psite_annotation.annotators.PSPRegulatoryAnnotator

class psite_annotation.annotators.PSPRegulatoryAnnotator(annotation_file, organism='human')

Bases: object

Annotate pandas dataframe with regulatory functions according to PhosphositePlus.

Example

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

Initialize the input files and options for PSPRegulatoryAnnotator.

Parameters:

annotation_file (str) – tab separated file with PhosphositePlus annotations

Methods

annotate

Adds columns with number of studies.

load_annotations

Reads in tab separated file with PhosphositePlus annotations and stores it as a dictionary.
annotate(df)

Adds columns with number of studies.

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

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 and stores it as a dictionary.

Return type:

None