[Shen-YuFei]

Summary

Moves the LFQ group splitter of bigbio/quantms#734 (bin/split_lfq_groups.py) into quantms-utils, as requested in that review, so quantms can run it from the quantms-utils container.

quantmsutilsc splitlfqgroups --sdrf full.sdrf.tsv --design full_openms_design.tsv \
    --column 'comment[instrument]' --column 'comment[gradient duration]' [--output DIR]

• Each combination of the given SDRF column values is one group. The command writes <group>.sdrf.tsv and <group>_openms_design.tsv per group, and the manifest lfq_groups.tsv (group, run, files and grouping values).
• No run is dropped. The command fails when a grouping value is missing, a run belongs to two groups, the SDRF and design run sets differ, a fractionated sample crosses groups, or the design references missing sample metadata.
• Group IDs are hashes of the column names and values, so they do not depend on row order. Sample and fraction-group IDs are renumbered within each group; conditions and biological replicates are kept.
• The code is the same as in quantms; only the entry point is now a click command. It uses the standard library only, so there is no new dependency.

Verification

• pytest: 36 passed, 1 skipped (27 before). tests/test_split_lfq_groups.py ports the 8 quantms tests and adds one CLI test.
• flake8 . --select=E9,F63,F7,F82: 0.
• The new module with the tools Codacy runs here: Prospector (pycodestyle, pydocstyle, pyflakes, dodgy) and Bandit report nothing; Lizard is below its thresholds.

Follow-up

After a release, bigbio/quantms#734 will call quantmsutilsc splitlfqgroups and drop bin/split_lfq_groups.py.

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[codacy-production]

Up to standards ✅

🟢 Issues 0 issues

Results:
0 new issues

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🟢 Metrics 54 complexity

Metric	Results
Complexity	54

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