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`eris` 🧬🍏✨\n\n[![PyPI version](https://img.shields.io/pypi/v/eris.svg)](https://pypi.org/project/pyeris/)\n[![Python versions](https://img.shields.io/pypi/pyversions/eris.svg)](https://pypi.org/project/pyeris/)\n[![Documentation](https://img.shields.io/badge/docs-GitHub_Pages-blue.svg)](https://tomdstanton.github.io/eris/)\n[![License](https://img.shields.io/github/license/tomdstanton/eris.svg)](LICENSE)\n\n⋆⁺‧₊☽◯☾₊‧⁺⋆ **Graph-aware contextual annotation of targeted genomic features.** ⋆⁺‧₊☽◯☾₊‧⁺⋆\n\n`eris` is a bioinformatics pipeline designed to resolve and annotate shattered genomic\nfeatures (like mobile genetic elements or structural variants) directly from assembly graphs.\nBy employing a dynamic \"Anchor-and-Traverse\" depth-first search through de Bruijn/string graphs (GFA),\n`eris` stitches together split alignments across multiple micro-contigs, seamlessly bridging sequence\nbubbles and gaps.\n\nCrucially, it utilizes fractional read depth flow to distinguish between dominant wild-type structures and rare\nsub-clonal insertions, returning detailed evolutionary context including upstream flanks, downstream flanks, and\ntrapped passenger genes.\n\n---\n\n## 🚀 Features\n\n* **Graph-Aware Traversal:** Overcomes aligner limitations by traversing assembly graph topology to bridge unaligned micro-contigs and resolve shattered targets.\n* **Sub-Clonal Resolution:** Integrates graph read-depth (`dp`/`rd` tags) to calculate fractional copy number, easily distinguishing low-frequency variant bubbles from dominant paths.\n* **Contextual Annotation:** Sweeps across stitched paths to identify internal passenger genes (e.g., AMR genes trapped inside transposons) and flanking genomic context.\n* **High Performance:** Built for speed with a hybrid architecture utilizing `numpy`, `numba`, and `mappy` (Minimap2).\n* **Standardized Outputs:** Generates detailed tabular reports (TSV), locus-specific FASTAs, and standard annotations (`pyfgs` powered GFF3/FAA).\n\n## 📦 Installation\n\n`eris` requires **Python 3.11 or later**.\n\nInstall directly from PyPI:\n```bash\npip install pyeris\n```\n\n### Dependencies\n\n`eris` relies on the following core libraries:\n\n* `numpy` (\u003e=2.4)\n* `numba` (\u003e=0.65)\n* `mappy` (\u003e=2.3)\n* `pyfgs` (\u003e=0.0.1)\n* `biopython` (\u003e=1.87)\n\n## 🛠️ Usage\n\n`eris` installs a command-line interface `eris` for immediate use.\n\n```bash\neris -i assembly.gfa -d targets.fasta -o results/sample_A\n```\n\n### Basic Arguments\n* `-i`, `--genome`: Path to a genome in fasta or GFA format (can be compressed). GFA is heavily recommended to utilize topological stitching.\n* `-d`, `--targets`: Path to target nucleotide features (fasta or pre-indexed `.mmi`).\n* `-o`, `--outprefix`: Prefix for all generated output files.\n* `-f`, `--feature-type`: The type of feature to annotate (default: `CDS`).\n* `--hops`: Maximum number of contextual genes to sweep upstream/downstream (default: `3`).\n* `--tolerance`: Distance tolerance in base pairs for merging clustered alignments (default: `0`).\n\n### Outputs\nDepending on the arguments provided, eris will output:\n\n1. **`{prefix}_report.tsv`**: A detailed report of every resolved locus, including targets, context (INSIDE, UPSTREAM, DOWNSTREAM), biological effects, topological hops, and fractional depths.\n2. **`{prefix}_loci.fasta`**: The stitched nucleotide sequences for each assembled structural variant.\n3. **`{prefix}_assembly.gff`**: GFF3 annotation of the global features.\n4. **`{prefix}_proteins.faa`**: Amino acid fasta of the global features.\n\n## 📚 Documentation\n\nFor detailed guides, API reference, and advanced configuration, visit the [eris Documentation](https://tomdstanton.github.io/eris/).\n\n## 💻 Development\n\n`eris` uses [`hatch`](https://hatch.pypa.io/) for build and environment management.\n\nTo set up a local development environment ([uv](https://docs.astral.sh/uv/getting-started/installation/) needs to be installed):\n```bash\n# Clone the repository\ngit clone [https://github.com/tomdstanton/eris.git](https://github.com/tomdstanton/eris.git)\ncd eris\nmake dev\n```\n\n### Running Tests \u0026 Linting\n\n`eris` enforces rigorous type checking and linting.\n\n```bash\n# Run tests\npytest\n\n# Run static type checking\nmypy\n\n# Run linting and formatting\nruff check\nruff format\n```\n\n## 📝 License\n\nThis project is licensed under the terms of the LICENSE file included in the repository.\n\n## 🤝 Authors\n\n* **Tom Stanton** - [tomdstanton@gmail.com](mailto:tomdstanton@gmail.com)\n\n---\n\n![eris](https://static.wikia.nocookie.net/dreamworks/images/6/6f/Sinbad-disneyscreencaps.com-1100.jpg/revision/latest?cb=20240311205845)","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftomdstanton%2Feris","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftomdstanton%2Feris","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftomdstanton%2Feris/lists"}