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All Samples(2)  |  Call(1)  |  Derive(0)  |  Import(1)
Calculates pairwise semantic similarity scores between two given annotation sets

        def GOSet_PWSimilarity(G, GO1, GO2, metric="GS2", **kargs):
    """
    Calculates pairwise semantic similarity scores between two given annotation sets
    """
    
    if metric=="GS2":
        sim, l=G.GS2([G.GOtoInt(GO1), G.GOtoInt(GO2)])
    elif metric=="CzekanowskiDice":
        sim = G.CzekanowskiDice(G.GOtoInt(GO1), G.GOtoInt(GO2))
        l=[sim,sim]
    elif metric=="Resnik":
        sim,l = G.Resnik(G.GOtoInt(GO1), G.GOtoInt(GO2), kargs.get('IC', dict()))
    else:
        logger.handleWarning ("Sorry, unknown semnatic similarity %s " % metric)
        sim,l=None,None
    
    return sim, l
        


src/a/i/AIGO-0.1.0/AIGO/Compare.py   AIGO(Download)
 
from AIGO import allAspect, logger, logFun
from AIGO.Similarity import GOSet_PWSimilarity
 
class CompareFA(dict):
                D=dict()
                for g in commonGene:
                    sim,l=GOSet_PWSimilarity(FA1.G, FA1.GPtoGO[aspect][g], FA2.GPtoGO[aspect][g])
                    D[g]=(l[0],l[1])