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))
