esmrank 0.1.0__tar.gz

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esmrank-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: esmrank
+Version: 0.1.0
+Summary: A learn-to-rank approach for protein variant effect prediction
+Author: Riccardo Arnese, Gennaro Gambardella
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://github.com/gambalab/ESMRank
+Project-URL: Issues, https://github.com/gambalab/ESMRank/issues
+Keywords: protein,variant effect prediction,learning to rank,protein language model,bioinformatics
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=2.0
+Requires-Dist: pandas>=2.2
+Requires-Dist: scikit-learn>=1.5
+Requires-Dist: scipy>=1.13
+Requires-Dist: tqdm>=4.66
+Requires-Dist: xgboost<3,>=2.1
+Requires-Dist: edlib>=1.3.9
+Requires-Dist: pyhmmer<0.12,>=0.11
+Requires-Dist: biopython>=1.85
+Requires-Dist: transformers<5,>=4.57
+Requires-Dist: torch>=2.1
+Requires-Dist: accelerate>=0.26.0
+Requires-Dist: matplotlib
+Requires-Dist: pyarrow
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Dynamic: license-file
+
+# ESMRank  
+**A learn-to-rank approach for protein variant effect prediction**
+
+ESMRank is a pipeline for ranking protein variants according to their predicted functional impact.  
+The method frames variant effect prediction as a **learning-to-rank problem**, leveraging protein language models and sequence-derived features to prioritize mutations based on fitness, activity, or stability.
+
+---
+
+## Installation
+
+### Requirements
+- Python **3.10+**
+- Linux / macOS
+- A CUDA GPU (the ESM-2 feature step needs one)
+
+### Install with pip
+
+Install a `torch` build that matches your CUDA setup first (see https://pytorch.org), then:
+
+```bash
+pip install git+https://github.com/gambalab/ESMRank.git
+```
+
+This provides the `esmrank` command (and `python -m esmrank`).
+
+### Download the pretrained models
+
+The package does not bundle the models (~830 MB, hosted on Zenodo: https://zenodo.org/records/18773439). Fetch them once with:
+
+```bash
+esmrank download-models
+```
+
+They are stored in `~/.cache/esmrank/model` (or `--dest DIR`). If the installation fails the downloaded archive is kept, so re-running does not download it again; an archive you already have can be used with `esmrank download-models --archive ESMRank.tar.gz`. At run time the model directory is looked up in this order: `--model-dir`, `$ESMRANK_MODEL_DIR`, `./model`, then the cache directory above.
+
+### Install from source (development)
+
+```bash
+git clone https://github.com/gambalab/ESMRank.git
+cd ESMRank
+python -m venv ESMRank_venv && source ESMRank_venv/bin/activate
+pip install -e ".[test]"
+esmrank download-models
+pytest
+```
+
+`requirements.txt` still lists the exact versions the pipeline was developed against; `pyproject.toml` declares compatible ranges.
+
+---
+
+## Usage
+
+### From Python
+
+```python
+import pandas as pd
+import esmrank
+
+# make sure the pretrained files are available (downloads them only if missing)
+model_dir = esmrank.ensure_models()
+
+# a protein sequence instead of a FASTA file
+seq = "MSEQNNTEMTFQIQRIYTKDISFEAPNAPHVFQKDWQPEVKLDLDTASSQLADDVYEVVLRVTVTASLG"
+df = esmrank.rank_variants(seq, sub=True)                    # all missense variants
+df = esmrank.rank_variants(sequence=seq, alanines=True)      # explicit form, any length
+
+# a DataFrame instead of a CSV file (columns hgvsp, seq_wt, seq_mu; extra columns are kept)
+variants = pd.DataFrame({"hgvsp": ["p.Q12V"], "seq_wt": [seq], "seq_mu": [seq[:11] + "V" + seq[12:]]})
+df = esmrank.rank_variants(variants)
+
+# files work as well
+df = esmrank.rank_variants("protein.fasta", sub=True, model_dir=model_dir)
+df = esmrank.rank_variants("variants.csv", csv=True)
+
+# download the models first if they are not there yet
+df = esmrank.rank_variants(seq, alanines=True, auto_download=True)
+```
+
+`rank_variants` returns a DataFrame with columns `ids` and `prediction`.
+
+How the input is interpreted:
+
+| You pass | Treated as |
+|----------|------------|
+| a `pandas.DataFrame` | table of variants (same as CSV mode); `sub` / `indel` / `alanines` do not apply |
+| a string that is an existing file | FASTA file, or CSV file with `csv=True` |
+| a string starting with `>` | text of a single-record FASTA |
+| an all-uppercase string of at least 10 letters that is not an existing file | protein sequence |
+| `sequence="..."` | protein sequence, explicitly (any length, any case) |
+
+A sequence needs at least one of `sub`, `indel`, `alanines`, and may only contain the 20 standard amino acids. Any other string that is not a file raises `FileNotFoundError`, so a mistyped file name is never read as a sequence (use `sequence=` for short ones). Results are still written to `<outdir>/<name>/`: `name` defaults to the file name, the FASTA header, or a short hash of the sequence / DataFrame, and can be set with `name="..."`. The command line only accepts files.
+
+| Function | What it does |
+|----------|--------------|
+| `esmrank.ensure_models(model_dir=None)` | Returns the model directory; downloads the files only if they are missing (into `model_dir`, `$ESMRANK_MODEL_DIR`, or `~/.cache/esmrank/model`) |
+| `esmrank.download_models(dest=None, force=False, verify=True)` | Always downloads (unless already present and not `force`) |
+| `esmrank.find_model_dir(explicit=None)` | Locates existing model files, raises `FileNotFoundError` if none |
+| `esmrank.rank_variants(data, ...)` | Runs the pipeline and returns the predictions as a DataFrame |
+| `esmrank.run_pipeline(data, ...)` | Runs the pipeline and returns the output directory (also has `profile.tsv` / `profile.png`) |
+
+`rank_variants` and `run_pipeline` take the same options as the CLI: `csv`, `sub`, `indel`, `alanines`, `outdir`, `model_dir`, `esm_model`, `batch_size`, `gpu_ids`, plus `sequence`, `name` and `auto_download`. On the command line the equivalent of `auto_download` is `esmrank run --download ...`.
+
+### From command line
+
+```bash
+esmrank run --input INPUT [-csv] [-sub] [-indel] [-alanines]
+            [--outdir DIR] [--model-dir DIR] [--download] [--gpus 0,1] [--batch-size N] [--esm-model NAME]
+```
+
+Results are written to `<outdir>/<input file name>/` (default `output/<name>/`): `predictions.csv`, plus `profile.tsv` and `profile.png` in `-sub` / `-alanines` mode.
+
+---
+
+## Input modes
+
+ESMRank supports **two input modes**: CSV mode and FASTA mode.
+
+From the command line the input is always a file. From Python the input can also be given in memory: a **pandas DataFrame** instead of the CSV file, and a **protein sequence string** instead of the FASTA file (see [From Python](#from-python) for all the details).
+
+---
+
+### CSV mode
+
+In CSV mode, the input must be a CSV file (or, from Python, a pandas DataFrame) containing **three mandatory columns**:
+
+| Column name | Description |
+|------------|-------------|
+| `hgvsp` | Variant identifier |
+| `seq_wt` | Wild-type protein sequence |
+| `seq_mu` | Mutant protein sequence |
+
+Example:
+```csv
+hgvsp,seq_wt,seq_mu
+p.A123V,MSEQNNTEMTFQIQRIYTKDISFEAPNAPHVFQ...,MSEQNNTEMTFQIQRIYTKDISFEVPNAPHVFQ...
+```
+
+To run in CSV mode:
+```bash
+esmrank run --input variants.csv -csv
+```
+
+From Python you can pass a DataFrame directly, without writing a CSV (extra columns are kept):
+```python
+import pandas as pd
+import esmrank
+
+variants = pd.read_csv("variants.csv")      # or any DataFrame with the three columns above
+df = esmrank.rank_variants(variants)        # DataFrame with columns `ids` and `prediction`
+```
+
+---
+
+### FASTA mode
+
+In FASTA mode, the input must be a **single wild-type protein sequence** in FASTA format (or, from Python, the sequence itself as a string).
+
+The pipeline will automatically generate variants based on the selected mutation types:
+
+- `-sub` : generate all possible **missense substitutions**
+- `-indel` : generate all possible **insertions and deletions**
+- `-alanines`: mutually exclusive to sub and indel, generate only alanines substitutions for each aminoacid
+
+Example FASTA:
+```fasta
+>protein_X
+MSEQNNTEMTFQIQRIYTKDISFEAPNAPHVFQ...
+```
+
+Example execution:
+
+generating all missenses variants:
+
+```bash
+esmrank run --input protein.fasta -sub
+```
+generating all single single indel
+
+```bash
+esmrank run --input protein.fasta -indel
+```
+generating all missenses and single indel
+
+```bash
+esmrank run --input protein.fasta -sub -indel
+```
+generate alanine scanning ( alanines substitution only ) 
+
+```bash
+esmrank run --input protein.fasta -alanines
+```
+
+From Python you can pass the sequence as a string instead of a FASTA file; the same `sub`, `indel` and `alanines` options apply:
+```python
+import esmrank
+
+seq = "MSEQNNTEMTFQIQRIYTKDISFEAPNAPHVFQKDWQPEVKLDLDTASSQLADDVYEVVLRVTVTASLG"
+df = esmrank.rank_variants(seq, sub=True)                  # all missense variants
+df = esmrank.rank_variants(sequence=seq, alanines=True)    # alanine scanning
+```
+
+---
+
+## Command-line arguments
+
+| Argument | Description |
+|--------|-------------|
+| `-h` | Show help message |
+| `--input`, `-i` | Path to input file (CSV or FASTA) |
+| `-csv` | Enable CSV input mode (default: FASTA mode) |
+| `-sub` | Generate all possible missense substitutions |
+| `-indel` | Generate all possible insertions and deletions |
+| `-alanines` | Generate alanine substitutions for each position |
+| `--outdir` | Output root directory (default: `output`) |
+| `--model-dir` | Directory with the pretrained model files |
+| `--download` | Download the model files first if they are not already present |
+| `--gpus` | Comma-separated CUDA device ids (default: all) |
+| `--batch-size` | Worker batch size for the ESM step (default: 128) |
+| `--esm-model` | ESM-2 checkpoint name (default: `esm2_t33_650M_UR50D`) |
+
+The command line only accepts files. Sequence strings and DataFrames are available from Python, see [From Python](#from-python).
+
+The environment variables `ESM_GPU_IDS`, `ESM_WORKER_BATCH_SIZE`, `ESM_MODEL_NAME` and `ESM_CHECKPOINT_DIR` are still honoured.
+
+---
+
+## Notes
+
+- CSV and FASTA modes are **mutually exclusive**.
+- In FASTA mode, at least one of `-sub`, `-indel` or `-alanines` must be specified.
+- Runtime and memory usage scale with protein length and number of generated variants.
+
+---
+
+## License
+
+- **Source code**: Apache License 2.0, see [`LICENSE`](LICENSE).
+- **Pretrained model parameters** (downloaded with `esmrank download-models`): ESMRank Model Parameters Non-Commercial Research License, see [`LICENSE_WEIGHTS.md`](LICENSE_WEIGHTS.md). They may be used for non-commercial research and educational purposes only; commercial use requires written permission from the authors.
+- Third-party resources (Pfam-A HMMs, ESM-2 weights) keep their own licenses.
+
+---
+
+## Citation
+
+If you use ESMRank in your research, please cite:
+
+```bibtex
+@article{esmrank,
+  title={ESMRank reveals a transferable axis of protein mutational constraint from overlapping variant effect assays},
+  author={Riccardo Arnese, Gennaro Gambardella},
+  journal={TBD},
+  year={TBD}
+}
+```