def full_mds(path1,
path2,
alpha=4,
penalty=0.05,
num_threads=3,
weight=0.05,
prefix=""):
"""MDS without partitioning"""
structure1 = dt.structureFromBed(path1)
structure2 = dt.structureFromBed(path2)
dt.make_compatible((structure1, structure2))
contactMat1 = dt.matFromBed(path1, structure1)
contactMat2 = dt.matFromBed(path2, structure2)
infer_structures(contactMat1, structure1, contactMat2, structure2, alpha,
penalty, num_threads, weight)
prefix1 = os.path.splitext(os.path.basename(path1))[0]
structure1.write("{}{}_structure.tsv".format(prefix, prefix1))
prefix2 = os.path.splitext(os.path.basename(path2))[0]
structure2.write("{}{}_structure.tsv".format(prefix, prefix2))
dists = la.calculate_distances(structure1, structure2)
with open("{}{}_{}_relocalization.bed".format(prefix, prefix1, prefix2),
"w") as out:
for gen_coord, dist in zip(structure1.getGenCoords(), dists):
out.write("\t".join(
(structure1.chrom.name, str(gen_coord),
str(gen_coord + structure1.chrom.res), str(dist))))
out.write("\n")
out.close()
print("Fractional compartment change: ")
print(calculate_compartment_fraction(structure1, structure2, path1, path2))
return structure1, structure2
def fullMDS(path1, path2, alpha, penalty, num_threads, weight):
"""MDS without partitioning"""
structure1 = dt.structureFromBed(path1)
structure2 = dt.structureFromBed(path2)
dt.make_compatible((structure1, structure2))
contactMat1 = dt.matFromBed(path1, structure1)
contactMat2 = dt.matFromBed(path2, structure2)
infer_structures(contactMat1, structure1, contactMat2, structure2, alpha,
penalty, num_threads, weight)
return structure1, structure2
import linear_algebra as la
from sklearn.manifold import MDS
chrom = sys.argv[1]
res_kb = 100
prefix1 = "GM12878_combined"
prefix2 = "K562"
path1 = "hic_data/{}_{}_{}kb.bed".format(prefix1, chrom, res_kb)
path2 = "hic_data/{}_{}_{}kb.bed".format(prefix2, chrom, res_kb)
structure1 = dt.structureFromBed(path1, None, None)
structure2 = dt.structureFromBed(path2, None, None)
#make structures compatible
dt.make_compatible((structure1, structure2))
#get distance matrices
dists1 = dt.normalized_dist_mat(path1, structure1)
dists2 = dt.normalized_dist_mat(path2, structure2)
#MDS
coords1 = MDS(n_components=3,
random_state=np.random.RandomState(),
dissimilarity="precomputed",
n_jobs=-1).fit_transform(dists1)
coords2 = MDS(n_components=3,
random_state=np.random.RandomState(),
dissimilarity="precomputed",
n_jobs=-1).fit_transform(dists2)
def partitioned_mds(path1,
path2,
prefix="",
centromere=0,
num_partitions=4,
maxmemory=32000000,
num_threads=3,
alpha=4,
res_ratio=10,
penalty=0.05,
weight=0.05):
"""Partitions structure into substructures and performs MDS"""
#create low-res structures
lowstructure1 = create_low_res_structure(path1, res_ratio)
lowstructure2 = create_low_res_structure(path2, res_ratio)
dt.make_compatible((lowstructure1, lowstructure2))
#get partitions
n = len(lowstructure1.getPoints())
if centromere == 0:
midpoint = int(n / 2)
else:
midpoint = lowstructure1.chrom.getAbsoluteIndex(centromere)
assert num_partitions % 2 == 0
partition_size1 = int(np.ceil(float(midpoint) / (num_partitions / 2)))
partition_size2 = int(np.ceil(float(n - midpoint) / (num_partitions / 2)))
lowpartitions = [
] #low substructures, defined on absolute indices not relative indices
for i in range(int(num_partitions / 2)):
lowpartitions.append(
(i * partition_size1, min(((i + 1) * partition_size1), midpoint)))
for i in range(int(num_partitions / 2)):
lowpartitions.append((midpoint + i * partition_size2,
min((midpoint + (i + 1) * partition_size2),
n - 1)))
lowpartitions = np.array(lowpartitions)
low_contactMat1 = dt.matFromBed(path1, lowstructure1)
low_contactMat2 = dt.matFromBed(path2, lowstructure2)
tad.substructuresFromAbsoluteTads(lowstructure1, lowpartitions)
tad.substructuresFromAbsoluteTads(lowstructure2, lowpartitions)
#create high-res chroms
size1, res1 = dt.basicParamsFromBed(path1)
highChrom1 = dt.ChromParameters(lowstructure1.chrom.minPos,
lowstructure1.chrom.maxPos, res1,
lowstructure1.chrom.name, size1)
size2, res2 = dt.basicParamsFromBed(path2)
highChrom2 = dt.ChromParameters(lowstructure2.chrom.minPos,
lowstructure2.chrom.maxPos, res2,
lowstructure2.chrom.name, size2)
#initialize high-res substructures
high_substructures1 = []
high_substructures2 = []
low_gen_coords = lowstructure1.getGenCoords()
offset1 = 0 #initialize
offset2 = 0
for partition in lowpartitions:
start_gen_coord = low_gen_coords[partition[0]]
end_gen_coord = low_gen_coords[partition[1]]
high_substructure1 = dt.structureFromBed(path1, highChrom1,
start_gen_coord,
end_gen_coord, offset1)
high_substructure2 = dt.structureFromBed(path2, highChrom2,
start_gen_coord,
end_gen_coord, offset2)
high_substructures1.append(high_substructure1)
high_substructures2.append(high_substructure2)
offset1 += (len(high_substructure1.points) - 1) #update
offset2 += (len(high_substructure2.points) - 1) #update
for high_substructure1, high_substructure2 in zip(high_substructures1,
high_substructures2):
dt.make_points_compatible((high_substructure1, high_substructure2))
highstructure1 = dt.Structure([], high_substructures1, highChrom1, 0)
highstructure2 = dt.Structure([], high_substructures2, highChrom2, 0)
infer_structures(low_contactMat1, lowstructure1, low_contactMat2,
lowstructure2, alpha, penalty, num_threads, weight)
print("Low-resolution MDS complete")
highSubstructures1 = pymp.shared.list(highstructure1.structures)
highSubstructures2 = pymp.shared.list(highstructure2.structures)
lowSubstructures1 = pymp.shared.list(lowstructure1.structures)
lowSubstructures2 = pymp.shared.list(lowstructure2.structures)
numSubstructures = len(highstructure1.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):
highSubstructure1 = highSubstructures1[substructurenum]
highSubstructure2 = highSubstructures2[substructurenum]
trueLow1 = lowSubstructures1[substructurenum]
trueLow2 = lowSubstructures2[substructurenum]
#joint MDS
structure_contactMat1 = dt.matFromBed(
path1,
highSubstructure1) #contact matrix for this structure only
structure_contactMat2 = dt.matFromBed(
path2,
highSubstructure2) #contact matrix for this structure only
infer_structures(structure_contactMat1, highSubstructure1,
structure_contactMat2, highSubstructure2, 2.5,
penalty, num_threads, weight)
transform(trueLow1, highSubstructure1, res_ratio)
transform(trueLow2, highSubstructure2, res_ratio)
highSubstructures1[substructurenum] = highSubstructure1
highSubstructures2[substructurenum] = highSubstructure2
print("MDS performed on structure {} of {}".format(
substructurenum + 1, numSubstructures))
highstructure1.setstructures(highSubstructures1)
highstructure2.setstructures(highSubstructures2)
highstructure1.set_rel_indices()
highstructure2.set_rel_indices()
return highstructure1, highstructure2