PROtein Feature Aggregation and Variants.
Protein Feature Aggregation and Variants
ProteoFAV is a Python module that address the challenge of cross-mapping protein structures and protein sequences, allowing for protein structures to be annotated with sequence features. It implements methods for working with protein structures (via mmCIF, PDB, PDB Validation, DSSP and SIFTS files), sequence Features (via UniProt GFF annotations) and genetic variants (via UniProt/EBI Proteins API and Ensembl REST API). Cross-mapping of structure and sequence is performed with the aid of SIFTS.
ProteFAV relies heavily in the Pandas library to quickly load data into DataFrames for fast data exploration and analysis. Structure and sequence data are parsed/fetched onto Pandas DataFrames that are then merged-together (collapsed) onto a single DataFrame.
ProteoFAV was developed to support Python 3.5+ and Pandas 0.20+.
Check requirements for specific requirements.
To install the stable release, run this command in your terminal:
$ pip install proteofav
Installing from source in a virtual environment
$ wget https://github.com/bartongroup/ProteoFAV/archive/master.zip -O ProteoFAV.zip
$ unzip ProteoFAV.zip
# alternatively, cloning the git repository
$ git clone https://github.com/bartongroup/ProteoFAV.git
Installing With Conda:
$ conda-env create -n proteofav -f path/to/ProteoFAV/requirements.txt
$ source activate proteofav
$ cd path/to/ProteoFAV
$ pip install .
Installing with Virtualenv:
$ virtualenv --python `which python` env
$ source env/bin/activate
$ pip install -r requirements.txt
$ python path/to/ProteoFAV/setup.py install
Testing the installation
Test dependencies should be resolved with:
$ python path/to/ProteoFAV/setup.py develop --user
Run the Tests with:
$ python path/to/ProteoFAV/setup.py test
$ cd path/to/ProteoFAV/tests
$ python -m unittest discover
ProteoFAV uses a configuration file config.ini where the user can specify the directory paths, as well as urls for commonly used data sources.
After installing run:
You can download the Jupyter notebook from GitHub and test it with your ProteoFAV’s installation.
Contributing and Bug tracking
Feel free to fork, clone, share and distribute. If you find any bugs or issues please log them in the issue tracker.
Before you submit your Pull-requests read the Contributing Guide.
See the Credits
See the Changelog
GNU General Public License v3 (GPLv3). See license for details.
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