{"id":24330913,"url":"https://github.com/code-jl/dna-sequence-analyzer","last_synced_at":"2025-03-11T11:19:21.896Z","repository":{"id":273003375,"uuid":"912592690","full_name":"Code-JL/DNA-Sequence-Analyzer","owner":"Code-JL","description":"A robust Python-based bioinformatics tool for comprehensive DNA sequence analysis and manipulation.","archived":false,"fork":false,"pushed_at":"2025-01-06T02:05:32.000Z","size":8,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-01-18T01:15:55.828Z","etag":null,"topics":["bio-tools","bioinformatics","biological-data","computational-biology","data-analysis","dna-analysis","dna-sequencing","fasta","gc-content","gene-detection","genetics","genomics","molecular-biology","motif-finding","nucleotide-analysis","python","python3","scientific-computing","sequence-analysis","sequence-manipulation"],"latest_commit_sha":null,"homepage":"","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/Code-JL.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":"2025-01-06T01:42:59.000Z","updated_at":"2025-01-06T02:09:27.000Z","dependencies_parsed_at":"2025-01-18T01:15:59.468Z","dependency_job_id":"f530bd6c-1430-4552-b83d-91621983b64c","html_url":"https://github.com/Code-JL/DNA-Sequence-Analyzer","commit_stats":null,"previous_names":["code-jl/dna-sequence-analyzer"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Code-JL%2FDNA-Sequence-Analyzer","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Code-JL%2FDNA-Sequence-Analyzer/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Code-JL%2FDNA-Sequence-Analyzer/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Code-JL%2FDNA-Sequence-Analyzer/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Code-JL","download_url":"https://codeload.github.com/Code-JL/DNA-Sequence-Analyzer/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243021779,"owners_count":20223068,"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":["bio-tools","bioinformatics","biological-data","computational-biology","data-analysis","dna-analysis","dna-sequencing","fasta","gc-content","gene-detection","genetics","genomics","molecular-biology","motif-finding","nucleotide-analysis","python","python3","scientific-computing","sequence-analysis","sequence-manipulation"],"created_at":"2025-01-18T01:15:40.222Z","updated_at":"2025-03-11T11:19:21.869Z","avatar_url":"https://github.com/Code-JL.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# DNA-Sequence-Analyzer\n\nA robust Python-based bioinformatics tool for comprehensive DNA sequence analysis and manipulation.\n\n## Features\n\n- **GC Content Analysis**: Precise calculation of GC content percentage\n- **Nucleotide Frequency**: Detailed nucleotide distribution analysis\n- **Motif Finding**: Advanced pattern recognition and position reporting\n- **Sequence Manipulation**: Generate complement and reverse complement sequences\n- **Gene Detection**: Identification of potential coding regions using start/stop codons\n- **FASTA Support**: Full support for standard FASTA file format\n\n## Installation\n\n1. Clone the repository:\n```bash\ngit clone https://github.com/yourusername/dna_analyzer.git\ncd dna_analyzer\n```\n\n2. Install dependencies:\n```bash\npip install -r requirements.txt\n```\n\n## Usage\n\n## Basic Analysis\n\n```bash\npython src/main.py -i data/example1.fasta -o results.txt -a\n```\n\n## Motif Search\n\n```bash\npython src/main.py -i data/example2.fasta -m ATCG -o motif_results.txt\n```\n\n## Command Line Arguments\n\n- `-i, --input`: Input FASTA file path\n- `-o, --output`: Output file path for results\n- `-a, --analyze`: Perform complete sequence analysis\n- `-m, --find-motif`: Search for specific DNA motif\n\n## Example Data\n\nThe repository includes two example FASTA files in the 'data/' directory:\n\n- `example1.fasta`: Contains human and mouse gene sequences\n- `example2.fasta`: Contains COVID-19 spike protein and insulin gene fragments\n\n## Testing\n\nRun the test suite:\n\n```bash\npytest tests/\n```\n\n## Project Structure\n\n```bash\ndna_analyzer/\n├── src/\n│   ├── sequence_analyzer.py\n│   ├── utils.py\n│   └── main.py\n├── tests/\n│   └── test_analyzer.py\n├── data/\n│   ├── example1.fasta\n│   └── example2.fasta\n└── docs/\n```\n\n## Technical Details\n\n- Python 3.8+\n- Modular architecture for easy extension\n- Comprehensive test coverage\n- Efficient sequence processing algorithms\n\n## Contributing\n\n- Fork the repository\n- Create your feature branch (`git checkout -b feature/AmazingFeature`)\n- Commit your changes (`git commit -m 'Add some AmazingFeature'`)\n- Push to the branch (`git push origin feature/AmazingFeature`)\n- Open a Pull Request\n\n## License\n\nDistributed under the MIT License. See [LICENSE](LICENSE) for more information.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcode-jl%2Fdna-sequence-analyzer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcode-jl%2Fdna-sequence-analyzer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcode-jl%2Fdna-sequence-analyzer/lists"}