Installation

Prerequisites

Psite-annotation requires python >=3.9,<=3.11.

Using pip (recommended)

pip install psite-annotation

Alternatively, you can clone this repository and install it with pip manually:

git clone https://github.com/kusterlab/psite_annotation.git
cd psite_annotation
pip install .

Installing annotation files

The easiest way to use the package is to supply the annotation files each time you call the respective functions. Alternatively, it is also possible to install a configuration file to automatically point to the annotation files.

To set the paths to the annotation files, create a config.json file with the following content:

{
    "domainMappingFile": "/path/to/uniprot_to_domain.csv",
    "inVitroKinaseSubstrateMappingFile": "/path/to/yasushi_supp_table2_kinase_substrate_relations_mapped_ids.tsv",
    "motifsFile": "/path/to/motifs_all.tsv",
    "turnoverFile": "/path/to/TurnoverSites.csv",
    "kinaseLibraryMotifsFile": "/path/to/Motif_Odds_Ratios.txt",
    "kinaseLibraryQuantilesFile": "/path/to/Kinase_Score_Quantile_Matrix.txt",
    "pspFastaFile": "/path/to/Phosphosite_seq.fasta",
    "pspKinaseSubstrateFile": "/path/to/Kinase_Substrate_Dataset",
    "pspAnnotationFile": "/path/to/Phosphorylation_site_dataset",
    "pspRegulatoryFile": "/path/to/Regulatory_sites"
}

Where /path/to should be replaced by the absolute path to the annotation files.

For Kusterlab internal users:

• ask Matthew for the config file.

For external users:

• PhosphoSitePlus annotation files can be downloaded from https://www.phosphosite.org/staticDownloads.action (account needed).

• The other annotation files are available from the annotations.zip file in this repository.

You can then install this config file with:

python -c "import psite_annotation.config as c; c.setUserConfig('./config.json')"