psite_annotation.addInVitroKinases

psite_annotation.addInVitroKinases(df, inVitroKinaseSubstrateMappingFile)

Annotate pandas dataframe with upstream in vitro kinases according to Sugiyama et al (2019).

Adds the following annotation columns to dataframe:

In Vitro Kinases = all phosphorylating kinases according to the Sugiyama in vitro kinase-substrate study

Example

df = pa.addPeptideAndPsitePositions(df, pa.pspFastaFile, pspInput = True)
df = pa.addInVitroKinases(df, pa.inVitroKinaseSubstrateMappingFile)

Required columns:

Site positions

Parameters:

df (DataFrame) – pandas dataframe with ‘Site positions’ column
inVitroKinaseSubstrateMappingFile (str) – tab separated file with in vitro kinase annotations

Returns:

annotated dataframe

Return type:

pd.DataFrame