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This was manually curated to ARO:3000175.","shortMessageHtmlLink":"BUG manually curate misannotated gene (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2366426508\" data-permission-text=\"Title is private\" data-url=\"https://github.com/BigDataBiology/argNorm/issues/52\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/BigDataBiology/argNorm/pull/52/hovercard\" href=\"https://github.com/BigDataBiology/argNorm/pull/52\">#52</a>)"}},{"before":"bb97433a4672d0ae7ee04a1c75e066751ed5e405","after":"7568296773acf3fbd48da2e5312954cf1a303710","ref":"refs/heads/main","pushedAt":"2024-06-17T08:17:33.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"luispedro","name":"Luis Pedro Coelho","path":"/luispedro","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/79334?s=80&v=4"},"commit":{"message":"ENH Add lib.DATABASES list\n\nAlso, refactor tests/test_database.py","shortMessageHtmlLink":"ENH Add lib.DATABASES list"}},{"before":"fc177616cc4d5e08fe3c1d24a1604673807dcde4","after":"bb97433a4672d0ae7ee04a1c75e066751ed5e405","ref":"refs/heads/main","pushedAt":"2024-06-11T05:03:14.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"luispedro","name":"Luis Pedro Coelho","path":"/luispedro","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/79334?s=80&v=4"},"commit":{"message":"TST Test database consistency","shortMessageHtmlLink":"TST Test database consistency"}},{"before":"7f639a8d7e12981da572b9db74bb578f809dfc89","after":"fc177616cc4d5e08fe3c1d24a1604673807dcde4","ref":"refs/heads/main","pushedAt":"2024-06-10T11:51:15.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"luispedro","name":"Luis Pedro Coelho","path":"/luispedro","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/79334?s=80&v=4"},"commit":{"message":"DOC Fix MD structure","shortMessageHtmlLink":"DOC Fix MD structure"}},{"before":"7da7beb92a4ce5fc09602976ff3b7e89805d3b28","after":"7f639a8d7e12981da572b9db74bb578f809dfc89","ref":"refs/heads/main","pushedAt":"2024-06-10T10:02:36.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"luispedro","name":"Luis Pedro Coelho","path":"/luispedro","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/79334?s=80&v=4"},"commit":{"message":"RLS Version 0.4.0\n\nMajor changes:\n- Bundle a specific version of ARO with the package instead of downloading it from the internet (ensures reproducibility)\n- Add missing ARO mappings to manual curation.\n- Command line tool accept database/tool names in case-independent way (by @sebastianLedzianowski)\n- `lib.map_to_aro` returns `None` if there is no mapping (raises an exception if the name is missing)","shortMessageHtmlLink":"RLS Version 0.4.0"}},{"before":null,"after":"7f639a8d7e12981da572b9db74bb578f809dfc89","ref":"refs/heads/v0.4.x","pushedAt":"2024-06-10T03:49:48.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"luispedro","name":"Luis Pedro Coelho","path":"/luispedro","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/79334?s=80&v=4"},"commit":{"message":"RLS Version 0.4.0\n\nMajor changes:\n- Bundle a specific version of ARO with the package instead of downloading it from the internet (ensures reproducibility)\n- Add missing ARO mappings to manual curation.\n- Command line tool accept database/tool names in case-independent way (by @sebastianLedzianowski)\n- `lib.map_to_aro` returns `None` if there is no mapping (raises an exception if the name is missing)","shortMessageHtmlLink":"RLS Version 0.4.0"}},{"before":"2619b845859ead8c74b9b2c651006caa71016032","after":"7da7beb92a4ce5fc09602976ff3b7e89805d3b28","ref":"refs/heads/main","pushedAt":"2024-06-09T06:03:34.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"luispedro","name":"Luis Pedro Coelho","path":"/luispedro","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/79334?s=80&v=4"},"commit":{"message":"ADD missing ARO mappings to manual curation (#48)\n\n* ADD missing ARO mappings to manual curation\r\n\r\nA few ARO mappings were missing in the manual curation and they have been added. A few more missing manual curation genes from NCBI, MEGARes, and DeepARG will be added.\r\n\r\nAdditions:\r\n- argannot_curation: (Phe)cpt_strepv:U09991:AAB36569:1412-1948:537 -> ARO: 3000249\r\n- megares_curation: MEG_2114 -> ARO: 3000249, MEG_2430 -> ARO: 3000016, MEG_985 -> ARO: 3000229\r\n- sarg_curation: AM180355.1.gene2260.p01 -> ARO: 3000250\r\n\r\n\r\n* ADD rest of missing manual curations in megares manual curation\r\n\r\nAdditions:\r\nMEG_2865 -> ARO:3000387\r\nMEG_7974 -> ARO:3000076\r\n\r\n* Added missing manual curations for resfinder & resfinderfg\r\n\r\nAdditions:\r\nresfinder_curation: dldHA2X_1_AL939117 -> ARO:3003970, grdA_1_QJX10702 -> ARO:3007382, EstDL136_1_JN242251 -> ARO:3000387\r\nresfinderfg_curation: UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase|KF629588.1|pediatric_fecal_sample|CYC -> ARO:3003970\r\n\r\n* Update outputs for addition of missing manual curations for resfinder & resfinderfg\r\n\r\n* DOC add descriptions for new manual curation files\r\n\r\n* Update tests\r\n\r\nUpdate test_lib expected output for updated manual curation\r\n\r\n- Add test case where map_to_aro() returns None\r\n\r\nThis had to be done as (Phe)cpt_strepv:U09991:AAB36569:1412-1948:537 was given an ARO mapping in the manual curation which previously was not present","shortMessageHtmlLink":"ADD missing ARO mappings to manual curation (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2329207360\" data-permission-text=\"Title is private\" data-url=\"https://github.com/BigDataBiology/argNorm/issues/48\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/BigDataBiology/argNorm/pull/48/hovercard\" href=\"https://github.com/BigDataBiology/argNorm/pull/48\">#48</a>)"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"Y3Vyc29yOnYyOpK7MjAyNC0wOS0xMVQwMDozNzo1MC4wMDAwMDBazwAAAASyo5JH","startCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wOS0xMVQwMDozNzo1MC4wMDAwMDBazwAAAASyo5JH","endCursor":"Y3Vyc29yOnYyOpK7MjAyNC0wNi0wOVQwNjowMzozNC4wMDAwMDBazwAAAARgOki-"}},"title":"Activity · BigDataBiology/argNorm"}