def fetch_data(self, gr: GenomeRange, **kwargs):
ma = self.peakachu.pval_ma
mask = ma.data > 0.87 # threshold to filter pvals
pixels = dict(zip(zip(ma.row[mask], ma.col[mask]), 1 / ma.data[mask]))
rows = [
(x, x + 1, y, y + 1) # call peakachu
for [x, y], *_ in peakacluster.local_clustering(pixels, res=10000)
]
# should return a pd.DataFrame with columns ['start1', 'end1', 'start2', 'end2']
peaks = pd.DataFrame(
rows, columns=['start1', 'end1', 'start2', 'end2'
]) * self.peakachu.fetched_binsize + gr.start
return peaks
def main(args):
import numpy as np
import pandas as pd
from collections import defaultdict
from peakachu import peakacluster
res = args.resolution
x = pd.read_table(args.infile,
index_col=0,
usecols=[0, 1, 4, 6, 7],
header=None)
chromosomes = list(set(x.index))
for chrom in chromosomes:
X = x.loc[chrom].values
r = X[:, 0].astype(int) // res
c = X[:, 1].astype(int) // res
p = X[:, 2].astype(float)
raw = X[:, 3].astype(float)
d = c - r
idx = (p > args.threshold)
r, c, p, raw, d = r[idx], c[idx], p[idx], raw[idx], d[idx]
tmpr, tmpc, tmpp, tmpraw, tmpd = r, c, p, raw, d
#rawmatrix={(r[i],c[i]): raw[i] for i in range(len(r))}
matrix = {(r[i], c[i]): p[i] for i in range(len(r))}
count = 40001
while count > 40000:
D = defaultdict(float)
P = defaultdict(float)
unique_d = list(set(tmpd.tolist()))
for distance in unique_d:
dx = (tmpd == distance)
dr, dc, dp, draw = tmpr[dx], tmpc[dx], tmpp[dx], tmpraw[dx]
dx = (dp > np.percentile(dp, 10))
dr, dc, dp, draw = dr[dx], dc[dx], dp[dx], draw[dx]
for i in range(dr.size):
D[(dr[i], dc[i])] += draw[i]
P[(dr[i], dc[i])] += dp[i]
count = len(D.keys())
tmpr = np.array([i[0] for i in P.keys()])
tmpc = np.array([i[1] for i in P.keys()])
tmpp = np.array([P.get(i) for i in P.keys()])
tmpraw = np.array([D.get(i) for i in P.keys()])
tmpd = tmpc - tmpr
del X
gc.collect()
final_list = peakacluster.local_clustering(D, res=res)
final_list = [i[0] for i in final_list]
r = [i[0] for i in final_list]
c = [i[1] for i in final_list]
p = np.array([matrix.get((r[i], c[i])) for i in range(len(r))])
if len(r) > 7000:
sorted_index = np.argsort(p)
r = [r[i] for i in sorted_index[-7000:]]
c = [c[i] for i in sorted_index[-7000:]]
for i in range(len(r)):
P = matrix.get((r[i], c[i]))
print(chrom,
r[i] * res,
r[i] * res + res,
chrom,
c[i] * res,
c[i] * res + res,
P,
sep='\t')
def main(args):
import gc
import sys
import numpy as np
import pandas as pd
from collections import defaultdict
from peakachu import peakacluster
res = args.resolution
x = {}
with open(args.infile, 'r') as source:
for line in source:
p = line.rstrip().split()
chrom = p[0]
if float(p[6]) > args.threshold:
if not chrom in x:
x[chrom] = []
x[chrom].append([int(p[1]), int(p[4]), float(p[6]), float(p[7])])
for c in x:
x[c] = np.r_[x[c]]
for chrom in x:
X = x[chrom]
r = X[:, 0].astype(int)//res
c = X[:, 1].astype(int)//res
p = X[:, 2].astype(float)
raw = X[:, 3].astype(float)
d = c-r
tmpr, tmpc, tmpp, tmpraw, tmpd = r, c, p, raw, d
#rawmatrix={(r[i],c[i]): raw[i] for i in range(len(r))}
matrix = {(r[i], c[i]): p[i] for i in range(len(r))}
count = 40001
while count > 40000:
D = defaultdict(float)
P = defaultdict(float)
unique_d = list(set(tmpd.tolist()))
for distance in unique_d:
dx = (tmpd == distance)
dr, dc, dp, draw = tmpr[dx], tmpc[dx], tmpp[dx], tmpraw[dx]
dx = (dp > np.percentile(dp, 10))
dr, dc, dp, draw = dr[dx], dc[dx], dp[dx], draw[dx]
for i in range(dr.size):
D[(dr[i], dc[i])] += draw[i]
P[(dr[i], dc[i])] += dp[i]
count = len(D.keys())
tmpr = np.array([i[0] for i in P.keys()])
tmpc = np.array([i[1] for i in P.keys()])
tmpp = np.array([P.get(i) for i in P.keys()])
tmpraw = np.array([D.get(i) for i in P.keys()])
tmpd = tmpc-tmpr
del X
gc.collect()
final_list = peakacluster.local_clustering(D, res=res)
final_list = [i[0] for i in final_list]
r = [i[0] for i in final_list]
c = [i[1] for i in final_list]
p = np.array([matrix.get((r[i], c[i])) for i in range(len(r))])
if len(r) > 7000:
sorted_index = np.argsort(p)
r = [r[i] for i in sorted_index[-7000:]]
c = [c[i] for i in sorted_index[-7000:]]
for i in range(len(r)):
P = matrix.get((r[i], c[i]))
print(chrom, r[i]*res, r[i]*res+res, chrom,
c[i]*res, c[i]*res+res,
P, sep='\t')