "path": "gffquant/counters/count_matrix.py",247   "sha256": "1dc71574fbbfe0632870c545cccfa1b94e2b31001659d7d7c2554c9be826c49e",248   "language": "Python",249   "lines": 163,250   "truncated": false,251   "block": 23,252   "row": 7244253  },254  {255   "path": "gffquant/counters/region_counter.py",256   "sha256": "824634aa3bb253a1a85490948029460c0b6c0cc48f2ab118071d791a3119a0d7",257   "language": "Python",258   "lines": 38,259   "truncated": false,260   "block": 23,261   "row": 175262  },263  {264   "path": "gffquant/db/__init__.py",265   "sha256": "e58f47c28aff4ac9b1224469094d2ee1630750dd7897362c5305addb34a77dc5",266   "language": "Python",267   "lines": 64,268   "truncated": false,269   "block": 23,270   "row": 1416271  },272  {273   "path": "gffquant/db/annotation_db.py",274   "sha256": "74adfbe9ad9c963a46d00ef072f1b18cbf769c4b311054caadb099e957c878ef",275   "language": "Python",276   "lines": 287,277   "truncated": false,278   "block": 23,279   "row": 10378280  },281  {282   "path": "gffquant/db/gff_dbm.py",283   "sha256": "026911b8cd2625223cbed11fe3083e89774d0543b9dfbe7a6ef839986064a278",284   "language": "Python",285   "lines": 253,286   "truncated": false,287   "block": 23,288   "row": 9739289  },290  {291   "path": "gffquant/db/importers/__init__.py",292   "sha256": "6a01f2cf912c153675e3f3bd9db45e25d06654c4ee3fa5e193f2b04ad420cdbc",293   "language": "Python",294   "lines": 10,295   "truncated": false,296   "block": 22,297   "row": 26783298  },299  {300   "path": "gffquant/db/importers/annstr_db_importer.py",301   "sha256": "4d13746a699acbb238954b5f981ff0cabac1617df00c7d23f65d4a35de1cd86c",302   "language": "Python",303   "lines": 113,304   "truncated": false,305   "block": 23,306   "row": 4770307  },308  {309   "path": "gffquant/db/importers/chunk_reader.py",310   "sha256": "8ee125c2ace1f6c6b51ee71872f930dd2489c9dedd4ecac601150637cf7d89f7",311   "language": "Python",312   "lines": 15,313   "truncated": false,314   "block": 22,315   "row": 26769316  },317  {318   "path": "gffquant/db/importers/custom_database_importer.py",319   "sha256": "7459bbc88a5888fe947195d553bc6f543aa6f271d89cef727ef1bf42d37365d8",320   "language": "Python",321   "lines": 89,322   "truncated": false,323   "block": 23,324   "row": 3589325  },326  {327   "path": "gffquant/db/importers/database_importer.py",328   "sha256": "49ea4b03a5df5c9df7aa61f8cf35d9435d52323dbd6ae55cb7cc359ec63e30a4",329   "language": "Python",330   "lines": 149,331   "truncated": false,332   "block": 23,333   "row": 6888334  },335  {336   "path": "gffquant/db/importers/gene_database_importer.py",337   "sha256": "5b64182a2f3ec1259677626c70be0efe52add1c22c4ea66cf069a68a863e53f9",338   "language": "Python",339   "lines": 66,340   "truncated": false,341   "block": 23,342   "row": 1249343  },344  {345   "path": "gffquant/db/importers/settings.py",346   "sha256": "bfc33b09d8f1b2c4555146b50db2261ece140b13e1073808f1804e612ec20ca7",347   "language": "Python",348   "lines": 35,349   "truncated": false,350   "block": 22,351   "row": 28581352  },353  {354   "path": "gffquant/db/importers/small_database_importer.py",355   "sha256": "d2ad02fcd728b9c6bd580da474652ae131e16f0b629f5af99f7303334c332f01",356   "language": "Python",357   "lines": 52,358   "truncated": false,359   "block": 23,360   "row": 455361  },362  {363   "path": "gffquant/db/importers/small_genome_database_importer.py",364   "sha256": "dce45b6e2dad5eda5b07e8752ec58f366d381b73e4afc5b62df5eed9a0a745a0",365   "language": "Python",366   "lines": 113,367   "truncated": false,368   "block": 23,369   "row": 4198370  },371  {372   "path": "gffquant/db/models/db.py",373   "sha256": "50861d37e78d1bfd8c23dadf552d70de069b8087dd64048e15d67b98b1ef9b19",374   "language": "Python",375   "lines": 83,376   "truncated": false,377   "block": 23,378   "row": 1376379  },380  {381   "path": "gffquant/db/models/meta.py",382   "sha256": "58312fe87770e9115b584b3faecc9425da9626b91410bff7161b6070cbe0c908",383   "language": "Python",384   "lines": 7,385   "truncated": false,386   "block": 22,387   "row": 26018388  },389  {390   "path": "gffquant/handle_args.py",391   "sha256": "63138d6f1b4351be2071aa6473cc28968a5d80789af33d083047496f5add5c40",392   "language": "Python",393   "lines": 392,394   "truncated": false,395   "block": 23,396   "row": 11352397  },398  {399   "path": "gffquant/profilers/__init__.py",400   "sha256": "d110fabd9644a66216fdca8acb6b32480a85e2260d3da6570c636c505d8cff49",401   "language": "Python",402   "lines": 7,403   "truncated": false,404   "block": 22,405   "row": 26013406  },407  {408   "path": "gffquant/profilers/feature_quantifier.py",409   "sha256": "66a7cebb6ba2431647ac467618968a0500fa1a4344495b1dec28883c7669faa9",410   "language": "Python",411   "lines": 506,412   "truncated": false,413   "block": 23,414   "row": 12992415  },416  {417   "path": "gffquant/profilers/gene_quantifier.py",418   "sha256": "cd83366809b4b840c976a955ccdd03f7e609887084ef82b2a0c8859a538eef47",419   "language": "Python",420   "lines": 37,421   "truncated": false,422   "block": 22,423   "row": 28806424  },425  {426   "path": "gffquant/profilers/panda_coverage_profiler.py",427   "sha256": "694ef6947a6ad377f1385e356d74bd80060660bb13e09e4d9e11ae7cafc70624",428   "language": "Python",429   "lines": 178,430   "truncated": false,431   "block": 23,432   "row": 8616433  },434  {435   "path": "gffquant/profilers/panda_profiler.py",436   "sha256": "7870e8816f5ff364fedd307b2a0fead73f7d9256f0f510f56c45791b6846b2a5",437   "language": "Python",438   "lines": 367,439   "truncated": false,440   "block": 23,441   "row": 12098442  },443  {444   "path": "gffquant/profilers/region_quantifier.py",445   "sha256": "19f1d1cc6d1a11196854ce17746e20460119e3c168ade5f5c0657c8854074b93",446   "language": "Python",447   "lines": 41,448   "truncated": false,449   "block": 22,450   "row": 29099451  },452  {453   "path": "gffquant/runners/alignment_runner.py",454   "sha256": "89d99b63098f52f7c33d4af87bcf9a962b0a544d9a7a96e2804b3bf4a19a8637",455   "language": "Python",456   "lines": 88,457   "truncated": false,458   "block": 23,459   "row": 3653460  },461  {462   "path": "gffquant/ui/validation.py",463   "sha256": "086402fa7e5819ee33adb1df7f00178a9f4e48aa5342f24c8d52137837f76ad9",464   "language": "Python",465   "lines": 64,466   "truncated": false,467   "block": 23,468   "row": 1172469  },470  {471   "path": "gffquant/util/fileio.py",472   "sha256": "3fb5ae9ecb8b8ee0966042aaa672a21e080f3053a7a2c6229bffde7d4372d082",473   "language": "Python",474   "lines": 11,475   "truncated": false,476   "block": 22,477   "row": 26527478  },479  {480   "path": "setup.py",481   "sha256": "220ca0ae3fe496d7d6a9265c8762ab197dd19c7f337e0aafefa7bbe849914397",482   "language": "Python",483   "lines": 70,484   "truncated": false,485   "block": 23,486   "row": 1963487  },488  {489   "path": "util/gff_indexer.py",490   "sha256": "a5487c76dadd549a1e0f83536e52b2a43e4c76218f4f5380ea84091023e21e39",491   "language": "Python",492   "lines": 49,493   "truncated": false,494   "block": 23,495   "row": 280496  }497 ]498}