psite_annotation.annotators.PSPStudiesAnnotator

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

Bases: object

Annotate pandas dataframe with number of high and low-throughput studies according to PhosphositePlus.

Example

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

Initialize the input files and options for PSPStudiesAnnotator.

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:

  • LT_LIT = number of low-throughput studies

  • MS_LIT = number of high-throughput Mass Spec studies

  • MS_CST = number of high-throughput Mass Spec studies by CellSignalingTechnologies

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