def test_calc_inbreeding_coeficient(self):
variations = {'/calls/GT': numpy.array([[[0, 0], [0, 1], [0, 1],
[0, 0], [0, 1], [0, 0],
[0, 0], [0, 1], [1, 1],
[0, 0]]]),
'/variations/alt': numpy.zeros((1, 1))}
result = calc_inbreeding_coef(variations, min_num_genotypes=0,
chunk_size=None)
expected = numpy.array([1 - (0.4 / 0.42)])
assert numpy.allclose(result, expected)
variations = {'/calls/GT': numpy.array([]),
'/variations/alt': numpy.array([])}
result = calc_inbreeding_coef(variations, min_num_genotypes=0,
chunk_size=None)
assert result.shape[0] == 0
def test_calc_inbreeding_coeficient(self):
variations = {'/calls/GT': numpy.array([[[0, 0], [0, 1], [0, 1],
[0, 0], [0, 1], [0, 0],
[0, 0], [0, 1], [1, 1],
[0, 0]]]),
'/variations/alt': numpy.zeros((1, 1))}
result = calc_inbreeding_coef(variations, min_num_genotypes=0,
chunk_size=None)
expected = numpy.array([1 - (0.4 / 0.42)])
assert numpy.allclose(result, expected)
variations = {'/calls/GT': numpy.array([]),
'/variations/alt': numpy.array([])}
result = calc_inbreeding_coef(variations, min_num_genotypes=0,
chunk_size=None)
assert result.shape[0] == 0
def plot_inbreeding_coefficient(variations, max_num_allele, data_dir,
window_size, chunk_size=SNPS_PER_CHUNK,
min_num_genotypes=MIN_NUM_GENOTYPES_FOR_POP_STAT,
write_bg=False, calc_genome_wise=False):
# Calculate Inbreeding coefficient distribution
inbreed_coef = calc_inbreeding_coef(variations, chunk_size=chunk_size,
min_num_genotypes=min_num_genotypes)
ic_distrib, bins = histogram(inbreed_coef, 50, range_=(-1, 1))
fpath = join(data_dir, 'inbreeding_coef_distribution.png')
fhand = open(fpath, 'w')
title = 'Inbreeding coefficient distribution all samples'
plot_distrib(ic_distrib, bins, fhand=fhand,
mpl_params={'set_xlabel': {'args': ['Inbreeding coefficient'],
'kwargs': {}},
'set_ylabel': {'args': ['Number of SNPs'],
'kwargs': {}},
'set_title': {'args': [title], 'kwargs': {}},
'set_xlim': {'args': [-1, 1], 'kwargs': {}}})
# Save in bedgraph file
if calc_genome_wise:
bg_fhand = open(join(data_dir, 'ic.bg'), 'w')
chrom = _load_matrix(variations, CHROM_FIELD)
pos = _load_matrix(variations, POS_FIELD)
pos_ic = PositionalStatsCalculator(chrom, pos, inbreed_coef)
if write_bg:
pos_ic.write(bg_fhand, 'IC', 'Inbreeding coefficient',
track_type='bedgraph')
# Plot Ic along genome taking sliding windows
pos_ic = pos_ic.calc_window_stat()
chrom, pos, ic_windows = pos_ic.chrom, pos_ic.pos, pos_ic.stat
fpath = join(data_dir, 'ic_manhattan.png')
fhand = open(fpath, 'w')
title = 'Inbreeding coefficient (IC) along the genome'
manhattan_plot(chrom, pos, ic_windows, fhand=fhand, figsize=(15, 7.5),
ylim=-1,
mpl_params={'set_xlabel': {'args': ['Chromosome'],
'kwargs': {}},
'set_ylabel': {'args': ['IC'],
'kwargs': {}},
'set_title': {'args': [title], 'kwargs': {}}})
def plot_inbreeding_coefficient(
variations,
max_num_allele,
data_dir,
window_size,
chunk_size=SNPS_PER_CHUNK,
min_num_genotypes=MIN_NUM_GENOTYPES_FOR_POP_STAT,
write_bg=False,
calc_genome_wise=False):
# Calculate Inbreeding coefficient distribution
inbreed_coef = calc_inbreeding_coef(variations,
chunk_size=chunk_size,
min_num_genotypes=min_num_genotypes)
ic_distrib, bins = histogram(inbreed_coef, 50, range_=(-1, 1))
fpath = join(data_dir, 'inbreeding_coef_distribution.png')
fhand = open(fpath, 'w')
title = 'Inbreeding coefficient distribution all samples'
plot_distrib(ic_distrib,
bins,
fhand=fhand,
mpl_params={
'set_xlabel': {
'args': ['Inbreeding coefficient'],
'kwargs': {}
},
'set_ylabel': {
'args': ['Number of SNPs'],
'kwargs': {}
},
'set_title': {
'args': [title],
'kwargs': {}
},
'set_xlim': {
'args': [-1, 1],
'kwargs': {}
}
})
# Save in bedgraph file
if calc_genome_wise:
bg_fhand = open(join(data_dir, 'ic.bg'), 'w')
chrom = _load_matrix(variations, CHROM_FIELD)
pos = _load_matrix(variations, POS_FIELD)
pos_ic = PositionalStatsCalculator(chrom, pos, inbreed_coef)
if write_bg:
pos_ic.write(bg_fhand,
'IC',
'Inbreeding coefficient',
track_type='bedgraph')
# Plot Ic along genome taking sliding windows
pos_ic = pos_ic.calc_window_stat()
chrom, pos, ic_windows = pos_ic.chrom, pos_ic.pos, pos_ic.stat
fpath = join(data_dir, 'ic_manhattan.png')
fhand = open(fpath, 'w')
title = 'Inbreeding coefficient (IC) along the genome'
manhattan_plot(chrom,
pos,
ic_windows,
fhand=fhand,
figsize=(15, 7.5),
ylim=-1,
mpl_params={
'set_xlabel': {
'args': ['Chromosome'],
'kwargs': {}
},
'set_ylabel': {
'args': ['IC'],
'kwargs': {}
},
'set_title': {
'args': [title],
'kwargs': {}
}
})
