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Ext tests 0.1.2 #1

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Merged
AxisAlexNT merged 2 commits into from
Oct 13, 2022
Merged

Ext tests 0.1.2 #1

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736af57
Added saving bin_weights
AxisAlexNT Sep 23, 2022
2cdaf5d
Fixed bug with weights dataset naming
AxisAlexNT Sep 26, 2022
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25 changes: 23 additions & 2 deletions hict_utils/cool_to_hict/flatten_conv.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
import copy
import datetime
import math
from typing import Any, Dict, Tuple
from typing import Any, Dict, Tuple, Union

import h5py
import numpy as np
Expand Down Expand Up @@ -105,6 +105,7 @@ def dump_stripe_data(
) == len(src_file[f'{path_to_name_and_length}/name'])
stripes_group: h5py.Group = dst_file.create_group(
f'/resolutions/{resolution}/stripes')
bins_group: h5py.Group = src_file[f'/resolutions/{resolution}/bins']
contig_start_bins: h5py.Dataset = src_file[f'/resolutions/{resolution}/indexes/chrom_offset'].astype(
np.int64)
contig_length_bins_ds: np.ndarray = contig_start_bins[1:] - \
Expand All @@ -113,6 +114,11 @@ def dump_stripe_data(
stripe_descriptors: List[StripeDescriptor] = []
stripe_index: np.int64 = 0

# bins_count: np.int64 = len(bins_group['chrom'])
bin_weights: Optional[h5py.Dataset] = bins_group['weight'] if 'weight' in bins_group.keys(
) else None

start_bin: np.int64 = np.int64(0)
# Split contigs into blocks
contigs_count: np.int64 = len(contig_length_bins_ds)
for contig_id in range(0, contigs_count):
Expand All @@ -135,7 +141,9 @@ def dump_stripe_data(
{resolution: contig_length_bins},
{resolution: ContigHideType.AUTO_SHOWN},
{}
)
),
np.array(bin_weights[start_bin:start_bin+min(submatrix_size, contig_length_bins -
contig_part_id * submatrix_size)]) if bin_weights is not None else None
)

for contig_part_id in range(0, contig_part_count)
Expand All @@ -157,6 +165,19 @@ def dump_stripe_data(
stripe.contig_descriptor.contig_id for stripe in stripe_descriptors],
dtype=np.int64,
**additional_dataset_creation_args)
if bin_weights is not None:
stripes_group.create_dataset('stripes_bin_weights',
shape=(len(stripe_descriptors), submatrix_size),
maxshape=(None, submatrix_size),
data=[
np.pad(
stripe.bin_weights,
[(0, submatrix_size-len(stripe.bin_weights))],
mode='constant',
constant_values=0
) for stripe in stripe_descriptors],
dtype=np.float64,
**additional_dataset_creation_args)
return stripe_descriptors


Expand Down