Bioinformatics with Python Cookbook电子书

Bioinformatics with Python Cookbook

Table of Contents

Bioinformatics with Python Cookbook

Credits

About the Author

About the Reviewers

www.PacktPub.com

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Preface

What this book covers

What you need for this book

Who this book is for

Sections

Getting ready

How to do it…

There's more…

See also

Conventions

Reader feedback

Customer support

Downloading the example code

Downloading the color images of this book

Errata

Piracy

Questions

1. Python and the Surrounding Software Ecology

Introduction

Installing the required software with Anaconda

Getting ready

How to do it…

There's more…

See also

Installing the required software with Docker

Getting ready

How to do it…

See also

Interfacing with R via rpy2

Getting ready

How to do it…

There's more…

See also

Performing R magic with IPython

Getting ready

How to do it…

See also

2. Next-generation Sequencing

Introduction

Accessing GenBank and moving around NCBI databases

Getting ready

How to do it…

There's more…

See also

Performing basic sequence analysis

Getting ready

How to do it…

There's more…

See also

Working with modern sequence formats

Getting ready

How to do it…

There's more…

See also

Working with alignment data

Getting ready

How to do it…

There's more…

See also

Analyzing data in the variant call format

Getting ready

How to do it…

There's more…

See also

Studying genome accessibility and filtering SNP data

Getting ready

How to do it…

There's more…

See also

3. Working with Genomes

Introduction

Working with high-quality reference genomes

Getting ready

How to do it...

There's more...

See also

Dealing with low-quality genome references

Getting ready

How to do it...

There's more...

See also

Traversing genome annotations

Getting ready

How to do it...

There's more...

See also

Extracting genes from a reference using annotations

Getting ready

How to do it…

There's more...

See also

Finding orthologues with the Ensembl REST API

Getting ready

How to do it...

There's more...

Retrieving gene ontology information from Ensembl

Getting ready

How to do it...

There's more...

See also

4. Population Genetics

Introduction

Managing datasets with PLINK

Getting ready

How to do it…

There's more...

See also

Introducing the Genepop format

Getting ready

How to do it…

See also

Exploring a dataset with Bio.PopGen

Getting ready

How to do it…

There's more...

See also

Computing F-statistics

Getting ready

How to do it…

See also

Performing Principal Components Analysis

Getting ready

How to do it…

There's more...

See also

Investigating population structure with Admixture

Getting ready

How to do it…

There's more...

5. Population Genetics Simulation

Introduction

Introducing forward-time simulations

Getting ready

How to do it...

There's more...

Simulating selection

Getting ready

How to do it…

There's more...

Simulating population structure using island and stepping-stone models

Getting ready

How to do it…

Modeling complex demographic scenarios

Getting ready

How to do it…

Simulating the coalescent with Biopython and fastsimcoal

Getting ready

How to do it…

There's more...

See also

6. Phylogenetics

Introduction

Preparing the Ebola dataset

Getting ready

How to do it...

There's more...

See also

Aligning genetic and genomic data

Getting ready

How to do it...

Comparing sequences

Getting ready

How to do it...

There's more…

Reconstructing phylogenetic trees

Getting ready

How to do it...

There's more...

Playing recursively with trees

Getting ready

How to do it...

There's more...

Visualizing phylogenetic data

Getting ready

How to do it...

There's more...

7. Using the Protein Data Bank

Introduction

Finding a protein in multiple databases

Getting ready

How to do it...

There's more...

Introducing Bio.PDB

Getting ready

How to do it...

There's more...

Extracting more information from a PDB file

Getting ready

How to do it...

Computing molecular distances on a PDB file

Getting ready

How to do it...

Performing geometric operations

Getting ready

How to do it...

There's more...

Implementing a basic PDB parser

Getting ready

How to do it...

There's more...

Animating with PyMol

Getting ready

How to do it...

There's more...

Parsing mmCIF files using Biopython

Getting ready

How to do it...

There's more...

8. Other Topics in Bioinformatics

Introduction

Accessing the Global Biodiversity Information Facility

How to do it...

There's more...

Geo-referencing GBIF datasets

Getting ready

How to do it...

There's more...

Accessing molecular-interaction databases with PSIQUIC

How to do it...

Plotting protein interactions with Cytoscape the hard way

Getting ready

How to do it...

There's more...

9. Python for Big Genomics Datasets

Introduction

Setting the stage for high-performance computing

Getting ready

How to do it...

Designing a poor human concurrent executor

Getting ready

How to do it...

There's more...

Performing parallel computing with IPython

Getting ready

How to do it...

There's more...

Computing the median in a large dataset

Getting ready

How to do it...

There's more...

Optimizing code with Cython and Numba

Getting ready

How to do it...

There's more...

Programming with laziness

Getting ready

How to do it...

There's more...

Thinking with generators

Getting ready

How to do it...

See also

Index