psite_annotation.annotators

Classes for annotating pandas dataframes with a variety of annotations.

Example

from psite_annotation import annotators

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

Classes

ClinicalBasketAnnotator	Annotate pandas dataframe with clinical baskets from Annika.
DomainAnnotator	Annotate pandas dataframe with domains from uniprot.
InVitroKinasesAnnotator	Annotate pandas dataframe with upstream in vitro kinases according to Sugiyama et al (2019).
KinaseLibraryAnnotator	Annotate pandas dataframe with highest scoring kinases from the kinase library.
ModifiedSequenceAggregatorAnnotator	Annotate and aggregate pandas dataframe with representative modified sequence from a modified sequence group.
ModifiedSequenceGroupAnnotator	Annotate pandas dataframe with modified sequence groups where localizations are within match_tolerance of each other.
MotifAnnotator	Annotate pandas dataframe with motifs from uniprot.
PSPKinasesAnnotator	Annotate pandas dataframe with upstream kinases according to PhosphositePlus.
PSPRegulatoryAnnotator	Annotate pandas dataframe with regulatory functions according to PhosphositePlus.
PSPStudiesAnnotator	Annotate pandas dataframe with number of high and low-throughput studies according to PhosphositePlus.
PTMTurnoverAnnotator	Annotate pandas dataframe with Jana's PTM Turnover data.
PeptidePositionAnnotator	Annotate pandas dataframe with positions of the peptide within the protein sequence based on a fasta file.
SiteSequenceContextAnnotator	Annotate pandas dataframe with +/- 15 amino acids around each of the modified sites, separated by semicolons.