Weaselytics

Python package to extract and analyse chromatographic data.

A Python 3 library for (hassle-free) plotting of HPLC chromatograms from output files with baseline correction, peak detection and retention time determination through curve fitting.

Quick start

pip install weaselytics
weaselytics [OPTION] filename

CLI usage

weaselytics [-h] [-s] [-p] [-e] [-o] [-os OUTPUT_STATS] [-n] [-nb] [-sm]
            [-x0 STARTX] [-x1 ENDX] [-od OUTPUT_DIR]
            path

Options

Argument	Description
path	Input .txt data file (required)
-s	Show the matplotlib window(s)
-p	Print/export the matplotlib window(s)
-e	Export baseline-corrected data to filename_bl.txt
-o	Output data to filename.csv
-os	Output fitted stats for the given label to filename_<label>.csv
-n	Disable peak fitting
-nb	Disable baseline correction
-sm	Enable signal smoothing
-x0	Start fitting at x0 min
-x1	End fitting at x1 min
-od	Output directory for exported files (default: results)

Library usage

import weaselytics as wl

data = wl.ParsedData("chromato.txt")
x, y = data.data

baseline, params, case = wl.auto_beads(y, x, freq_cutoff=0.01)

Requirements

See pyproject.toml for the full dependency list.

Install

Editable install (for development):

pip install -e .

With test dependencies:

pip install -e ".[test]"

Tests

pytest

Contributor

Contributed by Emmanuel Bourret

TO DO

• Generalize hardcoded __LPYE__ pattern in export_dist
• Make ParsedData parser more general (support different delimiters, extra columns, headers)
• Clean up #@EB, #@TEMP, #TODO markers
• Add examples/ directory with sample output images
• Add proper sample chromatogram data for demos
• Improve README with example CLI output images