alignment = u.SequenceSource(sys.argv[1]) quals_dict = cPickle.load(open(sys.argv[2])) quals_dict_filtered = {} ids_in_alignment_file = [] while alignment.next(): ids_in_alignment_file.append(alignment.id) ids_in_alignment_file = set(ids_in_alignment_file) for read_id in quals_dict: if read_id in ids_in_alignment_file: quals_dict_filtered[read_id] = quals_dict[read_id] ids_in_alignment_file.remove(read_id) qual_stats_dict = get_qual_stats_dict(quals_dict_filtered) colors = get_list_of_colors(21, colormap="RdYlGn") colors = [colors[0] for _ in range(0, 20)] + colors max_count = max([qual_stats_dict[q]['count'] for q in qual_stats_dict if qual_stats_dict[q]]) alignment_length = len(quals_dict.values()[0]) fig = plt.figure(figsize = (25, 8)) plt.rc('grid', color='0.50', linestyle='-', linewidth=0.1) plt.grid(True) plt.subplots_adjust(left=0.02, bottom = 0.09, top = 0.95, right = 0.98) for position in range(0, alignment_length): print position
alignment = u.SequenceSource(sys.argv[1]) quals_dict = cPickle.load(open(sys.argv[2])) quals_dict_filtered = {} ids_in_alignment_file = [] while alignment.next(): ids_in_alignment_file.append(alignment.id) ids_in_alignment_file = set(ids_in_alignment_file) for read_id in quals_dict: if read_id in ids_in_alignment_file: quals_dict_filtered[read_id] = quals_dict[read_id] ids_in_alignment_file.remove(read_id) qual_stats_dict = get_qual_stats_dict(quals_dict_filtered) colors = get_list_of_colors(21, colormap="RdYlGn") colors = [colors[0] for _ in range(0, 20)] + colors max_count = max([ qual_stats_dict[q]['count'] for q in qual_stats_dict if qual_stats_dict[q] ]) alignment_length = len(quals_dict.values()[0]) fig = plt.figure(figsize=(25, 8)) plt.rc('grid', color='0.50', linestyle='-', linewidth=0.1) plt.grid(True) plt.subplots_adjust(left=0.02, bottom=0.09, top=0.95, right=0.98)
def test_01_RunWeightedEntropy(self): output_file = os.path.join(self.output_directory_path, 'entropy.txt') QD = get_quals_dict(self.qual_scores_file, self.alignment, output_file_path = os.path.join(self.output_directory_path, 'QUALS_DICT'), verbose = False) QSD = get_qual_stats_dict(QD, output_file_path = os.path.join(self.output_directory_path, 'QUAL_STATS_DICT'), verbose = False) entropy_analysis(self.alignment, output_file = output_file, verbose = False, weighted = True, qual_stats_dict = QSD) self.assertTrue(files_are_the_same(self.expected_result, output_file))