Weaselytics

Extract HPLC data from Agilent out.txt file and much more.

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

Quick start

Start the script with:

python3 weaselytics.py [OPTION] filename

it will show the chromatogram... (to complete)

Command-line options

• filename , required: filename (.txt)
• -s , optional: shows the matplotlib window(s)
• -p , optional: prints the matplotlib window(s)
• -e , optional: exports the baseline corrected data to filename_bl.txt
• -o , optional: outputs the data to filename.csv
• -os str , optional: outputs the fitted data and statistiques for the peak labeled <ARG> to filename_<ARG>.csv
• -n , optional: does not try to fit a chromatographic peak
• -nb , optional: does not try to baseline correct the chromatogram
• -x0 float , optional: starts fitting procedure at x0 min (x0 > 0)
• -x1 float , optional: ends fitting procedure at x1 min (x1 > x0 > 0)

Script options

(TO UPDATE)

Code options

(TO UPDATE)

Remarks

(TO UPDATE)

Examples:

Requirements

• re

• sys

• os

• argparse

• numpy

• pandas

• matplotlib

• seaborn

• scipy

• pybaselines (development branch)

• numba

• statsmodels

• time

Contributor

Contributed by Emmanuel Bourret

TO TO

• Refactor the main code into a package.

• Add smoothing function before the baseline correction.