psite_annotation.addPSPRegulatoryAnnotations

psite_annotation.addPSPRegulatoryAnnotations(df, phosphoSitePlusRegulatoryFile, organism='human')

Annotate pandas dataframe with regulatory functions according to PhosphositePlus.

Adds the following annotation columns to dataframe:

  • PSP_ON_FUNCTION = functional annotations for downstream regulation

  • PSP_ON_PROCESS = process annotations for downstream regulation

  • PSP_ON_PROT_INTERACT = protein interactions

  • PSP_ON_OTHER_INTERACT = other interactions

  • PSP_NOTES = regulatory site notes

Example

df = pa.addPeptideAndPsitePositions(df, pa.pspFastaFile, pspInput = True)
df = pa.addPSPRegulatoryAnnotations(df, pa.pspRegulatoryFile)
Required columns:

Site positions

Parameters:

  • df (DataFrame) – pandas dataframe with ‘Site positions’ column

  • phosphoSitePlusRegulatoryFile (str) – tab separated file with PhosphositePlus regulatory annotations

Returns:

annotated dataframe

Return type:

pd.DataFrame