psite_annotation.annotators.PTMTurnoverAnnotator

class psite_annotation.annotators.PTMTurnoverAnnotator(annotation_file)

Bases: object

Annotate pandas dataframe with Jana’s PTM Turnover data.

https://www.nature.com/articles/s41467-021-27639-0

Example

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

Initialize the input files and options for PTMTurnoverAnnotator.

Parameters:

annotation_file (str) – comma separated file with PTM turnover annotations

Methods

annotate	Adds column regarding the PTM turnover behavior.
load_annotations	Reads in comma separated file with PTM turnover annotations.

annotate(df)

Adds column regarding the PTM turnover behavior.

Adds the following annotation columns to dataframe:

• ‘PTM Turnover’ = rate of turnover for the modification sites according to Jana’s PTM Turnover data

Parameters:

df (DataFrame) – pandas dataframe with ‘Modified sequence’ column

Returns:

annotated dataframe

Return type:

pd.DataFrame

Required columns:

Modified sequence

load_annotations()

Reads in comma separated file with PTM turnover annotations.

The “PTM_Turnover” column can contain one of the following values: - slower - faster - FALSE - “” FALSE indicates there as “no difference” in PTM turnover A missing value indicates there were “not enough replicates”

Return type:

None