Table Of ContentBioinformatics with Python
Cookbook
Second Edition
Learn how to use modern Python bioinformatics libraries and
applications to do cutting-edge research in computational
biology
Tiago Antao
BIRMINGHAM - MUMBAI
Bioinformatics with Python Cookbook
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About the author
Tiago Antao is a bioinformatician currently working in the field of genomics. He was
originally a computer scientist but he crossed over to computational biology with an MSc in
Bioinformatics from the Faculty of Sciences at the University of Porto, Portugal, and a PhD
on the spread of drug-resistant malaria from the Liverpool School of Tropical Medicine in
the UK. He is one of the co-authors of Biopython, a major bioinformatics package written in
Python.
In his post-doctoral career, he has worked with human datasets at the University of
Cambridge (UK) and with mosquito whole genome sequence data at the University of
Oxford (UK). He is currently working as a research scientist at the University of Montana.
About the reviewers
Cho-Yi Chen is an Assistant Professor of Biomedical Informatics at the National Yang-
Ming University. While growing up, he was an active athlete, with a passion for science
and technology, which led him to become an Olympic swimmer and later a scientist in
genomics and systems biology. He received his BSc, MSc, and PhD from the National
Taiwan University and Academia Sinica, and finished his postdoctoral training at the
Dana-Farber Cancer Institute and Harvard University. He is a founding member of
Taiwan's Society of Evolution and Computational Biology, and is a recipient of the MOST
Young Scholar Fellowship for his dedication to biomedical research. He and his group
strive to advance our understanding of cancer and other human diseases.
Pin-Jou Wu is a research assistant in Dr. Cho-Yi Chen's laboratory at the Institute of
Biomedical Informatics at National Yang-Ming University, Taiwan. Her research interests
lie in circadian rhythm and its relation to human aging and diseases. She enjoys multi-
omics data mining by using statistics and machine learning approaches and enjoys
discovering a new insight into chronobiology.
She was a research assistant at Tainan District Agriculture Research and Extension Station.
She completed her Master's degree in Plant Pathology and Microbiology at National
Taiwan University and also completed a full-year exchange program doing a Master's of
Science degree at University College Dublin, Ireland.
Yao-Chung Chen is a bioinformatician with a background in molecular biology. After
receiving his MS from National Taiwan University, he participated in a transcriptome
analysis research project on immune systems in commercial fishes at National Pingtung
University of Science and Technology. Previous research experience makes him believe that
biologists should know more about programming, especially those who aim to work in
bioinformatics.
Aiming to be a pioneer, he wishes to interpret bioinformatics in a more biology-friendly
way and encourage more biologists to join this field. Currently, he works as a research
assistant and studies chronobiology at the Institute of Biomedical Informatics, National
Yang-Ming University.
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Table of Contents
Preface 1
Chapter 1: Python and the Surrounding Software Ecology 8
Introduction 8
Installing the required software with Anaconda 9
Getting ready 9
How to do it... 12
There's more... 13
Installing the required software with Docker 13
Getting ready 13
How to do it... 14
See also 15
Interfacing with R via rpy2 15
Getting ready 15
How to do it... 16
There's more... 22
See also 22
Performing R magic with Jupyter Notebook 23
Getting ready 23
How to do it... 23
There's more... 25
See also 25
Chapter 2: Next-Generation Sequencing 26
Introduction 26
Accessing GenBank and moving around NCBI databases 27
Getting ready 28
How to do it... 28
There's more... 32
See also 33
Performing basic sequence analysis 33
Getting ready 33
How to do it... 34
There's more... 35
See also 36
Working with modern sequence formats 36
Getting ready 36
How to do it... 37
There's more... 43
See also 44
Table of Contents
Working with alignment data 45
Getting ready 45
How to do it... 46
There's more... 51
See also 52
Analyzing data in VCF 53
Getting ready 53
How to do it... 54
There's more... 55
See also 56
Studying genome accessibility and filtering SNP data 56
Getting ready 57
How to do it... 58
There's more... 68
See also 69
Processing NGS data with HTSeq 69
Getting ready 70
How to do it... 70
There's more... 73
Chapter 3: Working with Genomes 74
Introduction 74
Working with high-quality reference genomes 75
Getting ready 75
How to do it... 76
There's more... 81
See also 81
Dealing with low-quality genome references 81
Getting ready 82
How to do it... 82
There's more... 86
See also 87
Traversing genome annotations 87
Getting ready 87
How to do it... 88
There's more... 89
See also 90
Extracting genes from a reference using annotations 90
Getting ready 91
How to do it... 91
There's more... 93
See also 94
Finding orthologues with the Ensembl REST API 94
Getting ready 94
How to do it... 95
[ ii ]
Table of Contents
There's more... 98
Retrieving gene ontology information from Ensembl 98
Getting ready 98
How to do it... 99
There's more... 102
See also 103
Chapter 4: Population Genetics 104
Introduction 104
Managing datasets with PLINK 105
Getting ready 106
How to do it... 107
There's more... 111
See also 112
Introducing the Genepop format 112
Getting ready 113
How to do it... 113
See also 117
Exploring a dataset with Bio.PopGen 117
Getting ready 118
How to do it... 118
There's more... 123
See also 123
Computing F-statistics 123
Getting ready 123
How to do it... 124
See also 129
Performing Principal Components Analysis 130
Getting ready 130
How to do it... 130
There's more... 134
See also 135
Investigating population structure with admixture 135
Getting ready 135
How to do it... 136
There's more... 141
Chapter 5: Population Genetics Simulation 142
Introduction 142
Introducing forward-time simulations 143
Getting ready 143
How to do it... 143
There's more... 149
Simulating selection 149
Getting ready 150
How to do it... 150
[ iii ]
