{"id":31913476,"url":"https://github.com/alejandrogzi/postoga","last_synced_at":"2026-01-28T16:04:23.622Z","repository":{"id":198560781,"uuid":"701031071","full_name":"alejandrogzi/postoga","owner":"alejandrogzi","description":"The post-TOGA processing pipeline","archived":false,"fork":false,"pushed_at":"2026-01-22T12:41:14.000Z","size":5115,"stargazers_count":9,"open_issues_count":1,"forks_count":4,"subscribers_count":1,"default_branch":"master","last_synced_at":"2026-01-23T02:16:45.955Z","etag":null,"topics":["bioinformatics","gene-annotation","pipeline","post-processing"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/alejandrogzi.png","metadata":{"files":{"readme":"README.md","changelog":"Changelog.md","contributing":null,"funding":null,"license":"LICENSE","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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2023-10-05T19:12:27.000Z","updated_at":"2026-01-22T12:41:18.000Z","dependencies_parsed_at":"2024-02-25T23:21:34.314Z","dependency_job_id":"be453472-30e6-48aa-b153-c0133f6d8877","html_url":"https://github.com/alejandrogzi/postoga","commit_stats":{"total_commits":98,"total_committers":2,"mean_commits":49.0,"dds":"0.061224489795918324","last_synced_commit":"8c65899b9fc1caeb0e3cffab6cf6a71e21c6bade"},"previous_names":["alejandrogzi/postoga"],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/alejandrogzi/postoga","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alejandrogzi%2Fpostoga","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alejandrogzi%2Fpostoga/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alejandrogzi%2Fpostoga/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alejandrogzi%2Fpostoga/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/alejandrogzi","download_url":"https://codeload.github.com/alejandrogzi/postoga/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alejandrogzi%2Fpostoga/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28846769,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-28T15:15:36.453Z","status":"ssl_error","status_checked_at":"2026-01-28T15:15:13.020Z","response_time":57,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["bioinformatics","gene-annotation","pipeline","post-processing"],"created_at":"2025-10-13T18:49:33.558Z","updated_at":"2026-01-28T16:04:23.617Z","avatar_url":"https://github.com/alejandrogzi.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003e [!WARNING]\n\u003e\n\u003e postoga is dependent from [TOGA2](https://github.com/hillerlab/TOGA2). Any changes in TOGA2 will have a repercusion here. If you found any bug/errors, please report them here.\n\u003e This project is in constant development, any desired features are welcome!\n\n\n# postoga\n\nThe post-[TOGA](https://github.com/hillerlab/TOGA2) processing pipeline.\n\n![version](https://img.shields.io/badge/version-0.12-orange)\n\n\u003cp align=\"center\"\u003e\n    \u003cimg width=700 align=\"center\" src=\"./assets/postoga_logo_git.png\" \u003e\n\u003c/p\u003e\n\n\u003c!-- \u003cimg src=\"./supply/postoga_report.png\" align=\"center\"/\u003e --\u003e\n\n## What's new on version 0.12\n\n\u003e - Changed 'orthology_status' to 'loss_status' in CLI interface\n\u003e - Updated main runner and query table maker to use 'loss_status' terminology\n\n## Usage\n\nTo use postoga, just:\n\nClone the repository\n```bash\n# clone the repository\ngit clone --recursive https://github.com/alejandrogzi/postoga.git\ncd postoga\n```\n\nActivate the environment and configure binaries\n```bash\n# Recommended: bootstrap everything (uv venv + pip install + maturin develop)\n./setup_postoga.sh\n\n# Manual alternative using Hatch targets\npip install hatch\nmake configure\n```\n\nHere is a descrption of postoga features:\n\n\u003e [!TIP]\n\u003e\n\u003e If the only thing you want to do is apply some filters to a TOGA result or convert results to GTF/GFF files, I recommend the following command:\n\u003e\n\u003e ```bash\n\u003e ./postoga.py \\\n\u003e --togadir /your/TOGA/dir \\\n\u003e --outdir /your/out/dir \\\n\u003e -bc [YOUR CLASSES] \\\n\u003e -br [YOUR STATUS] \\\n\u003e -bs [YOUR THRESHOLD] \\\n\u003e -bp [YOUR PARALOG SCORE] \\\n\u003e -to [YOUR FORMAT GTF/GFF] \\\n\u003e --depure \\\n\u003e -L info\n\u003e ```\n\n```text\nusage: postoga.py [-h] --togadir TOGADIR [-bc ORTHOLOGY_STATUS]\n                       [-br ORTHOLOGY_CLASS] [-bs ORTHOLOGY_SCORE]\n                       [-to {gtf,gff,bed}] [-tg {bed,utr}]\n                       [-bp MIN_PARALOG_SCORE] [-w WITH_ISOFORMS]\n                       [-ext [{query,reference}]] [--outdir OUTDIR]\n                       [--only-table] [--only-convert]\n                       [-L {debug,info,warn,off}] [--depure] [--version]\n\noptional arguments:\n  -h, --help            show this help message and exit\n  --togadir TOGADIR, -td TOGADIR\n                        Path to TOGA results directory\n  -bc ORTHOLOGY_STATUS, --by-orthology-status ORTHOLOGY_STATUS\n                        Filter parameter to only include certain orthology\n                        classes (FI, I, PI, UL, M, PM, L, UL)\n  -br ORTHOLOGY_CLASS, --by-orthology-class ORTHOLOGY_CLASS\n                        Filter parameter to only include certain orthology\n                        relationships (o2o, o2m, m2m, m2m, o2z)\n  -bs ORTHOLOGY_SCORE, --by-orthology-score ORTHOLOGY_SCORE\n                        Filter parameter to preserve orthology scores greater\n                        or equal to a given threshold (0.0 - 1.0)\n  -to {gtf,gff,bed}, --to {gtf,gff,bed}\n                        Specify the conversion format for .bed\n                        (query_annotation/filtered) file (gtf, gff3) or just\n                        keep it as .bed (bed)\n  -tg {bed,utr}, --target {bed,utr}\n                        Specify the .bed input file to used by the program\n  -bp MIN_PARALOG_SCORE, --by-paralog-score MIN_PARALOG_SCORE\n                        Filter parameter to preserve transcripts with paralog\n                        projection probabilities less or equal to a given\n                        threshold (0.0 - 1.0)\n  -w WITH_ISOFORMS, --with-isoforms WITH_ISOFORMS\n                        Path to a custom isoform table (default: None)\n  -ext [{query,reference}], --extract [{query,reference}]\n                        Flag or option to extract sequences (only codon and\n                        protein alignments) from the filtered genes. Can be\n                        'query', 'reference', or just set as a flag (default:\n                        False). When used as a flag extracting 'query'\n                        sequences is assumed.\n  --outdir OUTDIR, -o OUTDIR\n                        Path to posTOGA output directory\n  --only-table, -ot    Only produce the toga.table file\n  --only-convert, -oc  Only convert the toga.table file to gtf/gff\n  -L {debug,info,warn,off}, --level {debug,info,warn,off}\n                        Logging verbosity (debug, info, warn, off)\n  --depure, -d          Remove any trace of other postoga runs/files\n  --version, -v         show this help message and exit\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falejandrogzi%2Fpostoga","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Falejandrogzi%2Fpostoga","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falejandrogzi%2Fpostoga/lists"}