psite_annotation.annotators.PSPKinasesAnnotator

class psite_annotation.annotators.PSPKinasesAnnotator(annotation_file, output_gene_names=False, organism='human')

Bases: object

Annotate pandas dataframe with upstream kinases according to PhosphositePlus.

Example

annotator = PSPKinasesAnnotator(<path_to_annotation_file>)
annotator.load_annotations()
df = annotator.annotate(df)

Initialize the input files and options for PSPKinasesAnnotator.

Parameters:

  • annotation_file (str) – tab separated file with PhosphositePlus kinase annotations

  • output_gene_names (bool) – set to True to output the gene names instead of the kinase names

Methods

annotate

Adds column with phosphorylating kinases.

load_annotations

Reads in tab separated file with PhosphositePlus annotations.
annotate(df)

Adds column with phosphorylating kinases.

Adds the following annotation columns to dataframe:

  • PSP Kinases = all phosphorylating kinases according to PhosphoSitePlus, no distinction is made between in vivo and in vitro evidence (this can be added in the future, if necessary)

Parameters:

df (DataFrame) – pandas dataframe with “Site positions” column

Returns:

annotated dataframe

Return type:

pd.DataFrame

Required columns:

Site positions

load_annotations()

Reads in tab separated file with PhosphositePlus annotations.

Return type:

None