Command-line tool#
clop#
Group command.
Usage
clop [OPTIONS] COMMAND [ARGS]...
Options
- --version#
Show the version and exit.
eq1#
Model Kd dependence on pH.
Usage
clop eq1 [OPTIONS] KD1 PKA PH
Arguments
- KD1#
Required argument
- PKA#
Required argument
- PH#
Required argument
fit-titration#
Fit Titration group command.
Usage
fit-titration [OPTIONS] COMMAND [ARGS]...
Options
- --version#
Show the version and exit.
- -v, --verbose#
Verbosity of messages.
- -o, --out <out>#
Output folder.
- --is-ph, --no-is-ph#
Concentrations are pH.
- Default:
True
glob#
Update old glob fit of multiple datasets.
Usage
fit-titration glob [OPTIONS] FILE
Options
- -b, --boot <boot>#
Number of booting iterations.
- --weight, --no-weight#
Use residue weights.
- Default:
True
Arguments
- FILE#
Required argument
spec#
Update old svd or band fit of titration spectra.
Usage
fit-titration spec [OPTIONS] CSV_F NOTE_F
Options
- -b, --band <band>#
Integration interval from <1> to <2>
Arguments
- CSV_F#
Required argument
- NOTE_F#
Required argument
ppr#
Parse Plate Reader ppr group command.
Usage
ppr [OPTIONS] COMMAND [ARGS]...
Options
- --version#
Show the version and exit.
- -v, --verbose#
Increase verbosity: -v for INFO, -vv for DEBUG. Default is WARNING.
- -q, --quiet#
Silence terminal output; show only ERROR messages.
- -o, --out <out>#
Output folder.
enspire#
Save spectra as csv tables from EnSpire xls file.
Usage
ppr enspire [OPTIONS] CSV_F [NOTE_F]
Options
- -b <bands>#
Label and band interval (format: LABEL LOWER UPPER)
Arguments
- CSV_F#
Required argument
- NOTE_F#
Optional argument
tecan#
Convert a list of Tecan-exported excel files into titrations.
LIST_FILE : Path to file containing Tecan files and concentration values.
Saves titrations as .dat files and fits all wells using 2 labels. The function produces:
K plot
csv tables for all labelblocks and global fittings.
Buffer is always subtracted if scheme indicates buffer well positions.
Usage
ppr tecan [OPTIONS] LIST_FILE
Options
- --cl <cl>#
Cl stock concentration (mM) of added aliquots.
- --bg#
Subtract buffer signal (from scheme.txt). Implied by –bg-adj.
- --bg-adj#
Heuristically adjust negative buffer values (implies –bg).
- --bg-mth <bg_mth>#
Buffer calculation method.
- Default:
'mean'- Options:
mean | median | fit | meansd | mediansd
- --nrm#
Normalize using label metadata.
- --raw-dir <raw_dir>#
Folder holding the Tecan .xls files, when they are not next to LIST_FILE.
- --sch <sch>#
Path to plate scheme file (buffers and controls).
- --add <add>#
Path to additions file (initial volume + additions); enables dilution correction.
- --all#
Export all bg/dil/nrm data combinations.
- --lim <lim>#
x-axis range MIN MAX for K plots.
- -t, --title <title>#
Title for plots.
- --fit, --no-fit#
Perform fitting.
- Default:
True
- --png, --no-png#
Export PNG files.
- Default:
True
- --fit-method <fit_method>#
Global fit method: lm (standard LS), huber (robust Huber loss), irls (iterative reweighting), odr (orthogonal distance regression, x-aware).
- Default:
'huber'- Options:
lm | huber | irls | odr
- --outlier <outlier>#
Outlier removal spec, e.g. ‘mad:3.5:4’ (method:threshold:min_keep).
- --mcmc <mcmc>#
MCMC sampling: None, single, single-refit (robust screening pass then refit), multi (all wells jointly, control K shared per group).
- Default:
'None'- Options:
None | single | single-refit | multi
- --nuts-sampler <nuts_sampler>#
NUTS backend: default (pytensor/CPU), blackjax/numpyro (JAX/CPU), nutpie (Rust/CPU).
- Default:
'default'- Options:
default | blackjax | numpyro | nutpie
- --mcmc-samples <mcmc_samples>#
Number of posterior draws per chain (tune = samples // 2).
- Default:
2000
- --noise-alpha <noise_alpha>#
Proportional noise coefficient per label. Adds proportional term to y_err variance. Obtain from MCMC multi-noise shared_noise_params.csv.
- --noise-gain <noise_gain>#
Poisson gain per label. Replaces hardcoded gain=1 in shot-noise term. Obtain from MCMC multi-noise shared_noise_params.csv.
- --mcmc-noise <mcmc_noise>#
Observation-noise family for –mcmc single-refit. ye_mag scales y_err by a learned multiplier; structured builds floor+gain*y+(alpha*y)^2 with floors from bg_noise and gain/alpha from –noise-gain/–noise-alpha.
- Default:
'ye_mag'- Options:
ye_mag | structured
- --noise-mode <noise_mode>#
For –mcmc-noise structured, how a supplied –noise-gain/–noise-alpha value is treated: centered (a hint the posterior may leave) or fixed (pinned). A parameter with no value supplied is always free.
- Default:
'centered'- Options:
centered | fixed
- --per-well-ye-mags, --no-per-well-ye-mags#
For –mcmc multi: scale y_err per well rather than per label. Unset lets the library resolve it from the noise family, which couples the two.
- --ye-mag-parameterization <ye_mag_parameterization>#
For –mcmc multi with per-well ye_mags: independent per label (centered), a shared well factor with per-label deviations (hierarchical), a per-label level plus one shared well factor (separable), or that plus a per-label pH axis on the noise (separable_step).
- Default:
'centered'- Options:
centered | hierarchical | separable | separable_step
- --plate-fit <plate_fit>#
Also fit the whole plate in one classical least-squares problem, with the noise scale profiled per label across the plate and each control group pooled onto one K. Writes plate_{method}_K.csv. Minutes rather than hours, and as accurate against known pKs as the sampler.
- Options:
lm | odr
- --mcmc-robust, --no-mcmc-robust#
Use a robust likelihood for –mcmc instead of a Normal. Student-t nu=3 was the best-calibrated arm on this campaign’s plates.
- Default:
False
- --student-t-nu <student_t_nu>#
Student-t degrees of freedom for –mcmc-robust. Lower is heavier-tailed; pass 0 to infer nu (support above 2).
- Default:
3.0
- --ctr-free-k, --ctr-shared-k#
For –mcmc multi: fit every well its own K rather than pooling each control group onto a shared one. Pooling buys no accuracy at the construct level and narrows the stated interval, and library wells have no group to pool with.
- Default:
False
- --mcmc-tune <mcmc_tune>#
Tuning draws per chain for –mcmc. Default is mcmc-samples // 2.
- --mcmc-target-accept <mcmc_target_accept>#
NUTS target acceptance for –mcmc. Default is latent-x aware.
- --print-spec#
Print the resolved analysis specification and its signature, then exit. Two runs with the same signature fit the same model, whatever flags were typed.
- --dry-run#
Validate inputs without processing data.
- --detect-bad, --no-detect-bad#
Run bad-well detection: discard outlier wells before fitting and write bad_wells.csv after fitting.
- Default:
True
- --mask-outliers, --no-mask-outliers#
Mask geometric point outliers before fitting.
- Default:
False
- --outlier-threshold <outlier_threshold>#
Threshold for geometric point outlier scoring (0-1).
- Default:
0.2
Arguments
- LIST_FILE#
Required argument
note_to_csv#
Convert a tab-separated data file into a CSV file.
Usage
note_to_csv [OPTIONS] NOTE
Options
- -o, --output <output>#
Output CSV file.
- -l, --labels <labels>#
Labels to be appended.
- -t, --temp <temp>#
Temperature to be appended.
Arguments
- NOTE#
Required argument