def get_binnary_peptide_overlap(exp1:Experiment, exp2:Experiment)->Peptides:
"""compare the peptide overlap between two experimental objects.
:param exp1: an instance of class Experiment.
:type exp1: Experiment
:param exp2: an instance of class Experiment.
:type exp2: Experiment
:return: a list of peptides that have been identified in both experiments.
:rtype: Peptides
"""
peptide_one=exp1.get_peptides()
peptide_two=exp2.get_peptides()
return list(peptide_one.intersection(peptide_two))
def compute_jaccard_index(exp1:Experiment,exp2:Experiment, level:str='peptide')->float:
"""Compute Jaccard index between samples two samples
Args:
exp1 (Experiment): The first experimental instance
exp2 (Experiment): The first experimental instance
level (str): The level of computing the overlap between samples, can be any of peptide or protein
Returns:
float: Jaccard index computed with regard to the to provide level
"""
if level != 'peptide' and level != 'protein':
raise ValueError(f"Level: {level} is not supported, currently only level, peptide and protein are supported")
if level=='peptide':
return (len(exp1.get_peptides().intersection(exp2.get_peptides())) / len(exp1.get_peptides().union(exp2.get_peptides())))
if level=='protein':
return (len(exp1.get_proteins().intersection(exp2.get_proteins())) / len(exp1.get_proteins().union(exp2.get_proteins())))