def _aggregate(self, span):
from cooler.api import Cooler
lo, hi = span
clr = Cooler(self.source_uri)
# convert_enum=False returns chroms as raw ints
table = clr.pixels(join=True, convert_enum=False)
chunk = table[lo:hi]
# logger.info('{} {}'.format(lo, hi))
print('{} {}'.format(lo, hi))
# use the "start" point as anchor for re-binning
# XXX - alternatives: midpoint anchor, proportional re-binning
binsize = self.gs.binsize
chrom_binoffset = self.gs.chrom_binoffset
chrom_abspos = self.gs.chrom_abspos
start_abspos = self.gs.start_abspos
chrom_id1 = chunk['chrom1'].values
chrom_id2 = chunk['chrom2'].values
start1 = chunk['start1'].values
start2 = chunk['start2'].values
if binsize is None:
abs_start1 = chrom_abspos[chrom_id1] + start1
abs_start2 = chrom_abspos[chrom_id2] + start2
chunk['bin1_id'] = np.searchsorted(
start_abspos, abs_start1, side='right') - 1
chunk['bin2_id'] = np.searchsorted(
start_abspos, abs_start2, side='right') - 1
else:
rel_bin1 = np.floor(start1 / binsize).astype(int)
rel_bin2 = np.floor(start2 / binsize).astype(int)
chunk['bin1_id'] = chrom_binoffset[chrom_id1] + rel_bin1
chunk['bin2_id'] = chrom_binoffset[chrom_id2] + rel_bin2
grouped = chunk.groupby(['bin1_id', 'bin2_id'], sort=False)
return grouped['count'].sum().reset_index()
new_bins = binnify(c.chromsizes, 2 * c.binsize)
iterator = CoolerAggregator(input_uri, new_bins, 1000000, batchsize=1, map=map)
# # last message before it fails ...
# # INFO:cooler:17868809 17872380
# for ii in iterator:
# print(ii)
# from cooler.api import Cooler
lo, hi = 17869999, 17872300
# lo, hi = 17868809, 17872380
clr = Cooler(input_uri)
# convert_enum=False returns chroms as raw ints
table = clr.pixels(join=True, convert_enum=False)
chunk = table[lo:hi]
# logger.info('{} {}'.format(lo, hi))
print('{} {}'.format(lo, hi))
# use the "start" point as anchor for re-binning
# XXX - alternatives: midpoint anchor, proportional re-binning
binsize = iterator.gs.binsize
chrom_binoffset = iterator.gs.chrom_binoffset
chrom_abspos = iterator.gs.chrom_abspos
start_abspos = iterator.gs.start_abspos
chrom_id1 = chunk['chrom1'].values
chrom_id2 = chunk['chrom2'].values
start1 = chunk['start1'].values
start2 = chunk['start2'].values
from cooler import Cooler
# input_uri = "unzoomifiable_5kb.cool"
input_uri = "missing_bin_cooler_40kb.cool"
clr = Cooler(input_uri)
print(clr.pixels(join=True)[17872226])
table = clr.pixels(join=True)[17800000:]
print(table[table['chrom2'].isnull()])
# chrom1 start1 end1 chrom2 start2 end2 count
# 17872226 chr88 2640000 2680000 NaN NaN NaN 1
########################
# TODO
#########################
# Now i'm on the same page with Nezar
# bad pixel is found ...
# FIND OUT - HOW that happened ?!?!?!?!?! ...
#
# processes that might be involved:
#
# pairix ${pairs_lib}
#
# cooler cload pairix \
# --nproc ${task.cpus} \
# --assembly ${params.input.genome.assembly} \