How to do it...

Let's take a look at the following steps:

  1. Let's start by listing the chromosomes of the A. gambiae genome:
import gzipfrom Bio import SeqIOgambiae_name = 'gambiae.fa.gz'atroparvus_name = 'atroparvus.fa.gz'recs = SeqIO.parse(gzip.open(gambiae_name, 'rt', encoding='utf-8'), 'fasta')for rec in recs:    print(rec.description)

This will produce the following output:

chromosome:AgamP3:2L:1:49364325:1 chromosome 2Lchromosome:AgamP3:2R:1:61545105:1 chromosome 2Rchromosome:AgamP3:3L:1:41963435:1 chromosome 3Lchromosome:AgamP3:3R:1:53200684:1 chromosome 3Rchromosome:AgamP3:UNKN:1:42389979:1 chromosome UNKNchromosome:AgamP3:X:1:24393108:1 chromosome Xchromosome:AgamP3:Y_unplaced:1:237045:1 chromosome Y_unplaced

The code is quite straightforward. ...

Get Bioinformatics with Python Cookbook - Second Edition now with the O’Reilly learning platform.

O’Reilly members experience books, live events, courses curated by job role, and more from O’Reilly and nearly 200 top publishers.

Start your free trial