June 2015
Intermediate to advanced
306 pages
6h 50m
English
Content preview from Bioinformatics with Python CookbookBecome an O’Reilly member and get unlimited access to this title plus top books and audiobooks from O’Reilly and nearly 200 top publishers, thousands of courses curated by job role, 150+ live events each month,
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Extracting genes from a reference using annotations
In this recipe, we will see how to extract a gene sequence with the help of an annotation file to get its coordinates against a reference FASTA. We will use the Anopheles gambiae genome, along with its annotation file (as per the previous two recipes). We will first extract the Voltage-gated sodium channel (VGSC) gene, which is involved in resistance to insecticides.
Getting ready
If you have followed the previous two recipes, you are ready. If not, download the Anopheles gambiae FASTA file, along with the GTF file. You also need to prepare the gffutils database:
import gffutils import sqlite3 try: db = gffutils.create_db('gambiae.gff.gz', 'ag.db') except sqlite3.OperationalError: db = gffutils.FeatureDB('ag.db') ...Become an O’Reilly member and get unlimited access to this title plus top books and audiobooks from O’Reilly and nearly 200 top publishers, thousands of courses curated by job role, 150+ live events each month,
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