def test_forward_only(self): filename = os.path.join(data_dir, 'test_plotgen') p = PlotGenerator([0,0,0,0,0,1,1,3], [], filename) self.assertTrue(p.construct_file()) self.assertTrue(os.path.exists(filename)) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'expected_plotgen'), filename)) os.remove(filename)
def create_normalised_files(self): plot_objs = self.normalise() output_files = [] for p in self.plotfiles: fd, output_filename = mkstemp() pg = PlotGenerator(plot_objs[p].forward, plot_objs[p].reverse, output_filename) pg.construct_file() output_files.append(output_filename) return output_files
def test_generate_and_read(self): filename = os.path.join(data_dir, 'plot.test') p = PlotGenerator([0,0,0,0,0,1,1,3], [9,9,0,9,9,1,1,3], filename) p.construct_file() d = PlotParser(filename,0) self.assertTrue(self.check_arrays_equal(d.forward, [0,0,0,0,0,1,1,3])) self.assertTrue(self.check_arrays_equal(d.reverse, [9,9,0,9,9,1,1,3])) self.assertTrue(self.check_arrays_equal(d.combined, [9,9,0,9,9,2,2,6])) os.remove(filename)
def masking(self):
masking_plot = PlotParser(self.masking_plot_file)
output_plot_files = {}
for insertion_filename in self.insertion_plot_files:
insertion_plot = PlotParser(insertion_filename)
for i, mask in enumerate(masking_plot.combined):
if mask == 0 and self.strict_signal:
insertion_plot.forward[i] = 0
insertion_plot.reverse[i] = 0
fd, output_filename = mkstemp()
pg = PlotGenerator(insertion_plot.forward, insertion_plot.reverse, output_filename)
pg.construct_file()
output_plot_files[insertion_filename] = output_filename
return output_plot_files
def create_split_plot_file(self, forward, reverse):
fd, filename = mkstemp()
p = PlotGenerator(forward, reverse, filename)
p.construct_file()
return filename