Cli for fitting macromolecule pH titration or binding assays data e.g. fluorescence spectra.
Project description
ClopHfit
Cli for fitting macromolecule pH titration or binding assay data, e.g. fluorescence spectra.
- Version: "0.4.2"
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.
Usage
-
Extract and fit titrations from a list of tecan files collected at various pH or chloride concentrations:
clop prtecan --helpFor example:
clop prtecan list.pH -k ph --scheme ../scheme.txt --dil additions.pH --norm --out prova2 --Klim 6.8,8.4 --sel 7.6,20To reproduce older pr.tecan add
--no-weightoption:clop prtecan list.pH -k ph --scheme ../scheme.txt --no-bg --no-weight --out 4old --Klim 6.8,8.4 --sel 7.6,20 -
Predict chloride dissociation constant
K_dat given pH:clop eq1 --help
To use clophfit in your python:
from clophfit import prtecan, binding
Installation
pipx install clophfit
You can get the library directly from PyPI:
pip install clophfit
Development
You need the following requirements:
hatchfor test automation and package dependency managements. If you don't have hatch, you can usepipx run hatchto run it without installing, orpipx install hatch. Dependencies are locked thanks to pip-deepfreeze. You can runhatch env showto list available environments and scripts.hatch run init # init repo with pre-commit hooks hatch run sync # sync venv with deepfreeze # other examples hatch run lint:run hatch run tests.py3.10:all
Hatch handles everything for you, including setting up an temporary virtual environment for each run.pre-commitfor all style and consistency checking. While you can run it with nox, this is such an important tool that it deserves to be installed on its own. If pre-commit fails during pushing upstream then stage changes, Commit Extend (into previous commit), and repeat pushing.
pip, pip-deepfreeze and hatch are pinned in
.github/workflows/constraints.txt for consistency with CI/CD.
pipx install pre-commit
pipx install hatch
pipx runpip hatch install hatch-pip-deepfreeze
Setting up a development with direnv
echo "layout hatch" > .envrc
hatch run init
Setting up a development environment manually
You can set up a development environment by running:
python3 -m venv .venv
source ./.venv/bin/activate
pip install -v -e .[dev,tests,docs]
With direnv for using Jupyter during development:
jupiter notebook
And only in case you need a system wide easy accessible kernel:
python -m ipykernel install --user --name="cloph-310"
Testing and coverage
Use pytest to run the unit checks:
pytest
Use coverage to generate coverage reports:
coverage run --parallel -m pytest
Or use hatch:
hatch run tests:all
hatch run coverage:combine
hatch run coverage:report
Building docs
You can build the docs using:
hatch run docs:sync
hatch run docs:build
You can see a preview with:
hatch run docs:serve
When needed (e.g. API updates):
sphinx-apidoc -f -o docs/api/ src/clophfit/
Bump and releasing
To bump version and upload build to test.pypi using:
hatch run bump
Usually after:
gh pr create --fill
gh pr merge --squash --delete-branch [-t “fix|ci|feat: msg”]
To update only changelog:
gatch run ch
Alternatively:
pipx run --spec commitizen cz bump --changelog-to-stdout --files-only (--prerelease alpha) --increment MINOR
Configuration files
Manually updated pinned dependencies for CI/CD:
- .github/workflows/constraints.txt (testing dependabot)
Configuration files:
- pre-commit configured in .pre-commit-config.yaml;
- flake8 (for rst-docstrings and bandit) configured in .flake8 (pinned in pre-commit);
- black configured in pyproject.toml (pinned in pre-commit);
- ruff configured in pyproject.toml (pinned in pre-commit);
- darglint configured in .darglint (pinned in pre-commit);
- codespell configured in .codespellrc (pinned in pre-commit);
- coverage configured in pyproject.toml (tests deps);
- mypy configured in pyproject.toml (tests deps);
- commitizen in pyproject.toml (dev deps and pinned in pre-commit).
pip-df generates requirements[-dev,docs,tests].txt.
TODO
-
Print sorted output.
-
Add info to results report:
- Brightness;
- flatness (SA - SB)/SA - fluorescence is constant? GREAT;
- presence of isosbestic (the fitting line cross / SA1 < SB1 and SA2 > SB2 sometime they do not cross anyway).
-
Robust fit considering sigma pH.
-
check metadata and report the diff REMEMBER 8.8 (2013-05-29); metadata rescaled; dataframe groupby per meta_pre, ma anche enspire
-
development
- readthedocs or ghpages? https://www.docslikecode.com/articles/github-pages-python-sphinx/
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