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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 Jun 2015
Publisher
ISBN-13 9781782175117
Length 306 pages
Edition 1st Edition
Languages
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Toc

Table of Contents (11) 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. Other Topics in Bioinformatics 9. Python for Big Genomics Datasets Index

Computing the median in a large dataset


As you have seen in the first recipe, computing the median requires having all the values available. With something like a mean, we just need an accumulator and a counter. The fundamental point of this recipe is to introduce the idea of approximate computing; with big data, it may not always be the best strategy to get the precise value (of course, this should be evaluated on a case-by-case basis).

Getting ready

We will require the first recipe to have been fully run.

Here, we will take two different strategies to compute the median: approximating the data points in a way that allows compression of data and subsampling of data.

As usual, this is available in the 08_Advanced/Median.ipynb notebook.

How to do it...

Take a look at the following steps:

  1. Our first approach will be to use approximations of all values, starting with creating a dictionary. This code should be run where the first recipe was run:

    from __future__ import division, print_function
    import...
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