Bioinformatics Data Skills by Oreilly学习笔记-1

Chapter1. How to learn bioinformatics

看起来是琐碎的小技巧,甚至是关于信仰的东西,可能要真正投入进去,才能慢慢体会,看得不太认真,许多略过的东西,以后可以再回头看。

Test Code, or Better Yet, Let Code Test Code
学到了用Code test code:

EPS = 0.00001 # a small number to use when comparing floating-point values
def add(x, y):
"""Add two things together."""
return x + y
def test_add():
"""Test that the add() function works for a variety of numeric types."""
assert(add(2, 3) == 5)
assert(add(-2, 3) == 1)
assert(add(-1, -1) == -2)
assert(abs(add(2.4, 0.1) - 2.5) < EPS)

尽管有时用于test 的code本身也可能成为bug,但是确实,当写得多了之后可以起到事半功倍的效果。

多用短小可重复的代码块,这样可以避免总是写相同作用的代码。

记得写README files

This practical book teaches the skills that scientists need for turning large sequencing datasets into reproducible and robust biological findings. Many biologists begin their bioinformatics training by learning scripting languages like Python and R alongside the Unix command line. But there's a huge gap between knowing a few programming languages and being prepared to analyze large amounts of biological data. Rather than teach bioinformatics as a set of workflows that are likely to change with this rapidly evolving field, this book demsonstrates the practice of bioinformatics through data skills. Rigorous assessment of data quality and of the effectiveness of tools is the foundation of reproducible and robust bioinformatics analysis. Through open source and freely available tools, you'll learn not only how to do bioinformatics, but how to approach problems as a bioinformatician. Go from handling small problems with messy scripts to tackling large problems with clever methods and tools Focus on high-throughput (or "next generation") sequencing data Learn data analysis with modern methods, versus covering older theoretical concepts Understand how to choose and implement the best tool for the job Delve into methods that lead to easier, more reproducible, and robust bioinformatics analysis Table of Contents Part I. Ideology: Data Skills for Robust and Reproducible Bioinformatics Chapter 1. How to Learn Bioinformatics Part II. Prerequisites: Essential Skills for Getting Started with a Bioinformatics Project Chapter 2. Setting Up and Managing a Bioinformatics Project Chapter 3. Remedial Unix Shell Chapter 4. Working with Remote Machines Chapter 5. Git for Scientists Chapter 6. Bioinformatics Data Part III. Practice: Bioinformatics Data Skills Chapter 7. Unix Data Tools Chapter 8. A Rapid Introduction to the R Language Chapter 9. Working with Range Data Chapter 10. Working with Sequence Data Chapter 11. Working with Alignment Data Chapter 12. Bioinformatics Shell Scripting, Writing Pipelines, and Parallelizing Tasks Chapter 13. Out-of-Memory Approaches: Tabix and SQLite Chapter 14. Conclusion
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