Add create_obs_over_exp_cooler() and CLI tool (sandbox)

[Phlya]

Summary

Add a function and standalone CLI tool that divides a cooler's contact matrix by expected values and saves the O/E (observed/expected) ratios to a new cooler file.

New files

cooltools/sandbox/obs_over_exp_cooler.py (extended)

• create_obs_over_exp_cooler(): Streams pixel chunks from an input cooler, divides balanced values by cis/trans expected, and writes a new .cool file via cooler.create_cooler().
• Supports pre-computed or on-the-fly expected computation
• Cis-only mode (expected_trans_df=False) — trans pixels are written as NaN
• Smoothed expected columns with automatic trans fallback to base column
• Configurable chunksize for memory-efficient streaming

cooltools/sandbox/cli_obs_over_exp.py (new)

Standalone Click CLI wrapping the function. Key options:

• --cis-expected / --trans-expected: Paths to pre-computed TSV files
• --no-trans: Skip trans O/E computation
• --smooth / --aggregate-smoothed: Smoothing when computing on the fly
• --view: BED file with genomic regions
• Auto-adjusts expected_value_col when smoothing is requested on the fly

Can be run as: python -m cooltools.sandbox.cli_obs_over_exp --help

tests/test_obs_over_exp_cooler.py (new)

16 tests organized in 3 classes:

• TestCreateObsOverExpCooler (9 tests): API-level tests covering precomputed expected, cis-only, smoothed columns, on-the-fly computation, no-view fallback, trans fallback column, invalid column error, no-weights in output, and O/E values near 1
• TestObsOverExpCLI (6 tests): CLI tests covering precomputed expected, cis-only with --no-trans, on-the-fly computation, --smooth auto-adjustment, --help, and missing output error
• TestAPIvsCLIConsistency (1 test): Pixel-by-pixel comparison of API vs CLI output

Uses the fast 10 Mb-resolution test cooler (CN.mm9.10000kb.cool, ~38K pixels) with module-scoped pytest fixtures for shared expected computation. Full suite runs in ~14 seconds.

Usage example

from cooltools.sandbox.obs_over_exp_cooler import create_obs_over_exp_cooler
import cooler

clr = cooler.Cooler('data.cool')
create_obs_over_exp_cooler(
    clr, 'data_oe.cool',
    expected_cis_df=cis_expected,
    expected_trans_df=trans_expected,
    view_df=view_df,
    expected_value_col='balanced.avg.smoothed.agg',
)

Or via CLI:

python -m cooltools.sandbox.cli_obs_over_exp data.cool \
    --cis-expected cis_exp.tsv \
    --trans-expected trans_exp.tsv \
    --expected-value-col balanced.avg.smoothed.agg \
    -o data_oe.cool

[Phlya]

Old tests are failing, not the new ones... And locally everything passes for me, not sure what's going on