week2-1_bash.md

Command Line III

Karthik Gangavarapu, Huitian (Yolanda) Diao

Running one command on multiple inputs

Loops

1. for

   for i in {a..e}
   do
     echo $i
   done
   

   For loop + wildcard

   cd ../data/
   mkdir fastq
   mv *.fastq fastq
   

   Exercise: Rename all the files in the folder data from .fq to .fastq

   cd ../data/
   for i in $(ls)
   do
     mv $i ${i/.fq/.fastq}
   done
   

   Bash string manipulation

2. while

Logic

1. if else

2. Logic operators

find

xargs

More on fastq files

Version control with Git

What is git?