def assert_final_peaks_equals_input_peaks(self):
final_peaks = IntervalCollection.create_list_from_file(
"test_max_paths.intervalcollection")
for peak in self.peaks:
self.assertTrue(
peak in final_peaks.intervals,
"Peak %s not in final peaks. Final peaks: \n%s" %
(peak, final_peaks.intervals))
self.assertEqual(len(self.peaks), len(final_peaks.intervals))
def __init__(self, graph, sequence_retriever, linear_path_file_name,
peaks1_file_name, peaks2_file_name):
self.graph = graph
self.sequence_retriever = sequence_retriever
self.peaks1 = PeakCollection.create_list_from_file(peaks1_file_name,
graph=graph)
self.peaks2 = PeakCollection.create_list_from_file(peaks2_file_name,
graph=graph)
print("Number of intervals in set 1/2: %d / %d" %
(len(self.peaks1.intervals), len(self.peaks2.intervals)))
if linear_path_file_name is not None:
self.linear_path = IntervalCollection.create_list_from_file(
linear_path_file_name, self.graph).intervals[0]
def do_asserts(self):
for i, chromosome in enumerate(self.chromosomes):
final_peaks = IntervalCollection.create_list_from_file(
"multigraphs_" + chromosome + "_max_paths.intervalcollection")
for peak in self.peaks[i]:
assert peak in final_peaks