def __init__(self, maf_file, annotations_file, regions_names, coding=True):
Seq.__init__(self)
self.coding = coding
annotations = Importer.get_lines_from_file(annotations_file)
maf_file = Importer.get_lines_from_file(maf_file)
for region_name in regions_names:
print(region_name)
self.tri_num = 0
self.mutation_number = 0
self.trinucleotides_occurences = self.generate_empty_params()
self.neutral_matrix = self.generate_empty_params()
print('extracting annotations')
regions = self.extract_regions_from_annotations(
annotations, region_name)
print('analysing sequence')
self.analyse_maf_file(maf_file, regions)
self.export_tri_occ_and_mutations(region_name)
self.normalize_neutral_matrix()
self.export_results(region_name)
print()
def __init__(self, l=None):
Seq.__init__(self)
if l is None:
self.data = []
else:
self.data = l