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respect dtypes of input file #557

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Merged
Phlya merged 4 commits into from
Jul 7, 2025
Merged

respect dtypes of input file #557

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bf0a842
respect dtypes of input file
Jul 7, 2025
b9259f3
add test for dtype propagation
Jul 7, 2025
f20d8fe
fix test fail due to differing order
Jul 7, 2025
072819c
fix comment type
dmalzl Jul 7, 2025
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3 changes: 3 additions & 0 deletions cooltools/api/rearrange.py
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Original file line number Diff line number Diff line change
Expand Up @@ -202,6 +202,8 @@ def rearrange_cooler(
bins_old, view_df, new_chrom_col=new_chrom_col, orientation_col=orientation_col
)
logging.info("Creating a new cooler")
# fetching pixel dtypes to avoid implicit casts of count column
dtypes = clr.pixels().dtypes.to_dict()
cooler.create_cooler(
out_cooler,
bins_new,
Expand All @@ -210,6 +212,7 @@ def rearrange_cooler(
bin_mapping,
chunksize=chunksize,
),
dtypes = dtypes,
assembly=assembly,
mode=mode,
mergebuf=int(2e7),
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Binary file added tests/data/float_counts.cool
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14 changes: 13 additions & 1 deletion tests/test_rearrange_cooler.py
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Expand Up @@ -62,7 +62,7 @@ def test_rearrange_cooler(request):

# III.
# Check that when taking two chromosomes in a different order and inverting one,
# all is ax espected
# all is as espected

reorder_invert_view = (
orig_view.iloc[1::-1].assign(strand=["+", "-"]).reset_index(drop=True)
Expand Down Expand Up @@ -136,3 +136,15 @@ def test_rearrange_cooler(request):
::-1, :
]
assert np.array_equal(old_trans_m, reordered_inverted_trans_m, equal_nan=True)

# IV.
# Check that pixel datatypes are propagted to output cooler
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@Phlya Phlya Jul 7, 2025

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propagAted

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@dmalzl dmalzl Jul 7, 2025

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thanks for pointing this out. already fixed it

float_clr = cooler.Cooler(op.join(request.fspath.dirname, "data/float_counts.cool"))
new_view = bioframe.make_viewframe(float_clr.chromsizes)
rearrange_cooler(float_clr, new_view, "test_propagated_datatypes.cool")

propagate_clr = cooler.Cooler("test_propagated_datatypes.cool")
assert_frame_equal(
float_clr.pixels()[:],
propagate_clr.pixels()[:]
)