Book Image

Bioinformatics with Python Cookbook - Second Edition

By : Tiago Antao
Book Image

Bioinformatics with Python Cookbook - Second Edition

By: Tiago Antao

Overview of this book

Bioinformatics is an active research field that uses a range of simple-to-advanced computations to extract valuable information from biological data. This book covers next-generation sequencing, genomics, metagenomics, population genetics, phylogenetics, and proteomics. You'll learn modern programming techniques to analyze large amounts of biological data. With the help of real-world examples, you'll convert, analyze, and visualize datasets using various Python tools and libraries. This book will help you get a better understanding of working with a Galaxy server, which is the most widely used bioinformatics web-based pipeline system. This updated edition also includes advanced next-generation sequencing filtering techniques. You'll also explore topics such as SNP discovery using statistical approaches under high-performance computing frameworks such as Dask and Spark. By the end of this book, you'll be able to use and implement modern programming techniques and frameworks to deal with the ever-increasing deluge of bioinformatics data.
Table of Contents (16 chapters)
Title Page
About Packt
Contributors
Preface
Index

Performing geometric operations


We will now perform computations with geometry information, including computing the center of the mass of chains and of whole models.

Getting ready

You can find this content in the Chapter07/Mass.ipynb Notebook file.

How to do it...

Let's take a look at the following steps:

  1. First, let's retrieve the data:
from Bio import PDB
repository = PDB.PDBList()
parser = PDB.PDBParser()
repository.retrieve_pdb_file('1TUP', pdir='.', file_format='pdb')
p53_1tup = parser.get_structure('P 53', 'pdb1tup.ent')
  1. Then, let's recall the type of residues that we have with the following code:
my_residues = set()
for residue in p53_1tup.get_residues():
    my_residues.add(residue.id[0])
print(my_residues)

So, we have H_ ZN (zinc) and W (water), which are HETATMs; the vast majority are standard PDB atoms.

  1. Let's compute the masses for all chains, zincs, and waters using the following code:
def get_mass(atoms, accept_fun=lambda atom: atom.parent.id[0] != 'W'):
    return sum([atom.mass for atom...