nx_supplement_batch.nx

nx_supplement_batch.nx -- C5.4 + C4.4: batch CLI with user-extensible compound DB + RT calibration + multi-file processing. USAGE (3 positional args, then peak files): nx_supplement_batch <compounds-or-dash> <cal-or-dash> <peak1> [peak2] ... compounds-or-dash: path to user-defined compound TSV file, or "-" to use only the 24-compound built-in seed DB. Format (one per line, '#' comments): id|name|SMILES|reg_code|citation reg_code: 0=UNK 1=APPROVED 2=RESTRICTED 3=BANNED 4=RX cal-or-dash: path to RT calibration CSV, or "-" for mass-only. Format (per C7.1): # id ref_rt_seconds tolerance_seconds 4 740.0 30.0 peak1, peak2, ...: one or more peak text files to process. EXAMPLES: # Built-in DB, no RT cal, 3 samples $ nx_supplement_batch - - lot_A.txt lot_B.txt lot_C.txt # Built-in DB + RT cal, 3 samples $ nx_supplement_batch - rt_cal.csv lot_A.txt lot_B.txt lot_C.txt # Lab's extended DB + RT cal, 50 samples $ nx_supplement_batch lab_compounds.tsv rt_cal.csv samples/*.txt EXIT CODE: Total banned detections summed across all samples. Pipe straight to LIMS: $ nx_supplement_batch - - samples/*.txt | \ jq -r 'select(.verdict.recommendation=="REJECT") | .sample_id'