Browse Library
Sign In Start Free Trial
Close icon Search icon
Account
Browse Library Advanced Search Sign In Start Free Trial

Add to playlist

Create a Playlist

Modal Close icon
You need to login to use this feature.
  • Bioinformatics with Python Cookbook
  • Toc
  • feedback
Bioinformatics with Python Cookbook

Bioinformatics with Python Cookbook

By : Tiago R Antao, Tiago Antao
4.7 (6)
close
Bioinformatics with Python Cookbook

Bioinformatics with Python Cookbook

4.7 (6)
By: Tiago R Antao, Tiago Antao

Overview of this book

If you have intermediate-level knowledge of Python and are well aware of the main research and vocabulary in your bioinformatics topic of interest, this book will help you develop your knowledge further.
Table of Contents (11 chapters)
close
close
Preface
Preface
What this book covers
What you need for this book
Who this book is for
Sections
Conventions
Reader feedback
Customer support
Free Chapter
1
1. Python and the Surrounding Software Ecology
1. Python and the Surrounding Software Ecology
Introduction
Installing the required software with Anaconda
Installing the required software with Docker
Interfacing with R via rpy2
Performing R magic with IPython
2
2. Next-generation Sequencing
2. Next-generation Sequencing
Introduction
Accessing GenBank and moving around NCBI databases
Performing basic sequence analysis
Working with modern sequence formats
Working with alignment data
Analyzing data in the variant call format
Studying genome accessibility and filtering SNP data
3
3. Working with Genomes
3. Working with Genomes
Introduction
Working with high-quality reference genomes
Dealing with low-quality genome references
Traversing genome annotations
Extracting genes from a reference using annotations
Finding orthologues with the Ensembl REST API
Retrieving gene ontology information from Ensembl
4
4. Population Genetics
chevron up
4. Population Genetics
Introduction
Managing datasets with PLINK
Introducing the Genepop format
Exploring a dataset with Bio.PopGen
Computing F-statistics
Performing Principal Components Analysis
Investigating population structure with Admixture
5
5. Population Genetics Simulation
5. Population Genetics Simulation
Introduction
Introducing forward-time simulations
Simulating selection
Simulating population structure using island and stepping-stone models
Modeling complex demographic scenarios
Simulating the coalescent with Biopython and fastsimcoal
6
6. Phylogenetics
6. Phylogenetics
Introduction
Preparing the Ebola dataset
Aligning genetic and genomic data
Comparing sequences
Reconstructing phylogenetic trees
Playing recursively with trees
Visualizing phylogenetic data
7
7. Using the Protein Data Bank
7. Using the Protein Data Bank
Introduction
Finding a protein in multiple databases
Introducing Bio.PDB
Extracting more information from a PDB file
Computing molecular distances on a PDB file
Performing geometric operations
Implementing a basic PDB parser
Animating with PyMol
Parsing mmCIF files using Biopython
8
8. Other Topics in Bioinformatics
8. Other Topics in Bioinformatics
Introduction
Accessing the Global Biodiversity Information Facility
Geo-referencing GBIF datasets
Accessing molecular-interaction databases with PSIQUIC
Plotting protein interactions with Cytoscape the hard way
9
9. Python for Big Genomics Datasets
9. Python for Big Genomics Datasets
Introduction
Setting the stage for high-performance computing
Designing a poor human concurrent executor
Performing parallel computing with IPython
Computing the median in a large dataset
Optimizing code with Cython and Numba
Programming with laziness
Thinking with generators
10
Index
Index

Introducing the Genepop format

The Genepop format is used in many conservation genetics studies. It's the format of the Genepop application and is the de facto format for many population genetics analysis. If you come from other fields (for example, have a lot of sequencing experience), you may not have heard of it, but this format is widely used (as its citation record proves) and is worth a look. Here, we will convert some datasets from previous recipes to this format and introduce the Genepop parser from Biopython.

Getting ready

You will need to run the previous recipe because its output will be required for this one.

If you are not using Docker, you might not be using some of the code that I produced earlier (mostly to deal with the bread and butter of data conversion). You can find this code at https://github.com/tiagoantao/pygenomics and install it from

pip install pygenomics

Note that at this stage, we will not use the Genepop application (this will change in the next recipe), so...

End of Section 4
Next Section
bookmark search playlist font-size

Change the font size

margin-width

Change margin width

day-mode

Change background colour

Close icon Search
Country selected
Close icon Your notes and bookmarks

Delete Bookmark

Modal Close icon
Are you sure you want to delete it?
Cancel
Yes, Delete