psite_annotation

Convenience functions for annotating a pandas dataframe with a variety of annotations.

Functions

addDomains(df, domainMappingFile)	Adds column with domains the peptide overlaps with.
addInVitroKinases(df, ...)	Annotate pandas dataframe with upstream in vitro kinases according to Sugiyama et al (2019).
addKinaseLibraryAnnotations(df, motifs_file, ...)	Annotate pandas dataframe with highest scoring kinases from the kinase library.
addModifiedSequenceGroups(df[, match_tolerance])	Annotate DataFrame with representative sequences from grouped localizations.
addMotifs(df, motifsFile)	Adds column with motifs the site sequence context matches with.
addPSPAnnotations(df, phosphoSitePlusFile[, ...])	Annotate pandas dataframe with number of high and low-throughput studies according to PhosphositePlus.
addPSPKinaseSubstrateAnnotations(df, ...[, ...])	Annotate pandas dataframe with upstream kinases according to PhosphositePlus.
addPSPRegulatoryAnnotations(df, ...[, organism])	Annotate pandas dataframe with regulatory functions according to PhosphositePlus.
addPeptideAndPsitePositions(df, fastaFile[, ...])	Annotate pandas dataframe with positions of the peptide within the protein sequence based on a fasta file.
addSiteSequenceContext(df, fastaFile[, ...])	Annotate pandas dataframe with sequence context of a p-site.
addTurnoverRates(df, turnoverFile)	Annotate pandas dataframe with PTM turnover behavior.
aggregateModifiedSequenceGroups(df, ...[, ...])	Annotate and aggregate DataFrame with representative sequences from grouped localizations.