def test_calc_called_gts_distribution_per_depth(self):
hdf5 = VariationsH5(join(TEST_DATA_DIR, 'ril.hdf5'), mode='r')
dist, _ = calc_called_gts_distrib_per_depth(hdf5, depths=range(30),
chunk_size=10)
assert dist[1, 1] == 1
dist2, _ = calc_called_gts_distrib_per_depth(hdf5, depths=range(30),
chunk_size=None)
assert numpy.all(dist == dist2)
vars_ = VariationsArrays()
vars_['/calls/GT'] = numpy.array([[[0, 0], [0, 1], [0, 1],
[0, 0], [0, 1], [0, 0],
[0, 0], [0, 1], [1, 1],
[0, 0]]])
vars_['/calls/DP'] = numpy.array([[10, 5, 15, 7, 10,
0, 0, 25, 20, 10]])
vars_.samples = list(range(10))
dist, _ = calc_called_gts_distrib_per_depth(vars_, depths=[0, 5, 10,
30])
expected = [[0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
[0, 0, 0, 0, 0, 0, 0, 1, 0, 0],
[0, 0, 0, 0, 0, 1, 0, 0, 0, 0],
[1, 0, 0, 0, 0, 0, 0, 0, 0, 0]]
assert numpy.all(dist == expected)
def test_calc_called_gts_distribution_per_depth(self):
hdf5 = VariationsH5(join(TEST_DATA_DIR, 'ril.hdf5'), mode='r')
dist, _ = calc_called_gts_distrib_per_depth(hdf5, depths=range(30),
chunk_size=10)
assert dist[1, 1] == 1
dist2, _ = calc_called_gts_distrib_per_depth(hdf5, depths=range(30),
chunk_size=None)
assert numpy.all(dist == dist2)
vars_ = VariationsArrays()
vars_['/calls/GT'] = numpy.array([[[0, 0], [0, 1], [0, 1],
[0, 0], [0, 1], [0, 0],
[0, 0], [0, 1], [1, 1],
[0, 0]]])
vars_['/calls/DP'] = numpy.array([[10, 5, 15, 7, 10,
0, 0, 25, 20, 10]])
vars_.samples = list(range(10))
dist, _ = calc_called_gts_distrib_per_depth(vars_, depths=[0, 5, 10,
30])
expected = [[0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
[0, 0, 0, 0, 0, 0, 0, 1, 0, 0],
[0, 0, 0, 0, 0, 1, 0, 0, 0, 0],
[1, 0, 0, 0, 0, 0, 0, 0, 0, 0]]
assert numpy.all(dist == expected)
def plot_called_gts_distrib_per_depth(h5, depths, data_dir,
chunk_size=SNPS_PER_CHUNK):
# Distribution of the number of samples with a depth higher than
# given values
distribs, _ = calc_called_gts_distrib_per_depth(h5, depths=depths,
chunk_size=chunk_size)
fpath = join(data_dir, 'gts_distribution_per_depth.png')
title = 'Distribution of the number of samples with a depth higher than'
title += ' given values'
mpl_params = {'set_xlabel': {'args': ['Depth'], 'kwargs': {}},
'set_ylabel': {'args': ['Number of samples'], 'kwargs': {}},
'set_title': {'args': [title], 'kwargs': {}},
'set_xticklabels': {'args': [depths],
'kwargs': {'rotation': 90}}}
plot_boxplot_from_distribs(distribs, fhand=open(fpath, 'w'),
figsize=(15, 10), mpl_params=mpl_params,
color='tan')
def plot_called_gts_distrib_per_depth(h5,
depths,
data_dir,
chunk_size=SNPS_PER_CHUNK):
# Distribution of the number of samples with a depth higher than
# given values
distribs, _ = calc_called_gts_distrib_per_depth(h5,
depths=depths,
chunk_size=chunk_size)
fpath = join(data_dir, 'gts_distribution_per_depth.png')
title = 'Distribution of the number of samples with a depth higher than'
title += ' given values'
mpl_params = {
'set_xlabel': {
'args': ['Depth'],
'kwargs': {}
},
'set_ylabel': {
'args': ['Number of samples'],
'kwargs': {}
},
'set_title': {
'args': [title],
'kwargs': {}
},
'set_xticklabels': {
'args': [depths],
'kwargs': {
'rotation': 90
}
}
}
plot_boxplot_from_distribs(distribs,
fhand=open(fpath, 'w'),
figsize=(15, 10),
mpl_params=mpl_params,
color='tan')
