/gene_dictionary

Create your own gene dictionary

Primary LanguagePython

Gene Dictionary

Build simple gene dictionary using data from NCBI gene database.

How to Use

  1. Install the prerequisite and follow the installation steps shown below.
  2. Choose one of two methods:
    • Acquire data through NCBI's API
      1. edit the list of genes in search.py
      2. pipenv run search
    • Use local copy of NCBI gene database
      1. edit the list of genes in extract.py
      2. pipenv run extract
  3. result will be saved in data.json

Prerequisite

Installation

wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ASN_BINARY/Mammalia/Homo_sapiens.ags.gz -O Homo_sapiens.ags.gz
gene2xml -i ./Homo_sapiens.ags.gz -o ./gene_database.xml -c T -l T -b T
pipenv install

Run test

pipenv install --dev
pipenv run test