def action(args): controls, sample_groups = get_input(args.infile, split_description = args.split_desc) qadata = qa_from_csv(qafile) matrix = read_matrix(matrix_file) style = 'screen' if args.outfile == sys.stdout else 'file' outfile = get_outfile(args, label = 'results', ext = 'csv') if args.calculate_ion_ratios: qadata = add_ion_ratios(qadata, controls) samples = get_samples(controls, sample_groups, qadata, matrix) display_results(samples, outfile, style = style, grouped = args.grouped) if args.outfile is None: outfile.close()
def test03(self): display_results(self.samples, sys.stdout, grouped = False)
def test02(self): display_results(self.samples, sys.stdout, style = 'file')
def test01(self): display_results(self.samples, sys.stdout)
def test03(self): display_results(self.samples, sys.stdout, grouped=False)
def test02(self): display_results(self.samples, sys.stdout, style='file')