Mercurial > repos > scottx611x > cooler_convert

annotate recursive_agg_onefile.py @ 10:f0d4e43f95b5 draft

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planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
author scottx611x
date Mon, 21 Nov 2016 08:49:12 -0500
parents 4543c0fdd563
children 1745b88127c0
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1 from __future__ import division, print_function
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2 from multiprocessing import Pool
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3 import argparse
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4 import sys
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5
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6 import numpy as np
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7 import cooler
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8 from cooler.io import CoolerAggregator
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9 import cooler.ice
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10 import h5py
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12
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13 FACTOR = 2
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14 TILESIZE = 256
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15 N_CPU = 8
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17
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18 def set_postmortem_hook():
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19 import sys, traceback, ipdb
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20 def _excepthook(exc_type, value, tb):
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21 traceback.print_exception(exc_type, value, tb)
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22 print()
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23 ipdb.pm()
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24 sys.excepthook = _excepthook
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25
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26 set_postmortem_hook()
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29 def main(infile, outfile, chunksize):
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30 c = cooler.Cooler(infile)
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31 binsize = c.info['bin-size']
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32 chromtable = c.chroms()[:]
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33 chromsizes = chromtable.set_index('name')['length']
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34 chroms = chromtable['name'].values
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35 lengths = chromtable['length'].values
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36 total_length = np.sum(chromsizes.values)
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37 n_tiles = total_length / binsize / TILESIZE
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38 n_zooms = int(np.ceil(np.log2(n_tiles)))
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39
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40 print(
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41 "Copying base matrix to level {0} and producing {0} zoom levels starting from 0...".format(n_zooms),
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42 file=sys.stderr
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43 )
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44
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45 # transfer base matrix
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46 with h5py.File(outfile, 'w') as dest, \
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47 h5py.File(infile, 'r') as src:
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48
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49 zoomLevel = str(n_zooms)
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50 src.copy('/', dest, zoomLevel)
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51
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52 print(zoomLevel, file=sys.stderr)
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53
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54
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55 # produce aggregations
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56 with h5py.File(outfile, 'r+') as f:
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57 grp = f[str(n_zooms)]
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58 c = cooler.Cooler(grp)
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59 binsize = cooler.info(grp)['bin-size']
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60
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61 for i in range(n_zooms - 1, -1, -1):
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62 zoomLevel = str(i)
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63
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64 # aggregate
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65 new_binsize = binsize * FACTOR
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66 new_bins = cooler.util.binnify(chromsizes, new_binsize)
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67
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68 reader = CoolerAggregator(c, new_bins, chunksize)
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69
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70 grp = f.create_group(zoomLevel)
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71 f.attrs[zoomLevel] = new_binsize
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72 cooler.io.create(grp, chroms, lengths, new_bins, reader)
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73
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74 # balance
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75 #with Pool(N_CPU) as pool:
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76 too_close = 20000 # for HindIII
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77 ignore_diags = max(int(np.ceil(too_close / new_binsize)), 3)
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78
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79 bias = cooler.ice.iterative_correction(
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80 f, zoomLevel,
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81 chunksize=chunksize,
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82 min_nnz=10,
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83 mad_max=3,
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84 ignore_diags=ignore_diags,
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85 map=map)
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86 h5opts = dict(compression='gzip', compression_opts=6)
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87 grp['bins'].create_dataset('weight', data=bias, **h5opts)
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88
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89 print(zoomLevel, file=sys.stderr)
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90
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91 c = cooler.Cooler(grp)
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92 binsize = new_binsize
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93
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94
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95 if __name__ == '__main__':
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96 parser = argparse.ArgumentParser(
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97 description="Recursively aggregate a single resolution cooler file into a multi-resolution file.")
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98 parser.add_argument(
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99 "cooler_file",
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100 help="Cooler file",
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101 metavar="COOLER_PATH")
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102 parser.add_argument(
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103 "--out", "-o",
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104 help="Output text file")
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105 args = vars(parser.parse_args())
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106
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107
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108 infile = args['cooler_file']
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109 if args['out'] is None:
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110 outfile = infile.replace('.cool', '.multires.cool')
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111 else:
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112 outfile = args['out']
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113
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114 chunksize = int(1e6)
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115 main(infile, outfile, chunksize)
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116