laydi/scripts/lpls/rpy_go.py

""" Module for Gene ontology related functions called in R"""
import scipy
import rpy
silent_eval = rpy.with_mode(rpy.NO_CONVERSION, rpy.r)

def get_term_sim(termlist, method = "JiangConrath", verbose=False):
    """Returns the similariy matrix between go-terms.

    Arguments:
        termlist: character vector of GO terms
        method: one of
        ("JiangConrath","Resnik","Lin","CoutoEnriched","CoutoJiangConrath","CoutoResnik","CoutoLin")
        verbose: print out various information or not
    """
    _methods = ("JiangConrath","Resnik","Lin","CoutoEnriched","CoutoJiangConrath","CoutoResnik","CoutoLin")
    assert(method in _methods)
    assert(termlist[0][:2]=='GO')
    rpy.r.library("GOSim")
    return rpy.r.getTermSim(termlist, method = method, verbose = verbose)

def get_gene_sim(genelist, similarity='OA',
                 distance="Resnick"):
    rpy.r.library("GOSim")
    rpy.r.assign("ids", genelist)
    silent_eval('a<-getGeneSim(ids)', verbose=FALSE)

def goterms_from_gene(genelist, ontology=['BP'], garbage = ['IEA', 'ISS', 'ND']):
    """ Returns the go-terms from a specified genelist (Entrez id).
    
    """
    rpy.r.library("GO")
    _CODES = {"IMP" : "inferred from mutant phenotype",
              "IGI" : "inferred from genetic interaction",
              "IPI" :"inferred from physical interaction",
              "ISS" : "inferred from sequence similarity",
              "IDA" : "inferred from direct assay",
              "IEP" : "inferred from expression pattern",
              "IEA" : "inferred from electronic annotation",
              "TAS" : "traceable author statement",
              "NAS" : "non-traceable author statement",
              "ND" : "no biological data available",
              "IC" : "inferred by curator"
              }
    _ONTOLOGIES = ['BP', 'CC', 'MF']
    assert(scipy.all([(code in _CODES) for code in garbage]))
    assert(scipy.all([(ont in _ONTOLOGIES) for ont in ontology]))
    have_these = rpy.r('as.list(GOTERM)').keys()
    goterms = {}
    for gene in genelist:
        goterms[gene] = []
        info = rpy.r('GOENTREZID2GO[["' + str(gene) + '"]]')
        #print info
        if info:
            for term, desc in info.items():
                if term not in have_these:
                    print "GO miss:"
                    print term
                if desc['Ontology'] in ontology and desc['Evidence'] not in garbage:
                        goterms[gene].append(term)

    return goterms

def genego_matrix(goterms, tmat, gene_ids, term_ids, func=min):
    ngenes = len(gene_ids)
    nterms = len(term_ids)
    gene2indx = {}
    for i,id in enumerate(gene_ids):
        gene2indx[id]=i
    term2indx = {}
    for i,id in enumerate(term_ids):
        term2indx[id]=i
    #G = scipy.empty((nterms, ngenes),'d')
    G = []
    newindex = []
    for gene, terms in goterms.items():
        g_ind = gene2indx[gene]
        if len(terms)>0:
            t_ind = []
            newindex.append(g_ind)
            for term in terms:
                if term2indx.has_key(term): t_ind.append(term2indx[term])
            print t_ind
            subsim = tmat[t_ind, :]
            gene_vec = scipy.apply_along_axis(func, 0, subsim)
            G.append(gene_vec)

    return scipy.asarray(G), newindex

def goterm2desc(gotermlist):
    """Returns the go-terms description keyed by go-term
    """
    rpy.r.library("GO")
    term2desc = {}
    for term in gotermlist:
        try:
            desc = rpy.r('Term(GOTERM[["' +str(term)+ '"]])')
            term2desc[str(term)] = desc
        except:
            raise Warning("Description not found for %s\n Mapping incomplete" %term)
    return term2desc

def parents_dag(go_terms, ontology=['BP']):
    """ Returns a list of lists representation of a GO DAG parents of goterms.

    make the networkx graph by:
        G = networkx.Digraph()
        G = networkx.from_dict_of_lists(edge_dict, G)
    """
    try:
        rpy.r.library("GOstats")
    except:
        raise ImportError, "Gostats"
    assert(go_terms[0][:3]=='GO:')

    # go valid namespace
    go_env = {'BP':rpy.r.GOBPPARENTS, 'MF':rpy.r.GOMFPARENTS, 'CC': rpy.r.GOCCPARENTS}
    graph = rpy.r.GOGraph(go_terms, go_env[ontology[0]])
    edges = rpy.r.edges(graph)
    edges.pop('all')
    edge_dict = {}
    for head, neighbours in edges.items():
        for nn in neighbours.values():
            if edge_dict.has_key(nn):
                edge_dict[nn].append(head)
            else:
                edge_dict[nn] = [head]
    return edge_dict

def gene_GO_hypergeo_test(genelist, universe, ontology = ['BP']):
    
    pvals = geneGoHyperGeoTest(entrezGeneIds, lib=None, ontology=ontology[0], universe=universe)
    return pvals