CLI Reference

CLI reference

loqculate v0.4.1. Subcommands: fit, compare. Both take curve_data then filename_concentration_map.

loqculate --version
loqculate fit --help
loqculate compare --help

Shared flags (parsed for both commands)

Flag	Default	Who actually uses it
--std_mult	2	Passed to lod(std_mult) after fit. PiecewiseCF and PiecewiseWLS honor it. OriginalWLS computes LOD inside fit() and ignores the later argument.
--cv_thresh	0.20	Passed to loq(cv_thresh) after fit. Honored by PiecewiseCF, PiecewiseWLS, EmpiricalCV. OriginalWLS and OriginalCV ignore it after fit. Threshold sense is <= for find_loq_threshold, strict < for OriginalWLS.
--bootreps	100	Forwarded only when --model starts with piecewise. OriginalWLS keeps constructor n_boot=100.
--min_noise_points	2	Piecewise constructors only. OriginalWLS stores the value and does not use it in LOD.
--min_linear_points	1	Piecewise constructors only. Unused in OriginalWLS LOD.
--sliding_window	3	Piecewise constructors only. EmpiricalCV keeps constructor 3.
--multiplier_file	unset	All models. CSV peptide,multiplier. Inner join.
--output_path	cwd	Created if missing.
--plot	y	y or n.
--format	auto	See Input formats.
--chunk_size	100	Peptides per worker batch (fit).
--n_threads	cpu_count - 2	Worker processes. -1 means all CPUs.

The LOD formula is not noise + std_mult * sigma. For the piecewise models it is $(c + \mathrm{std_mult}\cdot\sigma - b)/a$. See PiecewiseCF.

fit

loqculate fit DATA MAP [--model piecewise_cf] [--fast]

--model: piecewise_cf, piecewise_wls, cv_empirical, original_wls, original_cv.

--fast: PiecewiseCF only. Delta LOQ first; bootstrap once if that value is infinite. Other models sys.exit with an error.

A peptide that raises during fit is logged to stderr and still written with infinite LOD/LOQ. The run continues.

compare

loqculate compare DATA MAP [--models piecewise_cf,piecewise_wls]

Unknown names exit and print MODEL_REGISTRY keys. Failed models on one peptide are logged and omitted from that peptide's overlay. No CSV of LOD/LOQ.