cellmaps-imagedownloader 0.1.1

Description:

cellmapsimagedownloader 0.1.1

Cell Maps ImmunoFluorescent Image Downloader












Downloads ImmunoFluorescent image data from Human Protein Atlas

Free software: MIT license
Documentation: https://cellmaps-imagedownloader.readthedocs.io.


Dependencies

cellmaps_utils
requests
mygene
tqdm



Compatibility

Python 3.8+



Installation
pip install cellmaps_imagedownloader
Or directly from source:
git clone https://github.com/idekerlab/cellmaps_imagedownloader
cd cellmaps_imagedownloader
make dist
pip install dist/cellmaps_imagedownloader*whl
Run make command with no arguments to see other build/deploy options including creation of Docker image
make
Output:
clean remove all build, test, coverage and Python artifacts
clean-build remove build artifacts
clean-pyc remove Python file artifacts
clean-test remove test and coverage artifacts
lint check style with flake8
test run tests quickly with the default Python
test-all run tests on every Python version with tox
coverage check code coverage quickly with the default Python
docs generate Sphinx HTML documentation, including API docs
servedocs compile the docs watching for changes
testrelease package and upload a TEST release
release package and upload a release
dist builds source and wheel package
install install the package to the active Python's site-packages
dockerbuild build docker image and store in local repository
dockerpush push image to dockerhub


Needed files

samples file: CSV file with list of IF images to download (see sample samples file in examples folder)
unique file: CSV file of unique samples (see sample unique file in examples folder)
provenance: file containing provenance information about input files in JSON format (see sample provenance file in examples folder)



Usage
For information invoke cellmaps_imagedownloadercmd.py -h
Example usage
cellmaps_imagedownloadercmd.py ./cellmaps_imagedownloader_outdir --samples examples/samples.csv --unique examples/unique.csv --provenance examples/provenance.json

Via Docker
Example usage
Coming soon...



Credits
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.



History

0.1.1 (2024-08-26)

Bug fix in adding gene node attributes. The bug was resulting in duplicate entries and
missing gene names, related to ambiguous antibodies.



0.1.0 (2024-01-01)

First release on PyPI.