PhaSePred
Predict the phase-separation propensity of a protein from its amino-acid sequence. Implementation of Chen et al. 2022 PNAS.
Install
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:
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
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:
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
1 maintainer
Metadata
1 maintainer
Release files for phasepred 1.0.1
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Source distribution (sdist)
| File | Size | Uploaded | |
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| phasepred-1.0.1.tar.gz | 2.4 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| phasepred-1.0.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 4.0 MB
Release files / phasepred-1.0.1.tar.gz
| Download URL | phasepred-1.0.1.tar.gz |
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| Size | 2.4 MB |
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Release files / phasepred-1.0.1-py3-none-any.whl
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| Tags | Python 3 |
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