selection.py 文件源码

def calculate(self):
        """
        Wrapper method to calculate counts and enrichment scores 
        for all data in the :py:class:`~selection.Selection`.
        """
        if len(self.labels) == 0:
            raise ValueError("No data present across all sequencing libraries [{}]".format(self.name))
        for label in self.labels:
            self.merge_counts_unfiltered(label)
            self.filter_counts(label)
        if self.is_barcodevariant() or self.is_barcodeid():
            self.combine_barcode_maps()
        if self.scoring_method == "counts":
            pass
        elif self.scoring_method == "ratios":
            for label in self.labels:
                self.calc_ratios(label)
        elif self.scoring_method == "simple":
            for label in self.labels:
                self.calc_simple_ratios(label)
        elif self.scoring_method in ("WLS", "OLS"):
            if len(self.timepoints) <= 2:
                raise ValueError("Regression-based scoring requires three or more time points.")
            for label in self.labels:
                self.calc_log_ratios(label)
                if self.scoring_method == "WLS":
                    self.calc_weights(label)
                self.calc_regression(label)
        else:
            raise ValueError('Invalid scoring method "{}" [{}]'.format(self.scoring_method, self.name))

        if self.scoring_method in ("ratios" , "WLS", "OLS") and self.component_outliers:
            if self.is_barcodevariant() or self.is_barcodeid():
                self.calc_outliers("barcodes")
            if self.is_coding():
                self.calc_outliers("variants")