def detect_from_summaries(cfg, chrom=1, detect_fmt=("%.1f", "%d")):
'''
Detect local concentrations based on existing summaries.
Parameters
----------
- cfg : dictionary
Dictionary of parameters containing at least those relevant MCMC
draw and summary output paths and parameters for summarization.
- chrom : int
Index of chromosome to analyze
Returns
-------
- status : int
Integer status for summarisation. 0 for success, > 0 for failure.
'''
# Reference useful information in local namespace
p_detect = cfg['mcmc_summaries']['p_detect']
# Extract window size information (+/-) from config
concentration_pm = cfg['mcmc_summaries']['concentration_pm']
if isinstance(concentration_pm, str):
pm_list = [int(s) for s in concentration_pm.split(',')]
else:
pm_list = [concentration_pm]
# Get path to posterior summaries
pattern_summaries = cfg['mcmc_output']['summary_pattern']
pattern_summaries = pattern_summaries.strip()
path_summaries = pattern_summaries.format(**cfg) % chrom
# Run detection
if p_detect is not None:
# Load summaries
summaries = np.genfromtxt(path_summaries, names=True)
# Iterate of +/- settings
for pm in pm_list:
# Find detected positions
key = 'p_local_concentration_pm%d' % pm
detected = np.where(summaries[key] > p_detect)[0]
# Condense regions
detected, n = condense_detections(detected)
# Write detections to text file
pattern_detections = cfg['mcmc_output']['detections_pattern']
pattern_detections = pattern_detections.strip()
path_detections = pattern_detections.format(**cfg) % (chrom, pm)
detections = np.rec.fromarrays([detected, n], names=('pos', 'n'))
libio.write_recarray_to_file(fname=path_detections,
data=detections,
header=True,
sep=' ',
fmt=detect_fmt)
return 0
def detect_from_summaries(cfg, chrom=1, detect_fmt=("%.1f", "%d")):
'''
Detect local concentrations based on existing summaries.
Parameters
----------
- cfg : dictionary
Dictionary of parameters containing at least those relevant MCMC
draw and summary output paths and parameters for summarization.
- chrom : int
Index of chromosome to analyze
Returns
-------
- status : int
Integer status for summarisation. 0 for success, > 0 for failure.
'''
# Reference useful information in local namespace
p_detect = cfg['mcmc_summaries']['p_detect']
# Extract window size information (+/-) from config
concentration_pm = cfg['mcmc_summaries']['concentration_pm']
if isinstance(concentration_pm, str):
pm_list = [int(s) for s in concentration_pm.split(',')]
else:
pm_list = [concentration_pm]
# Get path to posterior summaries
pattern_summaries = cfg['mcmc_output']['summary_pattern']
pattern_summaries = pattern_summaries.strip()
path_summaries = pattern_summaries.format(**cfg) % chrom
# Run detection
if p_detect is not None:
# Load summaries
summaries = np.genfromtxt(path_summaries, names=True)
# Iterate of +/- settings
for pm in pm_list:
# Find detected positions
key = 'p_local_concentration_pm%d' % pm
detected = np.where(summaries[key] > p_detect)[0]
# Condense regions
detected, n = condense_detections(detected)
# Write detections to text file
pattern_detections = cfg['mcmc_output']['detections_pattern']
pattern_detections = pattern_detections.strip()
path_detections = pattern_detections.format(**cfg) % (chrom, pm)
detections = np.rec.fromarrays([detected, n],
names=('pos', 'n'))
libio.write_recarray_to_file(fname=path_detections, data=detections,
header=True, sep=' ', fmt=detect_fmt)
return 0
def summarise_clusters(cfg, chrom=1, null=False):
'''
Coordinate summarisation of MCMC results by cluster.
Clusters are defined via Parzen window smoothing with a cfg-specified
bandwidth and minimum separation. Following clustering, all cluster-level
summaries are computed within each iteration (localization, structure,
occupancy, etc.). The reported outputs are posterior summaries of these
cluster-level summaries (mean, SD, etc.).
Parameters
----------
- cfg : dictionary
Dictionary of parameters containing at least those relevant MCMC
draw and summary output paths and parameters for summarization.
- chrom : int
Index of chromosome to analyze
- null : bool
Summarise null results?
Returns
-------
- status : int
Integer status for summarisation. 0 for success, > 0 for failure.
'''
# Reference useful information in local namespace
n_burnin = cfg['mcmc_params']['n_burnin']
scratch = cfg['mcmc_summaries']['path_scratch']
# Cluster-level summary information
cluster_min_spacing = cfg['mcmc_summaries']['cluster_min_spacing']
cluster_bw = cfg['mcmc_summaries']['cluster_bw']
cluster_width = cfg['mcmc_summaries']['cluster_width']
h = cluster_width / 2
# Extract q_sparsity information for n_large summaries from config
q_sparsity = cfg['mcmc_summaries']['q_sparsity']
if isinstance(q_sparsity, str):
q_sparsity = [float(s) for s in q_sparsity.split(',')]
else:
q_sparsity = [q_sparsity]
# Extract p_threshold information for n_large summaries from config
p_threshold = cfg['mcmc_summaries']['p_threshold']
if isinstance(p_threshold, str):
p_threshold = [float(s) for s in p_threshold.split(',')]
else:
p_threshold = [p_threshold]
# Check for existence and writeability of scratch directory
if os.access(scratch, os.F_OK):
# It exists, check for read-write
if not os.access(scratch, os.R_OK | os.W_OK):
print >> sys.stderr, ("Error --- Cannot read and write to %s" %
scratch)
return 1
else:
# Otherwise, try to make the directory
os.makedirs(scratch)
# Extract results to scratch directory
if null:
pattern_results = cfg['mcmc_output']['null_out_pattern']
else:
pattern_results = cfg['mcmc_output']['out_pattern']
pattern_results = pattern_results.strip()
path_results = pattern_results.format(**cfg) % chrom
archive = tarfile.open(name=path_results, mode='r:*')
archive.extractall(path=scratch)
names_npy = archive.getnames()
archive.close()
# Load results of interest
theta = np.load(scratch + '/theta.npy', mmap_mode='r')
mu = np.load(scratch + '/mu.npy', mmap_mode='r')
# Remove burnin
if n_burnin > 0:
mu = mu[n_burnin:]
theta = theta[n_burnin:]
# Compute posterior mean of coefficients
# This looks inefficient, but it saves memory --- a lot of memory
b_postmean = np.array([np.mean(np.exp(theta_k)) for theta_k in theta.T])
# Setup window for clustering
cluster_window = gaussian_window(h=h, sigma=cluster_bw)
# Get cluster centers
cluster_centers = get_cluster_centers(x=b_postmean,
window=cluster_window,
min_spacing=cluster_min_spacing,
edge_correction=True)
n_clusters = cluster_centers.size
# Create slices by cluster for efficient access
cluster_slices = [
slice(max(0, c - h), min(c + h + 1, theta.shape[1]), 1)
for c in cluster_centers
]
# Extract cluster sizes
cluster_sizes = np.array([s.stop - s.start for s in cluster_slices],
dtype=np.int)
# Create names for sparsity and n_large variables
names_sparsity = ["sparsityq%02.0f" % (q * 100) for q in q_sparsity]
names_sparsity_se = ["sparsityq%02.0f_se" % (q * 100) for q in q_sparsity]
names_nlarge = ["nlargep%02.0f" % (p * 100) for p in p_threshold]
names_nlarge_se = ["nlargep%02.0f_se" % (p * 100) for p in p_threshold]
# Allocate arrays for cluster-level summaries
cluster_summaries = collections.OrderedDict()
cluster_summaries['center'] = cluster_centers
cluster_summaries['cluster_length'] = cluster_sizes
cluster_summaries['occupancy'] = np.empty(n_clusters, dtype=np.float)
cluster_summaries['occupancy_se'] = np.empty(n_clusters, dtype=np.float)
cluster_summaries['localization'] = np.empty(n_clusters, dtype=np.float)
cluster_summaries['localization_se'] = np.empty(n_clusters, dtype=np.float)
cluster_summaries['structure'] = np.empty(n_clusters, dtype=np.float)
cluster_summaries['structure_se'] = np.empty(n_clusters, dtype=np.float)
cluster_summaries['sparsity'] = np.empty(n_clusters, dtype=np.float)
cluster_summaries['sparsity_se'] = np.empty(n_clusters, dtype=np.float)
for var in itertools.chain([
item for items in itertools.izip(names_sparsity, names_sparsity_se)
for item in items
], [
item for items in itertools.izip(names_nlarge, names_nlarge_se)
for item in items
]):
cluster_summaries[var] = np.empty(n_clusters, dtype=np.float)
# Compute cluster-level summaries, iterating over clusters
for i, center, cluster in itertools.izip(xrange(n_clusters),
cluster_centers, cluster_slices):
# Extract cluster coefficient draws
b_draws = np.exp(theta[:, cluster])
p_draws = (b_draws.T / np.sum(b_draws, 1)).T
# Compute posterior mean occupancy and its SD
cluster_summaries['occupancy'][i] = np.mean(b_draws) * cluster_sizes[i]
cluster_summaries['occupancy_se'][i] = np.std(np.sum(b_draws, axis=1))
# Compute localization index by draw
x = np.arange(cluster_sizes[i])[np.newaxis, :]
localization = localization_index(x=x, p=p_draws, axis=1)
cluster_summaries['localization'][i] = np.mean(localization)
cluster_summaries['localization_se'][i] = np.std(localization)
# Compute structure index by draw
structure = structure_index(x=b_draws, axis=1)
cluster_summaries['structure'][i] = np.mean(structure)
cluster_summaries['structure_se'][i] = np.std(structure)
# Compute sparsity index by draw
sparsity = sparsity_index(x=b_draws, q=q_sparsity, axis=1)
for i_q in xrange(len(q_sparsity)):
cluster_summaries[names_sparsity[i_q]][i] = np.mean(sparsity[i_q])
cluster_summaries[names_sparsity_se[i_q]][i] = np.std(
sparsity[i_q])
# Compute n_large by draw
n_large = compute_n_large(x=b_draws, p_threshold=p_threshold, axis=1)
for i_p in xrange(len(p_threshold)):
cluster_summaries[names_nlarge[i_p]][i] = np.mean(n_large[i_p])
cluster_summaries[names_nlarge_se[i_p]][i] = np.std(n_large[i_p])
# Provide nicely-formatted delimited output for analyses and plotting
if null:
pattern_summaries = cfg['mcmc_output']['null_cluster_pattern']
else:
pattern_summaries = cfg['mcmc_output']['cluster_pattern']
pattern_summaries = pattern_summaries.strip()
path_summaries = pattern_summaries.format(**cfg) % chrom
# Build recarray of summaries, starting with coefficients and diagnostics
summaries = np.rec.fromarrays(cluster_summaries.values(),
names=cluster_summaries.keys())
# Write summaries to delimited text file
libio.write_recarray_to_file(fname=path_summaries,
data=summaries,
header=True,
sep=' ')
# Clean-up scratch directory
for name in names_npy:
os.remove(scratch + '/' + name)
return 0
def summarise(cfg, chrom=1, null=False, mmap=False, detect_fmt=("%.1f", "%d")):
'''
Coordinate summarisation of MCMC results.
Parameters
----------
- cfg : dictionary
Dictionary of parameters containing at least those relevant MCMC
draw and summary output paths and parameters for summarization.
- chrom : int
Index of chromosome to analyze
- null : bool
Summarise null results?
Returns
-------
- status : int
Integer status for summarisation. 0 for success, > 0 for failure.
'''
# Reference useful information in local namespace
n_burnin = cfg['mcmc_params']['n_burnin']
scratch = cfg['mcmc_summaries']['path_scratch']
width_local = cfg['mcmc_summaries']['width_local']
p_detect = cfg['mcmc_summaries']['p_detect']
bp_per_nucleosome = cfg['mcmc_summaries']['bp_per_nucleosome']
# Extract window size information (+/-) from config
concentration_pm = cfg['mcmc_summaries']['concentration_pm']
if isinstance(concentration_pm, str):
pm_list = [int(s) for s in concentration_pm.split(',')]
else:
pm_list = [concentration_pm]
# Check for existence and writeability of scratch directory
if os.access(scratch, os.F_OK):
# It exists, check for read-write
if not os.access(scratch, os.R_OK | os.W_OK):
print >> sys.stderr, ("Error --- Cannot read and write to %s" %
scratch)
return 1
else:
# Otherwise, try to make the directory
os.makedirs(scratch)
# Extract results to scratch directory
if null:
pattern_results = cfg['mcmc_output']['null_out_pattern']
else:
pattern_results = cfg['mcmc_output']['out_pattern']
pattern_results = pattern_results.strip()
path_results = pattern_results.format(**cfg) % chrom
archive = tarfile.open(name=path_results, mode='r:*')
archive.extractall(path=scratch)
names_npy = archive.getnames()
archive.close()
# Load results of interest
if mmap:
mmap_mode = 'r+'
else:
mmap_mode = None
theta = np.load(scratch + '/theta.npy', mmap_mode=mmap_mode)
mu = np.load(scratch + '/mu.npy')
# Remove burnin
if n_burnin > 0:
mu = mu[n_burnin:]
theta = theta[n_burnin:]
# Compute effective sample sizes
n_eff = np.array([ess1d(theta_k) for theta_k in theta.T])
gc.collect()
# Compute concentration summaries
local_concentrations = collections.OrderedDict()
global_concentrations = collections.OrderedDict()
# Iteration over concentration window sizes (+/-)
for pm in pm_list:
# Estimate probability of +/-(pm) local concentrations
window_local = np.ones(width_local)
window_pm = np.ones(1 + 2 * pm)
baseline = (np.convolve(np.ones_like(theta[0]), window_pm, 'same') /
np.convolve(np.ones_like(theta[0]), window_local, 'same'))
# Setup array for estimates by basepair
p_local_concentration = np.zeros(theta.shape[1], dtype=np.float)
# Iterate over draws
mean_lro = np.zeros(theta.shape[1], dtype=np.float)
se_lro = np.zeros(theta.shape[1], dtype=np.float)
for t in xrange(theta.shape[0]):
bt = np.exp(theta[t])
local_occupancy_smoothed = local_relative_occupancy(
bt, window_pm, window_local)
delta = local_occupancy_smoothed - mean_lro
mean_lro += delta / (t + 1.)
se_lro += delta * (local_occupancy_smoothed - mean_lro)
p_local_concentration *= t / (t + 1.)
p_local_concentration += ((local_occupancy_smoothed > baseline) /
(t + 1.))
se_lro = np.sqrt(se_lro / (theta.shape[0] - 1))
# Store results in dictionary
key = 'p_local_concentration_pm%d' % pm
local_concentrations[key] = p_local_concentration
key = 'mean_local_concentration_pm%d' % pm
local_concentrations[key] = mean_lro
key = 'se_local_concentration_pm%d' % pm
local_concentrations[key] = se_lro
key = 'z_local_concentration_pm%d' % pm
local_concentrations[key] = mean_lro / se_lro
# Clean-up
del local_occupancy_smoothed
gc.collect()
# Posterior quantiles for global concentrations
baseline_global = (
np.array([np.sum(np.exp(theta_t)) for theta_t in theta]) /
theta.shape[1] * bp_per_nucleosome)
# Setup arrays for means and quantiles by basepair
q_global_concentration = np.zeros(theta.shape[1], dtype=np.float)
mean_global_concentration = np.zeros(theta.shape[1], dtype=np.float)
# Iterate over basepairs
for bp in xrange(theta.shape[1]):
w = slice(max(0, bp - pm), min(bp + pm + 1, theta.shape[1]))
prop = (np.sum(np.exp(theta[:, w]), 1) / baseline_global /
(w.stop - w.start))
mean_global_concentration[bp] = np.mean(prop)
q_global_concentration[bp] = mstats.mquantiles(prop, 1. - p_detect)
# Store results in dictionaries
key = 'q_global_concentration_pm%d' % pm
global_concentrations[key] = q_global_concentration
key = 'mean_global_concentration_pm%d' % pm
global_concentrations[key] = mean_global_concentration
# Compute posterior means
theta_postmean = np.mean(theta, 0)
b_postmean = np.array([np.mean(np.exp(theta_k)) for theta_k in theta.T])
# Compute standard errors
theta_se = np.array([np.std(theta_k) for theta_k in theta.T])
b_se = np.array([np.std(np.exp(theta_k)) for theta_k in theta.T])
# Compute posterior medians
theta_postmed = np.array([np.median(theta_k) for theta_k in theta.T])
b_postmed = np.exp(theta_postmed)
# Provide nicely-formatted delimited output for analyses and plotting
if null:
pattern_summaries = cfg['mcmc_output']['null_summary_pattern']
else:
pattern_summaries = cfg['mcmc_output']['summary_pattern']
pattern_summaries = pattern_summaries.strip()
path_summaries = pattern_summaries.format(**cfg) % chrom
# Build recarray of summaries, starting with coefficients and diagnostics
summaries = np.rec.fromarrays([
theta_postmean, theta_postmed, theta_se, b_postmean, b_postmed, b_se,
n_eff
],
names=(
'theta',
'theta_med',
'se_theta',
'b',
'b_med',
'se_b',
'n_eff',
))
# Append local concentration information
summaries = nprf.append_fields(base=summaries,
names=local_concentrations.keys(),
data=local_concentrations.values())
# Append global concentration information
summaries = nprf.append_fields(base=summaries,
names=global_concentrations.keys(),
data=global_concentrations.values())
# Write summaries to delimited text file
libio.write_recarray_to_file(fname=path_summaries,
data=summaries,
header=True,
sep=' ')
# Run detection, if requested
if p_detect is not None and not null:
for pm in pm_list:
# Find detected positions
key = 'p_local_concentration_pm%d' % pm
detected = np.where(local_concentrations[key] > p_detect)[0]
# Condense regions
detected, n = condense_detections(detected)
# Write detections to text file
pattern_detections = cfg['mcmc_output']['detections_pattern']
pattern_detections = pattern_detections.strip()
path_detections = pattern_detections.format(**cfg) % (chrom, pm)
detections = np.rec.fromarrays([detected, n], names=('pos', 'n'))
libio.write_recarray_to_file(fname=path_detections,
data=detections,
header=True,
sep=' ',
fmt=detect_fmt)
# Clean-up scratch directory
for name in names_npy:
os.remove(scratch + '/' + name)
return 0
def summarise_params(cfg, chrom=1, null=False):
'''
Coordinate summarisation of MCMC parameter draws.
Parameters
----------
- cfg : dictionary
Dictionary of parameters containing at least those relevant MCMC
draw and summary output paths and parameters for summarization.
- chrom : int
Index of chromosome to analyze
- null : bool
Summarise null results?
Returns
-------
- status : int
Integer status for summarisation. 0 for success, > 0 for failure.
'''
# Reference useful information in local namespace
n_burnin = cfg['mcmc_params']['n_burnin']
scratch = cfg['mcmc_summaries']['path_scratch']
# Check for existence and writeability of scratch directory
if os.access(scratch, os.F_OK):
# It exists, check for read-write
if not os.access(scratch, os.R_OK | os.W_OK):
print >> sys.stderr, ("Error --- Cannot read and write to %s" %
scratch)
return 1
else:
# Otherwise, try to make the directory
os.makedirs(scratch)
# Extract results to scratch directory
if null:
pattern_results = cfg['mcmc_output']['null_out_pattern']
else:
pattern_results = cfg['mcmc_output']['out_pattern']
pattern_results = pattern_results.strip()
path_results = pattern_results.format(**cfg) % chrom
archive = tarfile.open(name=path_results, mode='r:*')
archive.extractall(path=scratch)
names_npy = archive.getnames()
archive.close()
# Load results of interest
mu = np.load(scratch + '/mu.npy')
sigmasq = np.load(scratch + '/sigmasq.npy')
region_ids = np.load(scratch + '/region_ids.npy')
# Remove burnin
if n_burnin > 0:
mu = mu[n_burnin:]
sigmasq = sigmasq[n_burnin:]
# Compute posterior means
mu_postmean = np.mean(mu, 0)
sigmasq_postmean = np.mean(sigmasq, 0)
sigma_postmean = np.mean(np.sqrt(sigmasq), 0)
# Compute posterior medians
mu_postmed = np.median(mu, 0)
sigmasq_postmed = np.median(sigmasq, 0)
sigma_postmed = np.median(np.sqrt(sigmasq), 0)
# Compute standard errors
mu_se = np.std(mu, 0)
sigmasq_se = np.std(sigmasq, 0)
sigma_se = np.std(np.sqrt(sigmasq), 0)
# Provide nicely-formatted delimited output for analyses and plotting
if null:
pattern_summaries = cfg['mcmc_output']['null_param_pattern']
else:
pattern_summaries = cfg['mcmc_output']['param_pattern']
pattern_summaries = pattern_summaries.strip()
path_summaries = pattern_summaries.format(**cfg) % chrom
# Build recarray of summaries, starting with coefficients and diagnostics
summaries = np.rec.fromarrays([
region_ids, mu_postmean, mu_postmed, mu_se, sigmasq_postmean,
sigmasq_postmed, sigmasq_se, sigma_postmean, sigma_postmed, sigma_se
],
names=('region_id', 'mu_postmean',
'mu_postmed', 'mu_se',
'sigmasq_postmean', 'sigmasq_postmed',
'sigmasq_se', 'sigma_postmean',
'sigma_postmed', 'sigma_se'))
# Write summaries to delimited text file
libio.write_recarray_to_file(fname=path_summaries,
data=summaries,
header=True,
sep=' ')
# Clean-up scratch directory
for name in names_npy:
os.remove(scratch + '/' + name)
return 0
def summarise_clusters(cfg, chrom=1, null=False):
'''
Coordinate summarisation of MCMC results by cluster.
Clusters are defined via Parzen window smoothing with a cfg-specified
bandwidth and minimum separation. Following clustering, all cluster-level
summaries are computed within each iteration (localization, structure,
occupancy, etc.). The reported outputs are posterior summaries of these
cluster-level summaries (mean, SD, etc.).
Parameters
----------
- cfg : dictionary
Dictionary of parameters containing at least those relevant MCMC
draw and summary output paths and parameters for summarization.
- chrom : int
Index of chromosome to analyze
- null : bool
Summarise null results?
Returns
-------
- status : int
Integer status for summarisation. 0 for success, > 0 for failure.
'''
# Reference useful information in local namespace
n_burnin = cfg['mcmc_params']['n_burnin']
scratch = cfg['mcmc_summaries']['path_scratch']
# Cluster-level summary information
cluster_min_spacing = cfg['mcmc_summaries']['cluster_min_spacing']
cluster_bw = cfg['mcmc_summaries']['cluster_bw']
cluster_width = cfg['mcmc_summaries']['cluster_width']
h = cluster_width/2
# Extract q_sparsity information for n_large summaries from config
q_sparsity = cfg['mcmc_summaries']['q_sparsity']
if isinstance(q_sparsity, str):
q_sparsity = [float(s) for s in q_sparsity.split(',')]
else:
q_sparsity = [q_sparsity]
# Extract p_threshold information for n_large summaries from config
p_threshold = cfg['mcmc_summaries']['p_threshold']
if isinstance(p_threshold, str):
p_threshold = [float(s) for s in p_threshold.split(',')]
else:
p_threshold = [p_threshold]
# Check for existence and writeability of scratch directory
if os.access(scratch, os.F_OK):
# It exists, check for read-write
if not os.access(scratch, os.R_OK | os.W_OK):
print >> sys.stderr, ("Error --- Cannot read and write to %s" %
scratch)
return 1
else:
# Otherwise, try to make the directory
os.makedirs(scratch)
# Extract results to scratch directory
if null:
pattern_results = cfg['mcmc_output']['null_out_pattern']
else:
pattern_results = cfg['mcmc_output']['out_pattern']
pattern_results = pattern_results.strip()
path_results = pattern_results.format(**cfg) % chrom
archive = tarfile.open(name=path_results, mode='r:*')
archive.extractall(path=scratch)
names_npy = archive.getnames()
archive.close()
# Load results of interest
theta = np.load(scratch + '/theta.npy', mmap_mode='r')
mu = np.load(scratch + '/mu.npy', mmap_mode='r')
# Remove burnin
if n_burnin > 0:
mu = mu[n_burnin:]
theta = theta[n_burnin:]
# Compute posterior mean of coefficients
# This looks inefficient, but it saves memory --- a lot of memory
b_postmean = np.array([np.mean(np.exp(theta_k)) for theta_k in theta.T])
# Setup window for clustering
cluster_window = gaussian_window(h=h, sigma=cluster_bw)
# Get cluster centers
cluster_centers = get_cluster_centers(x=b_postmean, window=cluster_window,
min_spacing=cluster_min_spacing,
edge_correction=True)
n_clusters = cluster_centers.size
# Create slices by cluster for efficient access
cluster_slices = [slice(max(0, c-h), min(c+h+1, theta.shape[1]), 1) for c in
cluster_centers]
# Extract cluster sizes
cluster_sizes = np.array([s.stop - s.start for s in cluster_slices],
dtype=np.int)
# Create names for sparsity and n_large variables
names_sparsity = ["sparsityq%02.0f" % (q * 100) for q in q_sparsity]
names_sparsity_se = ["sparsityq%02.0f_se" % (q * 100) for q in q_sparsity]
names_nlarge = ["nlargep%02.0f" % (p * 100) for p in p_threshold]
names_nlarge_se = ["nlargep%02.0f_se" % (p * 100) for p in p_threshold]
# Allocate arrays for cluster-level summaries
cluster_summaries = collections.OrderedDict()
cluster_summaries['center'] = cluster_centers
cluster_summaries['cluster_length'] = cluster_sizes
cluster_summaries['occupancy'] = np.empty(n_clusters, dtype=np.float)
cluster_summaries['occupancy_se'] = np.empty(n_clusters, dtype=np.float)
cluster_summaries['localization'] = np.empty(n_clusters, dtype=np.float)
cluster_summaries['localization_se'] = np.empty(n_clusters, dtype=np.float)
cluster_summaries['structure'] = np.empty(n_clusters, dtype=np.float)
cluster_summaries['structure_se'] = np.empty(n_clusters, dtype=np.float)
cluster_summaries['sparsity'] = np.empty(n_clusters, dtype=np.float)
cluster_summaries['sparsity_se'] = np.empty(n_clusters, dtype=np.float)
for var in itertools.chain(
[item for items in itertools.izip(names_sparsity, names_sparsity_se) for
item in items],
[item for items in itertools.izip(names_nlarge, names_nlarge_se) for
item in items]):
cluster_summaries[var] = np.empty(n_clusters, dtype=np.float)
# Compute cluster-level summaries, iterating over clusters
for i, center, cluster in itertools.izip(xrange(n_clusters),
cluster_centers, cluster_slices):
# Extract cluster coefficient draws
b_draws = np.exp(theta[:,cluster])
p_draws = (b_draws.T / np.sum(b_draws, 1)).T
# Compute posterior mean occupancy and its SD
cluster_summaries['occupancy'][i] = np.mean(b_draws)*cluster_sizes[i]
cluster_summaries['occupancy_se'][i] = np.std(np.sum(b_draws, axis=1))
# Compute localization index by draw
x=np.arange(cluster_sizes[i])[np.newaxis,:]
localization = localization_index(x=x, p=p_draws, axis=1)
cluster_summaries['localization'][i] = np.mean(localization)
cluster_summaries['localization_se'][i] = np.std(localization)
# Compute structure index by draw
structure = structure_index(x=b_draws, axis=1)
cluster_summaries['structure'][i] = np.mean(structure)
cluster_summaries['structure_se'][i] = np.std(structure)
# Compute sparsity index by draw
sparsity = sparsity_index(x=b_draws, q=q_sparsity, axis=1)
for i_q in xrange(len(q_sparsity)):
cluster_summaries[names_sparsity[i_q]][i] = np.mean(sparsity[i_q])
cluster_summaries[names_sparsity_se[i_q]][i] = np.std(sparsity[i_q])
# Compute n_large by draw
n_large = compute_n_large(x=b_draws, p_threshold=p_threshold, axis=1)
for i_p in xrange(len(p_threshold)):
cluster_summaries[names_nlarge[i_p]][i] = np.mean(n_large[i_p])
cluster_summaries[names_nlarge_se[i_p]][i] = np.std(n_large[i_p])
# Provide nicely-formatted delimited output for analyses and plotting
if null:
pattern_summaries = cfg['mcmc_output']['null_cluster_pattern']
else:
pattern_summaries = cfg['mcmc_output']['cluster_pattern']
pattern_summaries = pattern_summaries.strip()
path_summaries = pattern_summaries.format(**cfg) % chrom
# Build recarray of summaries, starting with coefficients and diagnostics
summaries = np.rec.fromarrays(cluster_summaries.values(),
names=cluster_summaries.keys())
# Write summaries to delimited text file
libio.write_recarray_to_file(fname=path_summaries, data=summaries,
header=True, sep=' ')
# Clean-up scratch directory
for name in names_npy:
os.remove(scratch + '/' + name)
return 0
def summarise(cfg, chrom=1, null=False, mmap=False, detect_fmt=("%.1f", "%d")):
'''
Coordinate summarisation of MCMC results.
Parameters
----------
- cfg : dictionary
Dictionary of parameters containing at least those relevant MCMC
draw and summary output paths and parameters for summarization.
- chrom : int
Index of chromosome to analyze
- null : bool
Summarise null results?
Returns
-------
- status : int
Integer status for summarisation. 0 for success, > 0 for failure.
'''
# Reference useful information in local namespace
n_burnin = cfg['mcmc_params']['n_burnin']
scratch = cfg['mcmc_summaries']['path_scratch']
width_local = cfg['mcmc_summaries']['width_local']
p_detect = cfg['mcmc_summaries']['p_detect']
bp_per_nucleosome = cfg['mcmc_summaries']['bp_per_nucleosome']
# Extract window size information (+/-) from config
concentration_pm = cfg['mcmc_summaries']['concentration_pm']
if isinstance(concentration_pm, str):
pm_list = [int(s) for s in concentration_pm.split(',')]
else:
pm_list = [concentration_pm]
# Check for existence and writeability of scratch directory
if os.access(scratch, os.F_OK):
# It exists, check for read-write
if not os.access(scratch, os.R_OK | os.W_OK):
print >> sys.stderr, ("Error --- Cannot read and write to %s" %
scratch)
return 1
else:
# Otherwise, try to make the directory
os.makedirs(scratch)
# Extract results to scratch directory
if null:
pattern_results = cfg['mcmc_output']['null_out_pattern']
else:
pattern_results = cfg['mcmc_output']['out_pattern']
pattern_results = pattern_results.strip()
path_results = pattern_results.format(**cfg) % chrom
archive = tarfile.open(name=path_results, mode='r:*')
archive.extractall(path=scratch)
names_npy = archive.getnames()
archive.close()
# Load results of interest
if mmap:
mmap_mode = 'r+'
else:
mmap_mode = None
theta = np.load(scratch + '/theta.npy', mmap_mode=mmap_mode)
mu = np.load(scratch + '/mu.npy')
# Remove burnin
if n_burnin > 0:
mu = mu[n_burnin:]
theta = theta[n_burnin:]
# Compute effective sample sizes
n_eff = np.array([ess1d(theta_k) for theta_k in theta.T])
gc.collect()
# Compute concentration summaries
local_concentrations = collections.OrderedDict()
global_concentrations = collections.OrderedDict()
# Iteration over concentration window sizes (+/-)
for pm in pm_list:
# Estimate probability of +/-(pm) local concentrations
window_local = np.ones(width_local)
window_pm = np.ones(1 + 2*pm)
baseline = (np.convolve(np.ones_like(theta[0]), window_pm, 'same') /
np.convolve(np.ones_like(theta[0]), window_local, 'same'))
# Setup array for estimates by basepair
p_local_concentration = np.zeros(theta.shape[1], dtype=np.float)
# Iterate over draws
mean_lro = np.zeros(theta.shape[1], dtype=np.float)
se_lro = np.zeros(theta.shape[1], dtype=np.float)
for t in xrange(theta.shape[0]):
bt = np.exp(theta[t])
local_occupancy_smoothed = local_relative_occupancy(
bt, window_pm, window_local)
delta = local_occupancy_smoothed - mean_lro
mean_lro += delta / (t+1.)
se_lro += delta * (local_occupancy_smoothed - mean_lro)
p_local_concentration *= t/(t+1.)
p_local_concentration += (
(local_occupancy_smoothed > baseline)/(t+1.))
se_lro = np.sqrt(se_lro / (theta.shape[0] - 1))
# Store results in dictionary
key = 'p_local_concentration_pm%d' % pm
local_concentrations[key] = p_local_concentration
key = 'mean_local_concentration_pm%d' % pm
local_concentrations[key] = mean_lro
key = 'se_local_concentration_pm%d' % pm
local_concentrations[key] = se_lro
key = 'z_local_concentration_pm%d' % pm
local_concentrations[key] = mean_lro / se_lro
# Clean-up
del local_occupancy_smoothed
gc.collect()
# Posterior quantiles for global concentrations
baseline_global = (np.array([np.sum(np.exp(theta_t)) for theta_t in
theta]) / theta.shape[1]
* bp_per_nucleosome)
# Setup arrays for means and quantiles by basepair
q_global_concentration = np.zeros(theta.shape[1], dtype=np.float)
mean_global_concentration = np.zeros(theta.shape[1], dtype=np.float)
# Iterate over basepairs
for bp in xrange(theta.shape[1]):
w = slice(max(0,bp-pm), min(bp+pm+1, theta.shape[1]))
prop = (np.sum(np.exp(theta[:,w]), 1) / baseline_global /
(w.stop-w.start))
mean_global_concentration[bp] = np.mean(prop)
q_global_concentration[bp] = mstats.mquantiles(prop, 1.-p_detect)
# Store results in dictionaries
key = 'q_global_concentration_pm%d' % pm
global_concentrations[key] = q_global_concentration
key = 'mean_global_concentration_pm%d' % pm
global_concentrations[key] = mean_global_concentration
# Compute posterior means
theta_postmean = np.mean(theta, 0)
b_postmean = np.array([np.mean(np.exp(theta_k)) for theta_k in theta.T])
# Compute standard errors
theta_se = np.array([np.std(theta_k) for theta_k in theta.T])
b_se = np.array([np.std(np.exp(theta_k)) for theta_k in theta.T])
# Compute posterior medians
theta_postmed = np.array([np.median(theta_k) for theta_k in theta.T])
b_postmed = np.exp(theta_postmed)
# Provide nicely-formatted delimited output for analyses and plotting
if null:
pattern_summaries = cfg['mcmc_output']['null_summary_pattern']
else:
pattern_summaries = cfg['mcmc_output']['summary_pattern']
pattern_summaries = pattern_summaries.strip()
path_summaries = pattern_summaries.format(**cfg) % chrom
# Build recarray of summaries, starting with coefficients and diagnostics
summaries = np.rec.fromarrays([theta_postmean, theta_postmed, theta_se,
b_postmean, b_postmed, b_se, n_eff],
names=('theta', 'theta_med', 'se_theta', 'b',
'b_med', 'se_b', 'n_eff',))
# Append local concentration information
summaries = nprf.append_fields(base=summaries,
names=local_concentrations.keys(),
data=local_concentrations.values())
# Append global concentration information
summaries = nprf.append_fields(base=summaries,
names=global_concentrations.keys(),
data=global_concentrations.values())
# Write summaries to delimited text file
libio.write_recarray_to_file(fname=path_summaries, data=summaries,
header=True, sep=' ')
# Run detection, if requested
if p_detect is not None and not null:
for pm in pm_list:
# Find detected positions
key = 'p_local_concentration_pm%d' % pm
detected = np.where(local_concentrations[key] > p_detect)[0]
# Condense regions
detected, n = condense_detections(detected)
# Write detections to text file
pattern_detections = cfg['mcmc_output']['detections_pattern']
pattern_detections = pattern_detections.strip()
path_detections = pattern_detections.format(**cfg) % (chrom, pm)
detections = np.rec.fromarrays([detected, n],
names=('pos', 'n'))
libio.write_recarray_to_file(fname=path_detections, data=detections,
header=True, sep=' ', fmt=detect_fmt)
# Clean-up scratch directory
for name in names_npy:
os.remove(scratch + '/' + name)
return 0
def summarise_params(cfg, chrom=1, null=False):
'''
Coordinate summarisation of MCMC parameter draws.
Parameters
----------
- cfg : dictionary
Dictionary of parameters containing at least those relevant MCMC
draw and summary output paths and parameters for summarization.
- chrom : int
Index of chromosome to analyze
- null : bool
Summarise null results?
Returns
-------
- status : int
Integer status for summarisation. 0 for success, > 0 for failure.
'''
# Reference useful information in local namespace
n_burnin = cfg['mcmc_params']['n_burnin']
scratch = cfg['mcmc_summaries']['path_scratch']
# Check for existence and writeability of scratch directory
if os.access(scratch, os.F_OK):
# It exists, check for read-write
if not os.access(scratch, os.R_OK | os.W_OK):
print >> sys.stderr, ("Error --- Cannot read and write to %s" %
scratch)
return 1
else:
# Otherwise, try to make the directory
os.makedirs(scratch)
# Extract results to scratch directory
if null:
pattern_results = cfg['mcmc_output']['null_out_pattern']
else:
pattern_results = cfg['mcmc_output']['out_pattern']
pattern_results = pattern_results.strip()
path_results = pattern_results.format(**cfg) % chrom
archive = tarfile.open(name=path_results, mode='r:*')
archive.extractall(path=scratch)
names_npy = archive.getnames()
archive.close()
# Load results of interest
mu = np.load(scratch + '/mu.npy')
sigmasq = np.load(scratch + '/sigmasq.npy')
region_ids = np.load(scratch + '/region_ids.npy')
# Remove burnin
if n_burnin > 0:
mu = mu[n_burnin:]
sigmasq = sigmasq[n_burnin:]
# Compute posterior means
mu_postmean = np.mean(mu, 0)
sigmasq_postmean = np.mean(sigmasq, 0)
sigma_postmean = np.mean(np.sqrt(sigmasq), 0)
# Compute posterior medians
mu_postmed = np.median(mu, 0)
sigmasq_postmed = np.median(sigmasq, 0)
sigma_postmed = np.median(np.sqrt(sigmasq), 0)
# Compute standard errors
mu_se = np.std(mu, 0)
sigmasq_se = np.std(sigmasq, 0)
sigma_se = np.std(np.sqrt(sigmasq), 0)
# Provide nicely-formatted delimited output for analyses and plotting
if null:
pattern_summaries = cfg['mcmc_output']['null_param_pattern']
else:
pattern_summaries = cfg['mcmc_output']['param_pattern']
pattern_summaries = pattern_summaries.strip()
path_summaries = pattern_summaries.format(**cfg) % chrom
# Build recarray of summaries, starting with coefficients and diagnostics
summaries = np.rec.fromarrays([region_ids, mu_postmean, mu_postmed, mu_se,
sigmasq_postmean, sigmasq_postmed,
sigmasq_se, sigma_postmean, sigma_postmed,
sigma_se],
names= ('region_id', 'mu_postmean',
'mu_postmed', 'mu_se',
'sigmasq_postmean', 'sigmasq_postmed',
'sigmasq_se', 'sigma_postmean',
'sigma_postmed', 'sigma_se'))
# Write summaries to delimited text file
libio.write_recarray_to_file(fname=path_summaries, data=summaries,
header=True, sep=' ')
# Clean-up scratch directory
for name in names_npy:
os.remove(scratch + '/' + name)
return 0