{"id":20834933,"url":"https://github.com/robaina/seqpicker","last_synced_at":"2025-07-24T09:31:35.579Z","repository":{"id":260627460,"uuid":"881445282","full_name":"Robaina/seqpicker","owner":"Robaina","description":null,"archived":false,"fork":false,"pushed_at":"2024-11-01T13:34:12.000Z","size":25,"stargazers_count":1,"open_issues_count":1,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-07-19T14:33:51.054Z","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":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Robaina.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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2024-10-31T15:31:20.000Z","updated_at":"2024-11-03T09:51:17.000Z","dependencies_parsed_at":"2024-11-01T13:30:24.733Z","dependency_job_id":"bdbc4818-f833-44bd-ae40-33628f7f3255","html_url":"https://github.com/Robaina/seqpicker","commit_stats":null,"previous_names":["robaina/seqpicker"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/Robaina/seqpicker","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Robaina%2Fseqpicker","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Robaina%2Fseqpicker/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Robaina%2Fseqpicker/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Robaina%2Fseqpicker/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Robaina","download_url":"https://codeload.github.com/Robaina/seqpicker/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Robaina%2Fseqpicker/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":266821732,"owners_count":23989820,"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","status":"online","status_checked_at":"2025-07-24T02:00:09.469Z","response_time":99,"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":"2024-11-18T00:21:53.652Z","updated_at":"2025-07-24T09:31:33.321Z","avatar_url":"https://github.com/Robaina.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# 🔍 seqpicker\n\nA Python tool for selecting representative protein sequences from large datasets. It combines CD-HIT clustering with an advanced representative set selection algorithm: [Repset](https://onlinelibrary.wiley.com/doi/10.1002/prot.25461) to maintain sequence diversity while reducing redundancy.\n\n## ✨ Features\n\n- Reduce protein sequence redundancy using CD-HIT\n- Select representative sequences using submodular optimization\n- Maintain sequence diversity while minimizing dataset size\n- Easy-to-use command line interface\n- Flexible Python API for integration into bioinformatics pipelines\n\n## ⚙️ Installation\n\n```bash\nconda create -f environment.yml\nconda activate seqpicker\n(seqpicker) poetry build\n(seqpicker) pip install dist/seqpicker-0.1.0-py3-none-any.whl\n```\n\n## 🚀 Usage\n\n### 💻 Command Line\n\n```bash\n# Basic usage\nseqpick input.fasta -o output.fasta --maxsize 1000\n\n# Use only CD-HIT (faster but less sophisticated)\nseqpick input.fasta --cdhit-only --similarity 0.9\n\n# Use only RepSet selection (slower but more accurate)\nseqpick input.fasta --repset-only --maxsize 500\n\n# Fine-tune the selection process\nseqpick input.fasta \\\n    --maxsize 1000 \\\n    --mixture-weight 0.7 \\\n    --cdhit-args \"-c 0.9 -n 5\"\n```\n\n### 🐍 Python API\n\n```python\nfrom seqpicker import reduce_database_redundancy\n\n# Basic usage\nreduce_database_redundancy(\n    input_fasta=\"input.fasta\",\n    output_fasta=\"output.fasta\",\n    maxsize=1000\n)\n\n# Advanced usage with more control\nreduce_database_redundancy(\n    input_fasta=\"input.fasta\",\n    output_fasta=\"output.fasta\",\n    cdhit=True,\n    maxsize=1000,\n    cdhit_args=\"-c 0.9 -n 5\",\n    mixture_weight=0.7\n)\n```\n\n## 🧠 How It Works\n\nseqpicker uses a two-step approach to select representative sequences:\n\n1. **Initial Redundancy Reduction** (optional)\n   - Uses CD-HIT to quickly remove highly similar sequences\n   - Configurable similarity threshold and parameters\n\n2. **Representative Selection**\n   - Implements RepSet, a submodular optimization algorithm to select representative sequences\n   - Balances sequence diversity and coverage\n   - Uses sequence similarity and redundancy metrics\n   - Configurable mixture weight between objectives\n\n## 📦 Dependencies\n\n- [CD-HIT](http://weizhongli-lab.org/cd-hit/)\n- [RepSet](https://onlinelibrary.wiley.com/doi/10.1002/prot.25461)\n- [Mafft](https://mafft.cbrc.jp/alignment/software/)\n- [HMMER (esl-alipid)](http://hmmer.org/)\n\n\n## 🤝 Contributing\n\nContributions are welcome! Please feel free to submit a Pull Request.\n\n## 📜 License\n\nThis project is licensed under the MIT License - see the LICENSE file for details.\n\n## ✏️ Citation\n\nIf you use seqpicker in your research, please cite:\n\n```bibtex\n@software{seqpicker2024,\n  author = {Semidán Robaina Estévez},\n  title = {seqpicker: A tool for selecting representative protein sequences},\n  year = {2024},\n  publisher = {GitHub},\n  url = {https://github.com/Robaina/seqpicker}\n}\n```","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frobaina%2Fseqpicker","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frobaina%2Fseqpicker","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frobaina%2Fseqpicker/lists"}