Metadata-Version: 2.4
Name: phasepred
Version: 1.0.2
Summary: Paper-faithful re-implementation of the PhaSePred phase-separation predictor (Chen et al. 2022, PNAS).
Author: Tingting Li Lab, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University
License-Expression: MIT
Project-URL: Homepage, https://www.pnas.org/doi/10.1073/pnas.2115369119
Project-URL: Documentation, https://github.com/NotWhiteBlank/PhaSePred
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.12
Description-Content-Type: text/markdown
License-File: LICENSE
License-File: NOTICE
Requires-Dist: biopython>=1.85
Requires-Dist: catgranule<2,>=1.0
Requires-Dist: joblib>=1.5
Requires-Dist: localcider>=0.1.21
Requires-Dist: matplotlib>=3.8
Requires-Dist: numpy<3,>=1.26
Requires-Dist: openpyxl>=3.1
Requires-Dist: pandas>=2.2
Requires-Dist: pydantic>=2.11
Requires-Dist: pyarrow>=20.0
Requires-Dist: python-calamine>=0.3
Requires-Dist: requests>=2.32
Requires-Dist: scikit-learn>=1.5
Requires-Dist: scipy>=1.13
Requires-Dist: shap>=0.46
Requires-Dist: tqdm>=4.67
Requires-Dist: typer>=0.15
Requires-Dist: xgboost<3.3,>=3.2
Dynamic: license-file

# PhaSePred

Predict the phase-separation propensity of a protein from its amino-acid sequence.
Implementation of [Chen et al. 2022 *PNAS*](https://doi.org/10.1073/pnas.2115369119).

## Install

```bash
pip install phasepred
```

Requires Python >= 3.12. The models and the DeepPhase table ship inside the
package.

Four feature components cannot be redistributed and need a one-time install from
the repository:

```bash
git clone https://github.com/notwhiteblank/PhaSePred.git && cd PhaSePred
bash tools/PScore/install.sh
bash tools/ESpritz/install.sh
bash tools/DeepCoil/install.sh
bash tools/PhosphoSitePlus/install.sh   # only needed for hSaPS / hPdPS
```

The installers put their data under `~/.local/share/phasepred/`, where the
package finds it automatically. `phasepred check-tools` prints a status row per
component, and for every missing one the exact command that installs it. A
complete install reports `9 OK`.

## Use

```bash
phasepred predict --fasta proteins.fasta --mode SaPS --output scores.csv
```

Four modes: `SaPS` and `PdPS` (any species, 8 features), `hSaPS` and `hPdPS`
(human, 10 features). The output CSV carries the score plus every feature value.

Input can also be UniProt accessions:

```bash
phasepred predict --ids "P35637,Q9Y2W1" --mode SaPS --output scores.csv
```

## More

Source, training data, retraining and AUC validation against the paper:
<https://github.com/notwhiteblank/PhaSePred>
