def structureFromBed(path, chrom=None, start=None, end=None, offset=0):
"""Initializes structure from intrachromosomal BED file."""
if chrom is None:
chrom = chromFromBed(path)
if start is None:
start = chrom.minPos
if end is None:
end = chrom.maxPos
structure = Structure([], [], chrom, offset)
structure.points = np.zeros(int((end - start)/chrom.res) + 1, dtype=object) #true if locus should be added
tracker = Tracker("Identifying loci", structure.chrom.size)
#add loci
with open(path) as listFile:
for line in listFile:
line = line.strip().split()
pos1 = int(line[1])
pos2 = int(line[4])
if pos1 >= start and pos1 <= end and pos2 >= start and pos2 <= end:
abs_index1 = structure.chrom.getAbsoluteIndex(pos1)
abs_index2 = structure.chrom.getAbsoluteIndex(pos2)
if abs_index1 != abs_index2: #non-self-interacting
structure.points[int((pos1 - start)/chrom.res)] = Point((0,0,0), structure.chrom, abs_index1, 0)
structure.points[int((pos2 - start)/chrom.res)] = Point((0,0,0), structure.chrom, abs_index2, 0)
tracker.increment()
listFile.close()
structure.set_rel_indices()
return structure
def structureFromBed(path,
chrom=None,
start=None,
end=None,
offset=0,
tads=None):
"""Initializes structure from intrachromosomal BED file."""
if chrom is None:
chrom = chromFromBed(path)
if start is None:
start = chrom.minPos
if end is None:
end = chrom.maxPos
structure = Structure([], [], chrom, offset)
#get TAD for every locus
#if tads is None:
# tadNums = np.zeros(structure.chrom.getLength())
#else:
# tadNums = []
# for i, tad in enumerate(tads):
# for j in range(tad[0], tad[1]):
# tadNums.append(i)
#maxIndex = len(tadNums) - 1
structure.points = np.zeros((end - start) / chrom.res + 1,
dtype=object) #true if locus should be added
tracker = Tracker("Identifying loci", structure.chrom.size)
#add loci
with open(path) as listFile:
for line in listFile:
line = line.strip().split()
pos1 = int(line[1])
pos2 = int(line[4])
if pos1 >= start and pos1 <= end and pos2 >= start and pos2 <= end:
pointNum1 = structure.chrom.getPointNum(pos1)
pointNum2 = structure.chrom.getPointNum(pos2)
#tadNum1 = tadNums[min(pointNum1, maxIndex)]
#tadNum2 = tadNums[min(pointNum2, maxIndex)]
#if pointNum1 != pointNum2 and tadNum1 == tadNum2: #must be in same TAD
if pointNum1 != pointNum2: #non-self-interacting
structure.points[(pos1 - start) / chrom.res] = Point(
(0, 0, 0), pointNum1, structure.chrom, 0)
structure.points[(pos2 - start) / chrom.res] = Point(
(0, 0, 0), pointNum2, structure.chrom, 0)
tracker.increment()
listFile.close()
structure.indexPoints()
return structure
def clusterFromBed(path, chrom, tads):
"""Initializes cluster from intrachromosomal BED file."""
if chrom is None:
chrom = intraChromFromBed(path, None)
cluster = Cluster([], [], chrom, 0)
#get TAD for every locus
if tads is None:
tadNums = np.zeros(cluster.chrom.getLength())
else:
tadNums = []
tadNum = 1
for tad in tads:
for i in range(tad[0], tad[1]):
tadNums.append(tadNum)
tadNum += 1
maxIndex = len(tadNums) - 1
points_to_add = np.zeros(cluster.chrom.getLength(),
dtype=np.bool) #true if locus should be added
tracker = Tracker("Identifying loci", cluster.chrom.size)
#find which loci should be added
with open(path) as listFile:
for line in listFile:
line = line.strip().split()
pos1 = int(line[1])
pos2 = int(line[4])
pointNum1 = cluster.chrom.getPointNum(pos1)
pointNum2 = cluster.chrom.getPointNum(pos2)
if pointNum1 is not None and pointNum2 is not None:
tadNum1 = tadNums[min(pointNum1, maxIndex)]
tadNum2 = tadNums[min(pointNum2, maxIndex)]
if pointNum1 != pointNum2 and tadNum1 == tadNum2: #must be in same TAD
if points_to_add[pointNum1] == False:
points_to_add[pointNum1] = True
if points_to_add[pointNum2] == False:
points_to_add[pointNum2] = True
tracker.increment()
listFile.close()
#create points
points = np.zeros(cluster.chrom.getLength(), dtype=np.object)
pointNums = np.where(points_to_add == True)[0]
for pointNum in pointNums:
points[pointNum] = Point((0, 0, 0), pointNum, cluster.chrom, None)
cluster.points = points
cluster.indexPoints()
return cluster
def matFromDixon(path, chrom):
"""Creates contact matrix from Dixon tsv data"""
numBins = chrom.getLength()
mat = np.zeros((numBins, numBins))
tracker = Tracker("Reading " + path, chrom.size)
with open(path) as infile:
for line in infile:
line = line.strip().split()
pos1 = int(line[0])
pos2 = int(line[1])
if pos1 != pos2:
if pos1 >= chrom.minPos and pos1 <= chrom.maxPos and pos2 >= chrom.minPos and pos2 <= chrom.maxPos:
bin1 = chrom.getAbsoluteIndex(pos1)
bin2 = chrom.getAbsoluteIndex(pos2)
if bin1 > bin2:
row = bin1
col = bin2
else:
row = bin1
col = bin2
mat[row, col] += 1
tracker.increment()
infile.close()
return mat
import numpy as np
in_path = sys.argv[1]
out_path = sys.argv[2]
f = h5py.File(in_path)
counts = np.array(f["pixels"]["count"])
bin_ids1 = np.array(f["pixels"]["bin1_id"])
bin_ids2 = np.array(f["pixels"]["bin2_id"])
chroms = np.array(f["bins"]["chrom"])
starts = np.array(f["bins"]["start"])
ends = np.array(f["bins"]["end"])
f.close()
tracker = Tracker("Converting to BED", len(counts))
print "Begin converting to BED"
with open(out_path, "w") as out_file:
for count, bin_id1, bin_id2 in zip(counts, bin_ids1, bin_ids2):
if count != 0:
chrom1 = str(chroms[bin_id1] + 1) #switch to 1-indexed
chrom2 = str(chroms[bin_id2] + 1)
start1 = str(starts[bin_id1])
end1 = str(ends[bin_id1])
start2 = str(starts[bin_id2])
end2 = str(ends[bin_id2])
out_file.write("\t".join(
("chr" + chrom1, start1, end1, "chr" + chrom2, start2, end2,
str(count))))
out_file.write("\n")
""""Convert fixedStep wig to binned bed"""
import sys
sys.path.append("..")
from tools import Tracker
wig = sys.argv[1]
bin_size = int(sys.argv[2])
file_size = int(sys.argv[3])
prefix = wig.split(".")[0]
tracker = Tracker("Converting {}".format(wig), file_size)
tot = 0
count = 0
with open(wig) as in_file:
with open("{}_{}kb.bed".format(prefix, bin_size / 1000), "w") as out_file:
for line in in_file:
line = line.strip().split()
if line[0] == "fixedStep": #header
chrom = line[1].split("=")[1]
curr_pos = int(line[2].split("=")[1])
step = int(line[3].split("=")[1])
span = int(line[4].split("=")[1])
else:
tot += float(line[0])
count += span
if curr_pos % bin_size == 0: