Mercurial > repos > scottx611x > cooler_convert

annotate recursive_agg_onefile.py @ 42:ff10e8784d4e draft default tip

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planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
author scottx611x
date Tue, 22 Nov 2016 14:21:59 -0500
parents 1daf2cd88f17
children
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1 from __future__ import division, print_function
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2 import sys
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3
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4 sys.path.append("/usr/local/lib/python2.7/dist-packages")
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5
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6 from multiprocessing import Pool
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7 import argparse
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8 import warnings
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9
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10 import numpy as np
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11 import cooler
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12 from cooler.io import CoolerAggregator
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13 import cooler.ice
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14 import h5py
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17 FACTOR = 2
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18 TILESIZE = 256
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19 N_CPU = 8
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21 def main(infile, outfile, chunksize):
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22 c = cooler.Cooler(infile)
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23 binsize = c.info['bin-size']
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24 chromtable = c.chroms()[:]
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25 chromsizes = chromtable.set_index('name')['length']
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26 chroms = chromtable['name'].values
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27 lengths = chromtable['length'].values
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28 total_length = np.sum(chromsizes.values)
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29 n_tiles = total_length / binsize / TILESIZE
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30 n_zooms = int(np.ceil(np.log2(n_tiles)))
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31
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32 print(
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33 "Copying base matrix to level {0} and producing {0} zoom levels starting from 0...".format(n_zooms),
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34 file=sys.stdout
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35 )
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37 # transfer base matrix
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38 with h5py.File(outfile, 'w') as dest, \
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39 h5py.File(infile, 'r') as src:
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40 zoomLevel = str(n_zooms)
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41 src.copy('/', dest, zoomLevel)
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42 print(zoomLevel, file=sys.stdout)
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45 # produce aggregations
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46 with h5py.File(outfile, 'r+') as f:
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47 grp = f[str(n_zooms)]
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48 c = cooler.Cooler(grp)
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49 binsize = cooler.info(grp)['bin-size']
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50
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51 for i in range(n_zooms - 1, -1, -1):
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52 zoomLevel = str(i)
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54 # aggregate
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55 new_binsize = binsize * FACTOR
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56 new_bins = cooler.util.binnify(chromsizes, new_binsize)
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58 reader = CoolerAggregator(c, new_bins, chunksize)
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60 grp = f.create_group(zoomLevel)
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61 f.attrs[zoomLevel] = new_binsize
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62 cooler.io.create(grp, chroms, lengths, new_bins, reader)
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63
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64 # balance
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65 #with Pool(N_CPU) as pool:
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66 too_close = 20000 # for HindIII
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67 ignore_diags = max(int(np.ceil(too_close / new_binsize)), 3)
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68
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69 bias = cooler.ice.iterative_correction(
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70 f, zoomLevel,
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71 chunksize=chunksize,
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72 min_nnz=10,
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73 mad_max=3,
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74 ignore_diags=ignore_diags,
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75 map=map)
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76 h5opts = dict(compression='gzip', compression_opts=6)
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77 grp['bins'].create_dataset('weight', data=bias, **h5opts)
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78
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79 print(zoomLevel, file=sys.stdout)
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80
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81 c = cooler.Cooler(grp)
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82 binsize = new_binsize
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83
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84 if __name__ == '__main__':
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85 parser = argparse.ArgumentParser(
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86 description="Recursively aggregate a single resolution cooler file into a multi-resolution file.")
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87 parser.add_argument(
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88 "cooler_file",
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89 help="Cooler file",
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90 metavar="COOLER_PATH")
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91 parser.add_argument(
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92 "--out", "-o",
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93 help="Output text file")
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94 args = vars(parser.parse_args())
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96
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97 infile = args['cooler_file']
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98 if args['out'] is None:
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99 outfile = infile.replace('.cool', '.multires.cool')
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100 else:
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101 outfile = args['out']
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102
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103 chunksize = int(1e6)
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104 with warnings.catch_warnings():
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105 warnings.simplefilter("ignore")
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106 main(infile, outfile, chunksize)
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