def block_generator(self): masking_plot = PlotParser(self.combined_mask_file) blocks = self.increased_insertions_blocks(masking_plot) + self.decreased_insertions_blocks(masking_plot) '''Filter out blocks which are less than the window size''' filtered_blocks = [b for b in blocks if b.block_length >= self.window_size] forward_masking_plot = PlotParser(self.forward_mask_file) reverse_masking_plot = PlotParser(self.reverse_mask_file) for b in filtered_blocks: b.direction = self.direction_for_block(b, forward_masking_plot, reverse_masking_plot) return filtered_blocks
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 get_plot_objs(self, files):
plot_objs = {}
for f in files:
plot_objs[f] = PlotParser(f)
self.genome_size = len(plot_objs[f].combined)
if self.verbose:
print(plot_objs[f])
return plot_objs
def test_valid_threshold(self):
d = PlotParser(os.path.join(data_dir, 'valid'), 3)
self.assertTrue(
self.check_arrays_equal(d.forward, [0, 0, 0, 0, 0, 0, 0, 3]))
self.assertTrue(
self.check_arrays_equal(d.reverse, [0, 0, 4, 5, 0, 0, 0, 0]))
self.assertTrue(
self.check_arrays_equal(d.combined, [0, 0, 4, 5, 0, 0, 0, 3]))
def test_valid_ziped(self):
d = PlotParser(os.path.join(data_dir, 'valid.gz'), 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, [0, 1, 4, 5, 0, 0, 0, 0]))
self.assertTrue(
self.check_arrays_equal(d.combined, [0, 1, 4, 5, 0, 1, 1, 3]))
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 plot_parser(self):
return PlotParser(self.plotfile, self.minimum_threshold)
def read_plots(self):
plot_objs = {}
for p in self.plotfiles:
pp = PlotParser(p)
plot_objs[p] = pp
return plot_objs
def test_large_file_zipped(self):
d = PlotParser(
os.path.join(data_dir,
'Control2.out.CP009273.insert_site_plot.gz'), 3)
self.assertEqual(d.total_reads, 7684360)