def test_02_RunEntropyOnUnique(self):
output_file = os.path.join(self.output_directory_path, 'entropy.txt')
entropy_analysis(self.unique_alignment,
output_file=output_file,
uniqued=True,
verbose=False)
self.assertTrue(files_are_the_same(self.expected_result, output_file))
def vis_freq_curve(fasta_file_path,
output_file=None,
x_limit=20,
display=False,
freq_from_defline=None,
entropy_output_file=None,
verbose=False,
mini=False,
title=None):
if freq_from_defline == None:
freq_from_defline = lambda x: int(
[t.split(':')[1] for t in x.split('|') if t.startswith('freq')][0])
fasta = u.SequenceSource(fasta_file_path)
frequency_list = []
while next(fasta):
try:
frequency_list.append(freq_from_defline(fasta.id))
except:
print('frequency info can not be read from defline.')
sys.exit()
frequency_list_to_plot = frequency_list[0:x_limit] + [0] * (x_limit - len(frequency_list) \
if len(frequency_list) < x_limit else 0)
entropy_values = entropy_analysis(fasta_file_path,
output_file=entropy_output_file,
verbose=verbose,
uniqued=True)
if mini:
plt.figure(figsize=(2, 2))
plt.subplots_adjust(left=0.01, bottom=0, top=1, right=1)
plt.subplot(1, 1, 1)
plt.grid(False)
plt.xticks([])
plt.yticks([])
ax = plt.gca()
plt.setp(ax, frame_on=False)
y_maximum = 1.1
x_maximum = len(entropy_values)
ind = np.arange(len(entropy_values))
text_x, text_y = x_maximum / 2, y_maximum / 2
plt.text(text_x,
text_y,
title if title else 'title',
horizontalalignment='center',
verticalalignment='center',
backgroundcolor='white',
fontsize=40,
color='red')
plt.ylim(ymax=y_maximum)
plt.xlim(xmax=x_maximum)
plt.bar(ind, entropy_values, color='black', lw=0.5)
else:
plt.figure(figsize=(24, 10))
plt.subplots_adjust(left=0.05, bottom=0.15, top=0.95, right=0.99)
plt.subplot(2, 1, 1)
plt.grid(True)
plt.rcParams.update({'axes.linewidth': 0.9})
plt.rc('grid', color='0.50', linestyle='-', linewidth=0.1)
plt.xticks(list(range(0, len(entropy_values), 5)),
rotation=90,
size='x-small')
plt.plot(frequency_list_to_plot, lw=3, c='black')
plt.xlabel('Order in the File', size='x-large')
plt.ylabel('Frequency of the Unique Sequence', size='x-large')
if title:
plt.title(title)
else:
plt.title('Frequency Distribution of Unique Sequences in %s' %
os.path.basename(fasta_file_path))
plt.ylim(ymin=-max(frequency_list_to_plot) * 0.05,
ymax=max(frequency_list_to_plot) * 1.05)
plt.xlim(xmin=-0.05, xmax=x_limit - 1)
plt.xticks(list(range(0, x_limit)),
[str(i) for i in range(1, x_limit + 1)],
rotation=90,
size='small')
plt.subplot(2, 1, 2)
plt.subplots_adjust(left=0.05, bottom=0.1, top=0.95, right=0.99)
try:
plt.grid(axis='y')
except:
plt.grid(True)
plt.rcParams.update({'axes.linewidth': 0.9})
plt.rc('grid', color='0.40', linestyle='-', linewidth=0.1)
y_maximum = max(entropy_values) * 1.1
y_maximum = 1.1 if y_maximum < 1 else y_maximum
ind = np.arange(len(entropy_values))
plt.bar(ind, entropy_values, color='black', lw=0.5)
plt.xlim([0, len(entropy_values)])
plt.ylim([0, y_maximum])
plt.xticks(list(range(0, len(entropy_values), 5)),
rotation=90,
size='x-small')
plt.xlabel('Position in the Alignment', size='x-large')
plt.ylabel('Shannon Entropy', size='x-large')
if output_file:
plt.savefig(output_file)
if display:
plt.show()
plt.clf()
plt.close('all')
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))
def vis_freq_curve(fasta_file_path, output_file = None, x_limit = 20, display = False, freq_from_defline = None, entropy_output_file = None, verbose = False, mini = False, title = None):
if freq_from_defline == None:
freq_from_defline = lambda x: int([t.split(':')[1] for t in x.split('|') if t.startswith('freq')][0])
fasta = u.SequenceSource(fasta_file_path)
frequency_list = []
while fasta.next():
try:
frequency_list.append(freq_from_defline(fasta.id))
except:
print 'frequency info can not be read from defline.'
sys.exit()
frequency_list_to_plot = frequency_list[0:x_limit] + [0] * (x_limit - len(frequency_list) \
if len(frequency_list) < x_limit else 0)
entropy_values = entropy_analysis(fasta_file_path, output_file = entropy_output_file, verbose = verbose, uniqued = True)
if mini:
plt.figure(figsize=(2, 2))
plt.subplots_adjust(left=0.01, bottom = 0, top = 1, right = 1)
plt.subplot(1, 1, 1)
plt.grid(False)
plt.xticks([])
plt.yticks([])
ax=plt.gca()
plt.setp(ax, frame_on=False)
y_maximum = 1.1
x_maximum = len(entropy_values)
ind = np.arange(len(entropy_values))
text_x, text_y = x_maximum / 2, y_maximum / 2
plt.text(text_x, text_y, title if title else 'title',
horizontalalignment='center',
verticalalignment='center',
backgroundcolor='white',
fontsize=40, color='red')
plt.ylim(ymax = y_maximum)
plt.xlim(xmax = x_maximum)
plt.bar(ind, entropy_values, color = 'black', lw = 0.5)
else:
plt.figure(figsize=(24, 10))
plt.subplots_adjust(left=0.05, bottom = 0.15, top = 0.95, right = 0.99)
plt.subplot(2, 1, 1)
plt.grid(True)
plt.rcParams.update({'axes.linewidth' : 0.9})
plt.rc('grid', color='0.50', linestyle='-', linewidth=0.1)
plt.xticks( range(0, len(entropy_values), 5), rotation=90, size = 'x-small')
plt.plot(frequency_list_to_plot, lw = 3, c = 'black')
plt.xlabel('Order in the File', size = 'x-large')
plt.ylabel('Frequency of the Unique Sequence', size = 'x-large')
if title:
plt.title(title)
else:
plt.title('Frequency Distribution of Unique Sequences in %s' % os.path.basename(fasta_file_path))
plt.ylim(ymin = -max(frequency_list_to_plot) * 0.05, ymax = max(frequency_list_to_plot) * 1.05)
plt.xlim(xmin = -0.05, xmax = x_limit - 1)
plt.xticks(range(0, x_limit), [str(i) for i in range(1, x_limit + 1)], rotation=90, size='small')
plt.subplot(2, 1, 2)
plt.subplots_adjust(left=0.05, bottom = 0.1, top = 0.95, right = 0.99)
try:
plt.grid(axis='y')
except:
plt.grid(True)
plt.rcParams.update({'axes.linewidth' : 0.9})
plt.rc('grid', color='0.40', linestyle='-', linewidth=0.1)
y_maximum = max(entropy_values) * 1.1
y_maximum = 1.1 if y_maximum < 1 else y_maximum
ind = np.arange(len(entropy_values))
plt.bar(ind, entropy_values, color = 'black', lw = 0.5)
plt.xlim([0, len(entropy_values)])
plt.ylim([0, y_maximum])
plt.xticks( range(0, len(entropy_values), 5), rotation=90, size = 'x-small')
plt.xlabel('Position in the Alignment', size = 'x-large')
plt.ylabel('Shannon Entropy', size = 'x-large')
if output_file:
plt.savefig(output_file)
if display:
plt.show()
plt.clf()
plt.close('all')
def test_02_RunEntropyOnUnique(self):
output_file = os.path.join(self.output_directory_path, 'entropy.txt')
entropy_analysis(self.unique_alignment, output_file = output_file, uniqued = True, verbose = False)
self.assertTrue(files_are_the_same(self.expected_result, output_file))