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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Exploring a dataset with Bio.PopGen
In this chapter, we will perform an initial exploratory analysis of one of our generated datasets. We will analyze the 10 percent sampling of chromosome 2 without the offspring. We will look for monomorphic loci (in this case, SNPs) across populations along with how to research minimum allele frequencies and expected heterozygosities.
Getting ready
You will need to have run the previous two recipes and should have the hapmap10_auto_noofs_2.gp and hapmap10_auto_noofs_2.pops files. We will also use the metadata file downloaded in the first recipe.
For this code to work, you will need to install Genepop from http://kimura.univ-montp2.fr/~rousset/Genepop.htm. We will use the interface provided by Biopython to execute ...
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I wanted to learn C and C++, but it didn't click for me until I picked up an O'Reilly book. When I went on the O’Reilly platform, I was astonished to find all the books there, plus live events and sandboxes so you could play around with the technology.Addison B.
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