def interMDS(names, prefix, inter_res, intra_res, full, args):
inter_res_string = tools.get_res_string(inter_res)
intra_res_string = tools.get_res_string(intra_res)
#get low-res structures from intra files
low_structures = []
for name in names:
path = "{}_{}_{}.bed".format(prefix, name, intra_res_string)
chrom = dt.chromFromBed(path)
#reduce res
chrom.res = inter_res
chrom.minPos = int(np.floor(float(chrom.minPos)/chrom.res)) * chrom.res #round
chrom.maxPos = int(np.ceil(float(chrom.maxPos)/chrom.res)) * chrom.res
low_structures.append(dt.structureFromBed(path, chrom))
#for correct indexing
n = len(names)
offsets = np.zeros(n, dtype=int)
for i in range(1, n):
offsets[i] = offsets[i-1] + len(low_structures[i-1].getPoints())
inter_mat = get_inter_mat(prefix, inter_res_string, intra_res_string, low_structures, offsets)
#perform MDS at low resolution on all chroms
infer_structures(inter_mat, low_structures, offsets, args[3], args[4])
#perform MDS at high resolution on each chrom
high_structures = []
inferred_low_structures = []
ts = []
for true_low, name in zip(low_structures, names):
path = "{}_{}_{}.bed".format(prefix, name, intra_res_string)
if full:
high_structure = mm.fullMDS(path, False, args[4], args[3])
else:
high_structure = mm.partitionedMDS(path, args)
high_structures.append(high_structure)
inferred_low = dt.highToLow(high_structure, true_low.chrom.res/high_structure.chrom.res)
inferred_low_structures.append(inferred_low)
#rescale
rescaling_factor = la.radius_of_gyration(true_low)/la.radius_of_gyration(inferred_low)
rescaled_coords = [rescaling_factor * coord for coord in inferred_low.getCoords()]
for i, point in enumerate(inferred_low.getPoints()):
point.pos = rescaled_coords[i]
r, t = la.getTransformation(inferred_low, true_low)
high_structure.transform(r, None) #do not translate now (need to rescale)
ts.append(t)
#translate (with rescaling)
low_rgs = np.array([la.radius_of_gyration(structure) for structure in low_structures])
high_rgs = np.array([la.radius_of_gyration(structure) for structure in high_structures])
scaling_factor = np.mean(high_rgs/low_rgs)
for high_structure, t in zip(high_structures, ts):
high_structure.transform(None, scaling_factor*t) #rescale translation
return high_structures
def interMDS(names, inter_prefix, intra_prefix, inter_res, intra_res, intra_low_res, args):
inter_res_string = tools.get_res_string(inter_res)
intra_res_string = tools.get_res_string(intra_res)
if intra_low_res is None:
intra_low_res_string = None
else:
intra_low_res_string = tools.get_res_string(intra_low_res)
#get low-res clusters from intra files
low_clusters = [dt.clusterFromBed("{}_{}_{}.bed".format(intra_prefix, name, inter_res_string), None, None) for name in names]
#for correct indexing
n = len(names)
offsets = np.zeros(n, dtype=np.int32)
for i in range(1, n):
offsets[i] = offsets[i-1] + len(low_clusters[i-1].getPoints())
inter_mat = get_inter_mat(intra_prefix, inter_prefix, inter_res, low_clusters, offsets)
#perform MDS at low resolution on all chroms
mm.infer_clusters(inter_mat, low_clusters, offsets, args[4])
#perform MDS at high resolution on each chrom
high_clusters = []
inferred_low_clusters = []
ts = []
for true_low, name in zip(low_clusters, names):
path = "{}_{}_{}.bed".format(intra_prefix, name, intra_res_string)
if intra_low_res_string is None:
high_cluster = mm.fullMDS(path, False, args[4])
else:
low_path = "{}_{}_{}.bed".format(intra_prefix, name, intra_low_res_string)
high_cluster = mm.partitionedMDS(path, low_path, args)
high_clusters.append(high_cluster)
inferred_low = dt.highToLow(high_cluster, true_low.chrom.res/high_cluster.chrom.res)
inferred_low_clusters.append(inferred_low)
#rescale
rescaling_factor = la.radius_of_gyration(true_low)/la.radius_of_gyration(inferred_low)
rescaled_coords = [rescaling_factor * coord for coord in inferred_low.getCoords()]
for i, point in enumerate(inferred_low.getPoints()):
point.pos = rescaled_coords[i]
r, t = la.getTransformation(inferred_low, true_low)
high_cluster.transform(r, None) #do not translate now (need to rescale)
ts.append(t)
#translate (with rescaling)
low_rgs = np.array([la.radius_of_gyration(cluster) for cluster in low_clusters])
high_rgs = np.array([la.radius_of_gyration(cluster) for cluster in high_clusters])
scaling_factor = np.mean(high_rgs/low_rgs)
for high_cluster, t in zip(high_clusters, ts):
high_cluster.transform(None, scaling_factor*t) #rescale translation
return high_clusters
def rescale(self):
"""Rescale radius of gyration of structure to 1"""
rg = la.radius_of_gyration(self)
for i, point in enumerate(self.points):
if point != 0:
x, y, z = point.pos
self.points[i].pos = (x // rg, y // rg, z // rg)
def transform(trueLow, highSubstructure, res_ratio):
#approximate as low resolution
inferredLow = dt.highToLow(highSubstructure, res_ratio)
scaling_factor = la.radius_of_gyration(trueLow) / la.radius_of_gyration(
inferredLow)
for i, point in enumerate(inferredLow.points):
if point != 0:
x, y, z = point.pos
inferredLow.points[i].pos = (x * scaling_factor,
y * scaling_factor,
z * scaling_factor)
#recover the transformation for inferred from true low structure
r, t = la.getTransformation(inferredLow, trueLow)
t /= scaling_factor
#transform high structure
highSubstructure.transform(r, t)
def partitionedMDS(path, args):
"""Partitions structure into substructures and performs MDS"""
domainSmoothingParameter = args[0]
minSizeFraction = args[1]
maxmemory = args[2]
num_threads = args[3]
alpha = args[4]
res_ratio = args[5]
alpha2 = args[6]
#create low-res structure
low_chrom = dt.chromFromBed(path)
low_chrom.res *= res_ratio
lowstructure = dt.structureFromBed(path, low_chrom) #low global structure
#get TADs
low_contactMat = dt.matFromBed(path, lowstructure)
low_tad_indices = tad.getDomains(
low_contactMat, lowstructure, domainSmoothingParameter, minSizeFraction
) #low substructures, defined on relative indices not absolute indices
tad.substructuresFromTads(lowstructure, low_tad_indices)
#create high-res chrom
size, res = dt.basicParamsFromBed(path)
highChrom = dt.ChromParameters(lowstructure.chrom.minPos,
lowstructure.chrom.maxPos, res,
lowstructure.chrom.name, size)
highstructure = dt.Structure([], [], highChrom, 0)
high_substructures = []
low_gen_coords = lowstructure.getGenCoords()
offset = 0 #initialize
for td in low_tad_indices:
start_gen_coord = low_gen_coords[td[0]]
end_gen_coord = low_gen_coords[td[1]]
high_substructure = dt.structureFromBed(path, highChrom,
start_gen_coord, end_gen_coord,
offset)
high_substructures.append(high_substructure)
offset += len(high_substructure.points) #update
offset -= 1
highstructure.setstructures(high_substructures)
infer_structure(low_contactMat, lowstructure, alpha, num_threads)
print "Low-resolution MDS complete"
highSubstructures = pymp.shared.list(highstructure.structures)
lowSubstructures = pymp.shared.list(lowstructure.structures)
numSubstructures = len(highstructure.structures)
num_threads = min(
(num_threads, mp.cpu_count(), numSubstructures)
) #don't exceed number of requested threads, available threads, or structures
with pymp.Parallel(num_threads) as p:
for substructurenum in p.range(numSubstructures):
highSubstructure = highSubstructures[substructurenum]
if len(highSubstructure.getPoints()) > 0: #skip empty
trueLow = lowSubstructures[substructurenum]
#perform MDS individually
structure_contactMat = dt.matFromBed(
path,
highSubstructure) #contact matrix for this structure only
infer_structure(structure_contactMat, highSubstructure, alpha2,
num_threads)
#approximate as low resolution
inferredLow = dt.highToLow(highSubstructure, res_ratio)
#rescale
scaling_factor = la.radius_of_gyration(
trueLow) / la.radius_of_gyration(inferredLow)
for i, point in enumerate(inferredLow.points):
if point != 0:
x, y, z = point.pos
inferredLow.points[i].pos = (x * scaling_factor,
y * scaling_factor,
z * scaling_factor)
#recover the transformation for inferred from true low structure
r, t = la.getTransformation(inferredLow, trueLow)
t /= scaling_factor
#transform high structure
highSubstructure.transform(r, t)
highSubstructures[substructurenum] = highSubstructure
print "MDS performed on structure {} of {}".format(
substructurenum + 1, numSubstructures)
highstructure.setstructures(highSubstructures)
return highstructure
def partitionedMDS(path, lowpath, args):
"""Partitions cluster into subclusters and performs MDS"""
domainSmoothingParameter = args[0]
minSizeFraction = args[1]
maxmemory = args[2]
num_threads = args[3]
alpha = args[4]
#create low-res cluster
lowCluster = dt.clusterFromBed(lowpath, None, None)
#get TADs
low_contactMat = dt.matFromBed(lowpath, lowCluster)
lowTads = tad.getDomains(low_contactMat, lowCluster,
domainSmoothingParameter,
minSizeFraction) #low subclusters
#create high-res chrom
size, res = dt.basicParamsFromBed(path)
highChrom = dt.ChromParameters(lowCluster.chrom.minPos,
lowCluster.chrom.maxPos, res,
lowCluster.chrom.name, size)
#create high-res cluster
resRatio = lowCluster.chrom.res / highChrom.res
highTads = lowTads * resRatio
highCluster = dt.clusterFromBed(path, highChrom, highTads)
#create compatible subclusters
tad.subclustersFromTads(highCluster, lowCluster, lowTads)
infer_cluster(low_contactMat, lowCluster, alpha)
print "Low-resolution MDS complete"
highSubclusters = pymp.shared.list(highCluster.clusters)
lowSubclusters = pymp.shared.list(lowCluster.clusters)
numSubclusters = len(highCluster.clusters)
num_threads = min(
(num_threads, mp.cpu_count(), numSubclusters)
) #don't exceed number of requested threads, available threads, or clusters
with pymp.Parallel(num_threads) as p:
for subclusternum in p.range(numSubclusters):
highSubcluster = highSubclusters[subclusternum]
trueLow = lowSubclusters[subclusternum]
#perform MDS individually
cluster_contactMat = dt.matFromBed(
path, highSubcluster) #contact matrix for this cluster only
infer_cluster(cluster_contactMat, highSubcluster, alpha)
#approximate as low resolution
inferredLow = dt.highToLow(highSubcluster, resRatio)
#rescale
scaling_factor = la.radius_of_gyration(
trueLow) / la.radius_of_gyration(inferredLow)
for i, point in enumerate(inferredLow.points):
if point != 0:
x, y, z = point.pos
inferredLow.points[i].pos = (x * scaling_factor,
y * scaling_factor,
z * scaling_factor)
#recover the transformation for inferred from true low cluster
r, t = la.getTransformation(inferredLow, trueLow)
t *= resRatio**(2. / 3) #rescale
#transform high cluster
highSubcluster.transform(r, t)
highSubclusters[subclusternum] = highSubcluster
print "MDS performed on cluster {} of {}".format(
subclusternum + 1, numSubclusters)
highCluster.setClusters(highSubclusters)
return highCluster
