Bioinformatics with Python Cookbook - Second Edition

Getting ready

If you have followed the previous two recipes, you will be ready. If not, download the Anopheles gambiae FASTA file, along with the GTF file. You also need to prepare the gffutils database:

import gffutilsimport sqlite3try:    db = gffutils.create_db('gambiae.gff.gz', 'ag.db')except sqlite3.OperationalError: db = gffutils.FeatureDB('ag.db')

As usual, you will find all of this in the Chapter03/Getting_Gene.ipynb Notebook file.