gpubs

Enables easy fetch and parsing of NCBI pubmed abstracts into tabular format, and then tags them with gene symbols/accession id's.

Quick Start

Create environment for development

On linux (ubuntu), firt install conda or miniconda, install mamba for speed, and then create the environment and activate gpubs environment

mamba env create -f conda_env.yml

conda activate gpubs

Run pipeline to get 1 baseline and 1 update abstract XML file from NCBI

from gpubs.models import ReferenceData
from gpubs.api import pipeline
# set num_abstract_xml_files=-1 to get all; will need about 60GB
m=ReferenceData(num_abstract_xml_files=1, version="v1", verbose=2)

Install with pip

pip install gpubs

To upload the package to PyPi

cd src

Bump the VERSION variable in release-info.json, then:

make clean
make

Prepare for checkin

black the code (changes code in-place to fit style guide)

black src

Lint the code with flak8

flake8 src

Run tests

TBD

Make documents

cd docs
make clean
make html