{"id":15580605,"url":"https://github.com/sammyjava/pdcut","last_synced_at":"2026-06-23T13:31:48.656Z","repository":{"id":89729469,"uuid":"454481889","full_name":"sammyjava/PDcut","owner":"sammyjava","description":"Routines for the PDcut project","archived":false,"fork":false,"pushed_at":"2022-03-08T18:19:34.000Z","size":14244,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-02-26T16:27:49.605Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Shell","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/sammyjava.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2022-02-01T17:23:47.000Z","updated_at":"2022-02-01T21:02:12.000Z","dependencies_parsed_at":null,"dependency_job_id":"491c82ed-474c-4d85-8544-af83b534d00e","html_url":"https://github.com/sammyjava/PDcut","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/sammyjava/PDcut","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sammyjava%2FPDcut","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sammyjava%2FPDcut/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sammyjava%2FPDcut/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sammyjava%2FPDcut/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sammyjava","download_url":"https://codeload.github.com/sammyjava/PDcut/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sammyjava%2FPDcut/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":34691714,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-06-23T02:00:07.161Z","response_time":65,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":"2024-10-02T19:31:34.146Z","updated_at":"2026-06-23T13:31:48.628Z","avatar_url":"https://github.com/sammyjava.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"# PDcut routines\n\n## reformat-pho\nThis routine reformats the orthogroups in the `N0.tsv` file into a tab-delimited row format with only protein names.\nFor example, if you ran OrthoFinder in the At_Mus directory (containing the FASTAs), you'll get the following file:\n```\nAt_Mus/OrthoFinder/Results_Feb01/Phylogenetic_Hierarchical_Orthogroups/N0.tsv\n```\nIn this case, run reformat-pho as follows:\n```\n$ cd At_Mus/OrthoFinder/Results_Feb01/\n$ ../../../reformat-pho \u003e pho.tsv\n```\nThis will create a file `pho.tsv` which contains the orthogroup identifiers, e.g.\n```\nHOG     OG      Gene Tree Parent Clade  Arabidopsis_thaliana.TAIR10.pep.all     Mus_musculus-Cilia_proteome\nN0.HOG0000000   OG0000000       n0      AT5G09950.2     AT5G09950.3     AT5G09950.1     AT4G33170.1     AT1G16480.1 ...\n```\nNote that the top lines of this file are *very long* because they contain large At orthogroups. Groups that contain Mus genes are further down in the file.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsammyjava%2Fpdcut","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsammyjava%2Fpdcut","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsammyjava%2Fpdcut/lists"}