Bioinformatics with Python Cookbook - Second Edition

How to do it...

Let's take a look at the following steps:

1. Let's start by creating an annotation database with gffutils, based on our GFF file:

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

The gffutils library creates a SQLite database to store annotations efficiently. Here, we will try to create the database, but if it already exists, we will use the existing one. This step can be time-consuming.

2. Now, we will list all the available feature types and count them:

print(list(db.featuretypes()))for feat_type in db.featuretypes():    print(feat_type, db.count_features_of_type(feat_type))

These features will include contigs, genes, exons, transcripts, ...