Mercurial > repos > scottx611x > cooler_convert

annotate recursive_agg_onefile.py @ 18:e539ccf221fd draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
author scottx611x
date Mon, 21 Nov 2016 10:39:27 -0500
parents 1745b88127c0
children 70d6350f982d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
1 from __future__ import division, print_function
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
2 from multiprocessing import Pool
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
3 import argparse
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
4 import sys
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
5
5
4543c0fdd563 planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents: 4
diff changeset
6 import numpy as np
10
f0d4e43f95b5 planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents: 5
diff changeset
7 import cooler
5
4543c0fdd563 planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents: 4
diff changeset
8 from cooler.io import CoolerAggregator
4543c0fdd563 planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents: 4
diff changeset
9 import cooler.ice
0
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
10 import h5py
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
11
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
12
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
13 FACTOR = 2
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
14 TILESIZE = 256
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
15 N_CPU = 8
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
16
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
17 def main(infile, outfile, chunksize):
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
18 c = cooler.Cooler(infile)
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
19 binsize = c.info['bin-size']
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
20 chromtable = c.chroms()[:]
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
21 chromsizes = chromtable.set_index('name')['length']
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
22 chroms = chromtable['name'].values
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
23 lengths = chromtable['length'].values
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
24 total_length = np.sum(chromsizes.values)
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
25 n_tiles = total_length / binsize / TILESIZE
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
26 n_zooms = int(np.ceil(np.log2(n_tiles)))
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
27
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
28 print(
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
29 "Copying base matrix to level {0} and producing {0} zoom levels starting from 0...".format(n_zooms),
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
30 file=sys.stderr
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
31 )
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
32
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
33 # transfer base matrix
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
34 with h5py.File(outfile, 'w') as dest, \
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
35 h5py.File(infile, 'r') as src:
18
e539ccf221fd planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents: 17
diff changeset
36 try:
e539ccf221fd planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents: 17
diff changeset
37 zoomLevel = str(n_zooms)
e539ccf221fd planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents: 17
diff changeset
38 src.copy('/', dest, zoomLevel)
e539ccf221fd planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents: 17
diff changeset
39 except Exception as e:
e539ccf221fd planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents: 17
diff changeset
40 print("Error: %s" % e)
0
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
41 print(zoomLevel, file=sys.stderr)
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
42
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
43
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
44 # produce aggregations
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
45 with h5py.File(outfile, 'r+') as f:
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
46 grp = f[str(n_zooms)]
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
47 c = cooler.Cooler(grp)
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
48 binsize = cooler.info(grp)['bin-size']
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
49
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
50 for i in range(n_zooms - 1, -1, -1):
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
51 zoomLevel = str(i)
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
52
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
53 # aggregate
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
54 new_binsize = binsize * FACTOR
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
55 new_bins = cooler.util.binnify(chromsizes, new_binsize)
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
56
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
57 reader = CoolerAggregator(c, new_bins, chunksize)
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
58
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
59 grp = f.create_group(zoomLevel)
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
60 f.attrs[zoomLevel] = new_binsize
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
61 cooler.io.create(grp, chroms, lengths, new_bins, reader)
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
62
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
63 # balance
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
64 #with Pool(N_CPU) as pool:
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
65 too_close = 20000 # for HindIII
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
66 ignore_diags = max(int(np.ceil(too_close / new_binsize)), 3)
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
67
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
68 bias = cooler.ice.iterative_correction(
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
69 f, zoomLevel,
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
70 chunksize=chunksize,
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
71 min_nnz=10,
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
72 mad_max=3,
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
73 ignore_diags=ignore_diags,
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
74 map=map)
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
75 h5opts = dict(compression='gzip', compression_opts=6)
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
76 grp['bins'].create_dataset('weight', data=bias, **h5opts)
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
77
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
78 print(zoomLevel, file=sys.stderr)
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
79
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
80 c = cooler.Cooler(grp)
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
81 binsize = new_binsize
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
82
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
83
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
84 if __name__ == '__main__':
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
85 parser = argparse.ArgumentParser(
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
86 description="Recursively aggregate a single resolution cooler file into a multi-resolution file.")
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
87 parser.add_argument(
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
88 "cooler_file",
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
89 help="Cooler file",
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
90 metavar="COOLER_PATH")
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
91 parser.add_argument(
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
92 "--out", "-o",
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
93 help="Output text file")
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
94 args = vars(parser.parse_args())
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
95
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
96
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
97 infile = args['cooler_file']
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
98 if args['out'] is None:
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
99 outfile = infile.replace('.cool', '.multires.cool')
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
100 else:
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
101 outfile = args['out']
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
102
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
103 chunksize = int(1e6)
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
104 main(infile, outfile, chunksize)
c7d624661e8a planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
scottx611x
parents:
diff changeset
105