Cli for fitting macromolecule pH titration or binding assays data e.g. fluorescence spectra.
Project description
ClopHfit
This package provides a command line interface for fitting pH titration or binding assay data for macromolecules, such as fluorescence spectra. With this tool, users can easily analyze their data and obtain accurate fitting results.
- Version: "0.10.7"
Installation
You can get the library directly from PyPI
using pip:
pip install clophfit
Alternatively, you can use pipx to install it in an isolated environment:
pipx install clophfit
To enable auto completion for the clop command, follow these steps:
-
Generate the completion script by running the following command:
_CLOP_COMPLETE=bash_source clop > ~/.local/bin/clop-complete.bash -
Source the generated completion script to enable auto completion:
source ~/.local/bin/clop-complete.bash
Usage
You can check out the documentation on https://darosio.github.io/ClopHfit for up to date usage information and examples.
CLI
ClopHfit provides several command line interface tools for fitting and processing data.
prtecan
Extract and fit titrations from a list of Tecan files collected at various pH or chloride concentrations:
ppr -o prova2 --is-ph tecan list.pH --scheme ../scheme.txt --norm
--dil additions.pH --Klim 6.8,8.4 --sel 7.6,20
Use the --no-weight option to reproduce an older pr.tecan version.
eq1
Predict chloride dissociation constant K_d at a given pH:
clop eq1 --help
prenspire
Parser for EnSpire (PerkinElmer) file:
ppr -o folder enspire file.csv
Destination folder (default: "./Meas-${version}") will contain for each Measurement:
- a table (csv) in wide tabular form e.g. <lambda, A01, ..., H12>;
- corresponding graphical (png) representation of spectra from all wells.
By adding a note.csv file:
ppr -o folder enspire file.csv note.csv
destination folder (default: "./Meas-${version}") will also contain:
- a pdf for each titration and label;
- a pdf for global (multiband) analysis pdfalong with global and all_SVD;
- a pdf for SVD analysis of all concatenated spectra.
note_to_csv
note_to_csv -t 37.0 -l "B E F" -o 37 NTT-G03-Cl_note
note_to_csv -t 20.0 -l "A C D" -o 20 NTT-G03-Cl_note
cat 20 37 > G03_Cl_note.csv
Python
ClopHfit can be imported and used as a Python package. The following modules are available:
clophfit.prenspire - parser for EnSpire (PerkinElmer) files
clophfit.prtecan - perform fitting of pH titration or binding assay data
clophfit.binding - perform fitting of macromolecule binding assay data
To use clophfit in your python:
from clophfit import prenspire, prtecan, binding
Features
- Plate Reader data Parser.
- Perform non-linear least square fitting.
- Extract and fit pH and chloride titrations of GFP libraries.
- For 2 labelblocks (e.g. 400, 485 nm) fit data separately and globally.
- Estimate uncertainty using bootstrap.
- Subtract buffer for each titration point.
- Report controls e.g. S202N, E2 and V224Q.
- Correct for dilution of titration additions.
- Plot data when fitting fails and save txt file anyway.
License
We use a shared copyright model that enables all contributors to maintain the copyright on their contributions.
All code is licensed under the terms of the revised BSD license.
Contributing
If you are interested in contributing to the project, please read our contributing and development environment guides, which outline the guidelines and conventions that we follow for contributing code, documentation, and other resources.
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