| { |
| "format": "oscr-script-manifest/1", |
| "repository": "github.com/cschu/gff_quantifier", |
| "url": "https://github.com/cschu/gff_quantifier", |
| "host": "github.com", |
| "commit": "9d5cfb3c37c4c0d3a876afd0296618d9c513f1f9", |
| "license": "MIT", |
| "license_confirmed_by": "license file LICENSE", |
| "redistribution": "yes", |
| "files": [ |
| { |
| "path": "LICENSE", |
| "sha256": "dc248f5d5767d0996a04d5c933f13aef32bb81706430d50bb2c58bfc0507072d", |
| "language": "License", |
| "lines": 21, |
| "truncated": false, |
| "block": 22, |
| "row": 14071 |
| }, |
| { |
| "path": "README.md", |
| "sha256": "dd76dcac6c1b262df84b837e151a93a57d06ad85a11c83fa6bfbd78052140277", |
| "language": "Text", |
| "lines": 118, |
| "truncated": false, |
| "block": 24, |
| "row": 845 |
| }, |
| { |
| "path": "gffquant/__init__.py", |
| "sha256": "71da71aad176c8431ff0c9405d1a29e9424e9e54d68b631588791ec29eef3182", |
| "language": "Python", |
| "lines": 52, |
| "truncated": false, |
| "block": 23, |
| "row": 330 |
| }, |
| { |
| "path": "gffquant/__main__.py", |
| "sha256": "617e809630a8dab2d172fba4fe1fa6154f1f302c1ebfad3e3555518e1a81259b", |
| "language": "Python", |
| "lines": 167, |
| "truncated": false, |
| "block": 23, |
| "row": 6837 |
| }, |
| { |
| "path": "gffquant/alignment/__init__.py", |
| "sha256": "1b817c270502fa1d3be09d18193797dd6414c653ceea57fdf08aa42a72377074", |
| "language": "Python", |
| "lines": 58, |
| "truncated": false, |
| "block": 23, |
| "row": 457 |
| }, |
| { |
| "path": "gffquant/alignment/aln_group.py", |
| "sha256": "7657036c6e0648c079da4f891b021805e16ebbe3930dfe9506d55755882504fc", |
| "language": "Python", |
| "lines": 105, |
| "truncated": false, |
| "block": 23, |
| "row": 5331 |
| }, |
| { |
| "path": "gffquant/alignment/bamreader.py", |
| "sha256": "9b715d156af849d15f626a536590c68501d6b51ea1cfa8d20a82cc46a2e7c5cf", |
| "language": "Python", |
| "lines": 462, |
| "truncated": false, |
| "block": 23, |
| "row": 12106 |
| }, |
| { |
| "path": "gffquant/alignment/cigarops.py", |
| "sha256": "56bc06035e4cfd93076be6ddeb1da685938e9c4a78f07a54f5066616a4b4b17f", |
| "language": "Python", |
| "lines": 25, |
| "truncated": false, |
| "block": 22, |
| "row": 27925 |
| }, |
| { |
| "path": "gffquant/alignment/pysam_alignment_processor.py", |
| "sha256": "8af508ccfa9803a4416f16a3bbe5ed5b22c6cad48dbf9ae344fe9f3d8e9eddb9", |
| "language": "Python", |
| "lines": 133, |
| "truncated": false, |
| "block": 23, |
| "row": 5503 |
| }, |
| { |
| "path": "gffquant/alignment/reference_hit.py", |
| "sha256": "eb56a769b45f62d6dec670819f408166cdebfe19b4fdc90bf9d0abaae18eba78", |
| "language": "Python", |
| "lines": 34, |
| "truncated": false, |
| "block": 22, |
| "row": 28413 |
| }, |
| { |
| "path": "gffquant/alignment/samflags.py", |
| "sha256": "ae0ae5fc4bec7369142e7842a87fd78c1b634ac93e2482827f66705362aa95b6", |
| "language": "Python", |
| "lines": 24, |
| "truncated": false, |
| "block": 22, |
| "row": 27433 |
| }, |
| { |
| "path": "gffquant/annotation/__init__.py", |
| "sha256": "0f0a13b39ba3d46d0b66ef17ae86ee8a6dc584a2d2243904da5297e7cd47c58b", |
| "language": "Python", |
| "lines": 8, |
| "truncated": false, |
| "block": 22, |
| "row": 26274 |
| }, |
| { |
| "path": "gffquant/annotation/count_annotator.py", |
| "sha256": "8f4ebaaafe9774bb487b5accfef8feb037d12a86180d517f24f567ffeca83b4f", |
| "language": "Python", |
| "lines": 178, |
| "truncated": false, |
| "block": 23, |
| "row": 8234 |
| }, |
| { |
| "path": "gffquant/annotation/count_writer.py", |
| "sha256": "8a8733607563c6e0a97bd247d327ed829272d217fcad0cdc436bd6b5ecb17d6b", |
| "language": "Python", |
| "lines": 139, |
| "truncated": false, |
| "block": 23, |
| "row": 5749 |
| }, |
| { |
| "path": "gffquant/annotation/genecount_annotator.py", |
| "sha256": "b6e5d7b993b95474435e2a38d9804d4db83b41227e22794b5c345f588cd2aca7", |
| "language": "Python", |
| "lines": 87, |
| "truncated": false, |
| "block": 23, |
| "row": 4612 |
| }, |
| { |
| "path": "gffquant/annotation/regioncount_annotator.py", |
| "sha256": "2626637e98e015779aafec2aa22bf0c61618ad14ca2527646aa4f9d6dca911be", |
| "language": "Python", |
| "lines": 81, |
| "truncated": false, |
| "block": 23, |
| "row": 4250 |
| }, |
| { |
| "path": "gffquant/bin/build_bed_database.py", |
| "sha256": "db118ded0d51ff972cd8f1ef6fced94bb7656403aec5c35cd2b65b134c0ed45c", |
| "language": "Python", |
| "lines": 161, |
| "truncated": false, |
| "block": 23, |
| "row": 6600 |
| }, |
| { |
| "path": "gffquant/bin/build_custom_database.py", |
| "sha256": "f96ab18573da32b638ab3832526d14d8285f3338834bf6faa1add4a4641cc9e9", |
| "language": "Python", |
| "lines": 71, |
| "truncated": false, |
| "block": 23, |
| "row": 2019 |
| }, |
| { |
| "path": "gffquant/bin/build_domain_database.py", |
| "sha256": "0435964466fc4d1d865d7b360f8ddcc961d08bb5f55671df06ff85179a2b4748", |
| "language": "Python", |
| "lines": 162, |
| "truncated": false, |
| "block": 23, |
| "row": 6718 |
| }, |
| { |
| "path": "gffquant/bin/build_gene_database.py", |
| "sha256": "e56f4149e526d365985e2ad5432a9cfe2633ac159aef1fdf650d85d65d604b40", |
| "language": "Python", |
| "lines": 61, |
| "truncated": false, |
| "block": 23, |
| "row": 533 |
| }, |
| { |
| "path": "gffquant/bin/collate_counts.py", |
| "sha256": "d5fd5f9a59807ee87bb0af2e3e2ee3ef14d429a0449ea5af362d21a1a51d05d2", |
| "language": "Python", |
| "lines": 241, |
| "truncated": false, |
| "block": 23, |
| "row": 10012 |
| }, |
| { |
| "path": "gffquant/bin/collate_studies.py", |
| "sha256": "1d58c3b49f7a2c36387fa3290a7c027c0b6674bc3ab0740ad394f83c36a97b7c", |
| "language": "Python", |
| "lines": 58, |
| "truncated": false, |
| "block": 23, |
| "row": 1423 |
| }, |
| { |
| "path": "gffquant/bin/db_collate.py", |
| "sha256": "9c23621fed2dd1873b4a3c9d33ffb7f677526e952cab3f8ece5c60f382f15573", |
| "language": "Python", |
| "lines": 190, |
| "truncated": false, |
| "block": 23, |
| "row": 6696 |
| }, |
| { |
| "path": "gffquant/bin/split_table.py", |
| "sha256": "dd71da87432770343690004a03360a67a2fcbf7a87cf349702a1a7406d6a6a1e", |
| "language": "Python", |
| "lines": 62, |
| "truncated": false, |
| "block": 23, |
| "row": 1089 |
| }, |
| { |
| "path": "gffquant/counters/__init__.py", |
| "sha256": "10fce70e0bc074b3b10d52defb99deffaec5e2425b8bc42b0ac5f23c32a0b55b", |
| "language": "Python", |
| "lines": 8, |
| "truncated": false, |
| "block": 22, |
| "row": 26053 |
| }, |
| { |
| "path": "gffquant/counters/alignment_counter.py", |
| "sha256": "da099251ca9484ca4304e6a6239312225fa4b1b20fb169558a93112225adc9a4", |
| "language": "Python", |
| "lines": 164, |
| "truncated": false, |
| "block": 23, |
| "row": 7510 |
| }, |
| { |
| "path": "gffquant/counters/count_matrix.py", |
| "sha256": "1dc71574fbbfe0632870c545cccfa1b94e2b31001659d7d7c2554c9be826c49e", |
| "language": "Python", |
| "lines": 163, |
| "truncated": false, |
| "block": 23, |
| "row": 7244 |
| }, |
| { |
| "path": "gffquant/counters/region_counter.py", |
| "sha256": "824634aa3bb253a1a85490948029460c0b6c0cc48f2ab118071d791a3119a0d7", |
| "language": "Python", |
| "lines": 38, |
| "truncated": false, |
| "block": 23, |
| "row": 175 |
| }, |
| { |
| "path": "gffquant/db/__init__.py", |
| "sha256": "e58f47c28aff4ac9b1224469094d2ee1630750dd7897362c5305addb34a77dc5", |
| "language": "Python", |
| "lines": 64, |
| "truncated": false, |
| "block": 23, |
| "row": 1416 |
| }, |
| { |
| "path": "gffquant/db/annotation_db.py", |
| "sha256": "74adfbe9ad9c963a46d00ef072f1b18cbf769c4b311054caadb099e957c878ef", |
| "language": "Python", |
| "lines": 287, |
| "truncated": false, |
| "block": 23, |
| "row": 10378 |
| }, |
| { |
| "path": "gffquant/db/gff_dbm.py", |
| "sha256": "026911b8cd2625223cbed11fe3083e89774d0543b9dfbe7a6ef839986064a278", |
| "language": "Python", |
| "lines": 253, |
| "truncated": false, |
| "block": 23, |
| "row": 9739 |
| }, |
| { |
| "path": "gffquant/db/importers/__init__.py", |
| "sha256": "6a01f2cf912c153675e3f3bd9db45e25d06654c4ee3fa5e193f2b04ad420cdbc", |
| "language": "Python", |
| "lines": 10, |
| "truncated": false, |
| "block": 22, |
| "row": 26783 |
| }, |
| { |
| "path": "gffquant/db/importers/annstr_db_importer.py", |
| "sha256": "4d13746a699acbb238954b5f981ff0cabac1617df00c7d23f65d4a35de1cd86c", |
| "language": "Python", |
| "lines": 113, |
| "truncated": false, |
| "block": 23, |
| "row": 4770 |
| }, |
| { |
| "path": "gffquant/db/importers/chunk_reader.py", |
| "sha256": "8ee125c2ace1f6c6b51ee71872f930dd2489c9dedd4ecac601150637cf7d89f7", |
| "language": "Python", |
| "lines": 15, |
| "truncated": false, |
| "block": 22, |
| "row": 26769 |
| }, |
| { |
| "path": "gffquant/db/importers/custom_database_importer.py", |
| "sha256": "7459bbc88a5888fe947195d553bc6f543aa6f271d89cef727ef1bf42d37365d8", |
| "language": "Python", |
| "lines": 89, |
| "truncated": false, |
| "block": 23, |
| "row": 3589 |
| }, |
| { |
| "path": "gffquant/db/importers/database_importer.py", |
| "sha256": "49ea4b03a5df5c9df7aa61f8cf35d9435d52323dbd6ae55cb7cc359ec63e30a4", |
| "language": "Python", |
| "lines": 149, |
| "truncated": false, |
| "block": 23, |
| "row": 6888 |
| }, |
| { |
| "path": "gffquant/db/importers/gene_database_importer.py", |
| "sha256": "5b64182a2f3ec1259677626c70be0efe52add1c22c4ea66cf069a68a863e53f9", |
| "language": "Python", |
| "lines": 66, |
| "truncated": false, |
| "block": 23, |
| "row": 1249 |
| }, |
| { |
| "path": "gffquant/db/importers/settings.py", |
| "sha256": "bfc33b09d8f1b2c4555146b50db2261ece140b13e1073808f1804e612ec20ca7", |
| "language": "Python", |
| "lines": 35, |
| "truncated": false, |
| "block": 22, |
| "row": 28581 |
| }, |
| { |
| "path": "gffquant/db/importers/small_database_importer.py", |
| "sha256": "d2ad02fcd728b9c6bd580da474652ae131e16f0b629f5af99f7303334c332f01", |
| "language": "Python", |
| "lines": 52, |
| "truncated": false, |
| "block": 23, |
| "row": 455 |
| }, |
| { |
| "path": "gffquant/db/importers/small_genome_database_importer.py", |
| "sha256": "dce45b6e2dad5eda5b07e8752ec58f366d381b73e4afc5b62df5eed9a0a745a0", |
| "language": "Python", |
| "lines": 113, |
| "truncated": false, |
| "block": 23, |
| "row": 4198 |
| }, |
| { |
| "path": "gffquant/db/models/db.py", |
| "sha256": "50861d37e78d1bfd8c23dadf552d70de069b8087dd64048e15d67b98b1ef9b19", |
| "language": "Python", |
| "lines": 83, |
| "truncated": false, |
| "block": 23, |
| "row": 1376 |
| }, |
| { |
| "path": "gffquant/db/models/meta.py", |
| "sha256": "58312fe87770e9115b584b3faecc9425da9626b91410bff7161b6070cbe0c908", |
| "language": "Python", |
| "lines": 7, |
| "truncated": false, |
| "block": 22, |
| "row": 26018 |
| }, |
| { |
| "path": "gffquant/handle_args.py", |
| "sha256": "63138d6f1b4351be2071aa6473cc28968a5d80789af33d083047496f5add5c40", |
| "language": "Python", |
| "lines": 392, |
| "truncated": false, |
| "block": 23, |
| "row": 11352 |
| }, |
| { |
| "path": "gffquant/profilers/__init__.py", |
| "sha256": "d110fabd9644a66216fdca8acb6b32480a85e2260d3da6570c636c505d8cff49", |
| "language": "Python", |
| "lines": 7, |
| "truncated": false, |
| "block": 22, |
| "row": 26013 |
| }, |
| { |
| "path": "gffquant/profilers/feature_quantifier.py", |
| "sha256": "66a7cebb6ba2431647ac467618968a0500fa1a4344495b1dec28883c7669faa9", |
| "language": "Python", |
| "lines": 506, |
| "truncated": false, |
| "block": 23, |
| "row": 12992 |
| }, |
| { |
| "path": "gffquant/profilers/gene_quantifier.py", |
| "sha256": "cd83366809b4b840c976a955ccdd03f7e609887084ef82b2a0c8859a538eef47", |
| "language": "Python", |
| "lines": 37, |
| "truncated": false, |
| "block": 22, |
| "row": 28806 |
| }, |
| { |
| "path": "gffquant/profilers/panda_coverage_profiler.py", |
| "sha256": "694ef6947a6ad377f1385e356d74bd80060660bb13e09e4d9e11ae7cafc70624", |
| "language": "Python", |
| "lines": 178, |
| "truncated": false, |
| "block": 23, |
| "row": 8616 |
| }, |
| { |
| "path": "gffquant/profilers/panda_profiler.py", |
| "sha256": "7870e8816f5ff364fedd307b2a0fead73f7d9256f0f510f56c45791b6846b2a5", |
| "language": "Python", |
| "lines": 367, |
| "truncated": false, |
| "block": 23, |
| "row": 12098 |
| }, |
| { |
| "path": "gffquant/profilers/region_quantifier.py", |
| "sha256": "19f1d1cc6d1a11196854ce17746e20460119e3c168ade5f5c0657c8854074b93", |
| "language": "Python", |
| "lines": 41, |
| "truncated": false, |
| "block": 22, |
| "row": 29099 |
| }, |
| { |
| "path": "gffquant/runners/alignment_runner.py", |
| "sha256": "89d99b63098f52f7c33d4af87bcf9a962b0a544d9a7a96e2804b3bf4a19a8637", |
| "language": "Python", |
| "lines": 88, |
| "truncated": false, |
| "block": 23, |
| "row": 3653 |
| }, |
| { |
| "path": "gffquant/ui/validation.py", |
| "sha256": "086402fa7e5819ee33adb1df7f00178a9f4e48aa5342f24c8d52137837f76ad9", |
| "language": "Python", |
| "lines": 64, |
| "truncated": false, |
| "block": 23, |
| "row": 1172 |
| }, |
| { |
| "path": "gffquant/util/fileio.py", |
| "sha256": "3fb5ae9ecb8b8ee0966042aaa672a21e080f3053a7a2c6229bffde7d4372d082", |
| "language": "Python", |
| "lines": 11, |
| "truncated": false, |
| "block": 22, |
| "row": 26527 |
| }, |
| { |
| "path": "setup.py", |
| "sha256": "220ca0ae3fe496d7d6a9265c8762ab197dd19c7f337e0aafefa7bbe849914397", |
| "language": "Python", |
| "lines": 70, |
| "truncated": false, |
| "block": 23, |
| "row": 1963 |
| }, |
| { |
| "path": "util/gff_indexer.py", |
| "sha256": "a5487c76dadd549a1e0f83536e52b2a43e4c76218f4f5380ea84091023e21e39", |
| "language": "Python", |
| "lines": 49, |
| "truncated": false, |
| "block": 23, |
| "row": 280 |
| } |
| ] |
| } |
