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.
detect-bad-wells#
Flag unreliable wells from raw .dat files in DATA_DIR.
Reads every *.dat file (one per well, columns: x, y1[, y2, …]) and reports wells with very low signal or flat curves across all labels. No fitting is required.
Example:
ppr detect-bad-wells path/to/pH/dat_bg_adj_dil_nrm_1sd/
Usage
ppr detect-bad-wells [OPTIONS] DATA_DIR
Options
- --z-threshold <z_threshold>#
Z-score threshold for outlier detection on the max-vs-span trendline.
- Default:
3.0
- --ctr-cols <ctr_cols>#
Comma-separated 1-based column numbers for CTR wells (used for logging only).
- Default:
'1,12'
Arguments
- DATA_DIR#
Required argument
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 | fit | meansd
- --nrm#
Normalize using label metadata.
- --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).
- Default:
'huber'- Options:
lm | huber | irls
- --outlier <outlier>#
Outlier removal spec, e.g. ‘zscore:3.0:4’ (method:threshold:min_keep).
- --mcmc <mcmc>#
MCMC sampling: None, multi, multi-noise (learned noise), multi-noise-xrw (noise+per-well pH random walk), single.
- Default:
'None'- Options:
None | multi | multi-noise | multi-noise-xrw | single
- --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
- --ctr-free-k#
Hierarchical CTR K: each replicate well gets its own K drawn from Normal(K_mu, K_tau). The spread of posteriors quantifies between-replicate accuracy.
- --noise-alpha <noise_alpha>#
Proportional noise coefficient per label (y1, y2, …). Adds alpha^2*signal^2 to y_err^2. Obtain from MCMC multi-noise shared_noise_params.csv (alpha_y1, alpha_y2).
- --noise-gain <noise_gain>#
Poisson gain per label (y1, y2, …). Replaces hardcoded gain=1 in shot-noise term: y_err^2=gain*signal+bg_err^2+(alpha*signal)^2. Obtain from MCMC multi-noise shared_noise_params.csv (gain_y1, gain_y2).
- --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
- --discard-bad-wells, --no-discard-bad-wells#
Automatically detect and discard bad wells before 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