Example #1
0
    def test_result_exporter(self):
        polarity = -1
        exp_settings = ExperimentalSettings(10, polarity, is_dims_experiment=False)

        peakels = PeakListReader(op.normcase("mzos/ressources/peaks_matrix_NEG.tsv"), exp_settings).get_peakels()

        ##annotation##
        peakels_annotator = PeakelsAnnotator(peakels, exp_settings)
        best_monos = peakels_annotator.annotate_()

         ##database finding##
        db_search = DatabaseSearch('hmdb', exp_settings)
        nb_metabs, not_found = db_search.assign_formula(peakels, exp_settings.mz_tol_ppm)

        ##scoring
        #first simplistic
        model = StatsModel(peakels, exp_settings.mz_tol_ppm * 1.5)
        #populate annotations objects
        model.calculate_score()

        ##scoring 2##
        bi = BayesianInferer(peakels, exp_settings)
        #populate annotations object
        bi.infer_assignment_probabilities()

        exporter = ResultsExporter(op.normcase("annotations.tsv"), peakels)
        exporter.write()