psite_annotation.annotators.InVitroKinasesAnnotator

class psite_annotation.annotators.InVitroKinasesAnnotator(annotation_file)

Bases: object

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

https://www.nature.com/articles/s41598-019-46385-4

Example

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

Initialize the input files and options for InVitroKinasesAnnotator.

Parameters:

annotation_file (str) – tab separated file with in vitro kinase annotations

Methods

annotate

Adds column with phosphorylating kinases.

load_annotations

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

Adds column with phosphorylating kinases.

Adds the following annotation columns to dataframe:

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

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 in vitro annotations.

Columns: Type Kinase Uniprot ID Protein description Position SIDIC PTMscore UniprotId UniprotId_Site

Return type:

None