📗
Essential Python For Genome Science
  • Before Start
  • Chapter Contents
  • Prerequisites
    • About the UNIX system
    • About python
  • UNDERSTAND RAW DATA
    • Stages of Genome Data Generation
    • From Bulk To Single Cell
    • Introduction To the Datasets
      • bulk RNA-seq
      • single-cell data
  • Work Environment
    • Chapter Ensemble
    • All About Installations
    • Keep Running
    • Coding Environment
    • Git and Github
    • Other Tips
  • Python and UNIX System
    • Run Python
    • File I/O
    • Run Shell Command In Python - I
    • 🎉Case Study: Mapping bulk RNA-seq reads with salmon
  • Data Cleaning
    • 🎉Key Concept of Pandas
    • 🎉Case Study: Aggregate Salmon Quant
    • Case Study: Exploring The Dataset 🚩
    • The "copy" and "inplace" Parameter 🚩
    • Case Study: Extract and Reformat GTF file 🚩
    • the correct vs. the wrong way of using pandas 🚩
    • Case Study: Bulk Sample PCA 🚩
  • PYTHON BASICS
    • Python can be lightning-fast ⚡️ 🚩
    • Run Shell Command In Python - II 🚩
    • Pointers In Python 🚩
    • Everything is an object 🚩
    • Thread and Process 🚩
    • Resource For Intermediate Python Knowledge 🚩
    • Python magic method 🚩
  • Genome Science Data
    • NGS Data Formats and Tools 🚩
      • SAM/BAM 🚩
      • BED 🚩
      • GTF 🚩
      • Bigwig / Bigbed 🚩
      • VCF / BCF 🚩
    • The Python Packages 🚩
  • Data visualization
    • Matplotlib Basics 🚩
    • Seaborn Basics 🚩
    • Interactive Data Visualization 🚩
  • Use R in Python
    • Why? 🚩
    • rpy2 🚩
  • Gotchas
    • Check whether package X is installed
    • BAM to FASTQ
    • Genomic Websites
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  1. Prerequisites

About the UNIX system

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Last updated 4 years ago

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UNIX system knowledge

  • I/O (Input/Output, IMPORTANT): what is stdin, stdout, stderr. What does "|" (pipe) do.

  • Job control (IMPORTANT): top, kill, jobs, bg, fg, use "&" to put job in bg, nohup

  • What is process, what is thread?

  • What is , especially, what is the (most useful) PATH variable and .

  • Basic navigation: pwd, cd, ls (ls -l, ls -hl, ls -hal, understand output of ls -l)

  • Read files: cat, less, file(tell you whether a file is binary or is compressed), head, tail, grep, sort

  • Manipulate files:cp, mv, rm, mkdir, ln -s

  • Working with commands: type, which, help, man

  • Permissions: chmod

For quick introduction, I really recommend . The "" chapter is about all the must-know of using UNIX systems (Linux, Mac OS), fairly enough for a beginning. The above list is actually based on this chapter.

local variable
how to change the PATH variable in ~/.bashrc
this short book
Learning the Shell