cellink.tl.external.check_and_patch_ldsc_parse_bug

cellink.tl.external.check_and_patch_ldsc_parse_bug(runner)

Check whether the LDSC installation has the pandas column-sort bug and patch it.

See ldsc issue #342 / PR #341.

The bug: pd.concat in ldscore/parse.py alphabetically re-sorts annotation columns after pd.concat across chromosomes in ldscore/parse.py (line ~147), causing _check_variance() to raise an IndexError during --h2 --overlap-annot.

The fix (PR #341): reindex the concatenated DataFrame to the column order of the first chromosome file: pd.concat(chr_ld)[chr_ld[0].columns].

Works for local, Docker and Singularity execution modes.

Configuration — add parse_script to your runner config so cellink knows exactly where parse.py lives, especially for containerised setups:

runner = configure_ldsc_runner(
    config_dict={
        "execution_mode": "singularity",
        "singularity_image": "/path/to/ldsc.sif",
        "ldsc_command": "ldsc.py",
        "parse_script": "/ldsc/ldscore/parse.py",  # ← explicit path
    }
)

If parse_script is omitted, cellink tries to auto-discover the path from PATH (works for local installs; may fail for containers).

Behaviour by mode

• local — patches parse.py on disk and backs up the original as parse.py.bak.

• docker — patches the file inside the image via docker cp + docker commit. The image is updated in-place and the patch survives container restarts.

• singularity — SIF images are read-only, so cellink writes the patched parse.py to a host-side shadow directory (default: ~/.cellink/ldsc_patch/ldscore/) and injects PYTHONPATH=<shadow>:$PYTHONPATH into every subsequent ldsc.py call. Set ldsc_patch_shadow_dir in the runner config to override the shadow location.

type runner:

param runner:

A configured LDSCRunner instance.

rtype:

dict

returns:

dict with keys: "status" — "already_patched", "patched",

"patch_failed" or "not_found"

"mode" — "local", "docker" or "singularity" "parse_path" — resolved path to parse.py (or None) "detail" — human-readable explanation