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Bioinformatics with Python Cookbook

You're reading from   Bioinformatics with Python Cookbook Learn how to use modern Python bioinformatics libraries and applications to do cutting-edge research in computational biology

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Product type Paperback
Published in Nov 2018
Publisher Packt
ISBN-13 9781789344691
Length 360 pages
Edition 2nd Edition
Languages
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Author (1):
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Tiago Antao Tiago Antao
Author Profile Icon Tiago Antao
Tiago Antao
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Table of Contents (12) Chapters Close

Preface 1. Python and the Surrounding Software Ecology 2. Next-Generation Sequencing FREE CHAPTER 3. Working with Genomes 4. Population Genetics 5. Population Genetics Simulation 6. Phylogenetics 7. Using the Protein Data Bank 8. Bioinformatics Pipelines 9. Python for Big Genomics Datasets 10. Other Topics in Bioinformatics 11. Advanced NGS Processing

Doing parallel computing with Dask


The previous code is still quite slow, so now, we will use parallel processing to accelerate our data analysis. Our first approach will be using Dask, a Python-based library that provides scalable parallelism: most of the code that scales on your laptop will be able to scale on a large cluster. Dask is a fairly low-level and Python-related approach. Later in this chapter, we will discuss an alternative approach that is more high-level and language-agnostic.

Getting ready

We will make a parallel version of the previous code, so you will need to have the same dataset available. We will be using HDF5 processing, so you should be acquainted with the previous recipe anyway.

How to do it...

Take a look at the following steps:

  1. We will start by doing the necessary imports and checking Dask's version:
from multiprocessing.pool import Pool
from math import ceil

import numpy as np

import h5py

import dask
import dask.array as da
import dask.multiprocessing
print(dask...
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