{"id":26573283,"url":"https://github.com/linsalrob/qiime_scripts","last_synced_at":"2025-03-23T00:40:02.828Z","repository":{"id":146768186,"uuid":"43541291","full_name":"linsalrob/qiime_scripts","owner":"linsalrob","description":"A few scripts that Rob has written to handle qiime files","archived":false,"fork":false,"pushed_at":"2015-10-02T09:56:12.000Z","size":140,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2023-03-24T07:24:52.517Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/linsalrob.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2015-10-02T07:47:25.000Z","updated_at":"2023-04-09T01:34:11.927Z","dependencies_parsed_at":"2023-04-09T01:34:11.791Z","dependency_job_id":null,"html_url":"https://github.com/linsalrob/qiime_scripts","commit_stats":null,"previous_names":[],"tags_count":null,"template":null,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linsalrob%2Fqiime_scripts","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linsalrob%2Fqiime_scripts/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linsalrob%2Fqiime_scripts/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linsalrob%2Fqiime_scripts/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/linsalrob","download_url":"https://codeload.github.com/linsalrob/qiime_scripts/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245040190,"owners_count":20551299,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-03-23T00:40:02.116Z","updated_at":"2025-03-23T00:40:02.817Z","avatar_url":"https://github.com/linsalrob.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# qiime_scripts\nA few scripts that Rob has written to handle qiime files. This is not something we do all the time, but occassionally someone asks us to munge the data into a particular format.\n\nYou are welcome to use the scripts and/or use them as inspiration. You're on your own if you do.\n\n# number_taxonomy.py\n\nHere is the question:\n\nI need the attached otu_tablex.biom to look like the otu_tableQIME.biom, so the numbers in brackets after each classification need to be removed and the k_ / p_/ etc. needs to be added to the front of each classification. \n\ni.e. from this:\n\n```\n\"rows\": [{\"id\": \"OTUId\", \"metadata\": {\"taxonomy\": [\"None\"]}},{\"id\": \"OTU_1;size=18783;\", \"metadata\": {\"taxonomy\": [\"Bacteria(100.0),\\\"Proteobacteria\\\"(45.0),Alphaproteobacteria(33.1),Rhizobiales(33.1),Rhizobiaceae(33.1),Kaistia(33.1)\"]}},{\"id\": \"OTU_2;size=7463;\", \"metadata\": {\"taxonomy\": [\"Bacteria(100.0),\\\"Actinobacteria\\\"(66.7),Actinobacteria(52.0),Actinomycetales(48.6),Nocardioidaceae(41.2),Nocardioides(39.7)\"]}}\n```\n\nto this:\n\n```\n\"rows\": [{\"id\": \"denovo0\", \"metadata\": {\"taxonomy\": [\"k__Bacteria\", \"p__Bacteroidetes\", \"c__[Saprospirae]\", \"o__[Saprospirales]\", \"f__Chitinophagaceae\", \"g__Sediminibacterium\", \"s__\"]}},{\"id\": \"denovo1\", \"metadata\": {\"taxonomy\": [\"Unassigned\"]}},{\"id\": \"denovo2\", \"metadata\": {\"taxonomy\": [\"k__Bacteria\", \"p__Proteobacteria\", \"c__Betaproteobacteria\", \"o__Burkholderiales\", \"f__Comamonadaceae\", \"g__\", \"s__\"]}}\n```\n\nThis script uses our ncbi taxonomy module to create the list.\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flinsalrob%2Fqiime_scripts","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flinsalrob%2Fqiime_scripts","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flinsalrob%2Fqiime_scripts/lists"}