IND-UCSF Software Carpentry Notes

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Software Carpentry Course, UCSF

March 2019

• Learned foundational bioinformatic tools including Bash, R, markdown and Github, as well as tutuorials for differential expression.

Bash Notes

pwd - show what directory (folder) you are in

cd - navigate to directory

ls - list what is in your directory

mkdir - make new folder

write with nano - nano docname.txt

• save: cntrl o
• exit: cntrl x

read your (whole) file in bash window - cat docname.txt

look at just the first n lines of your file in bash window - head -n docname.txt

moving files - mv docname.txt directorymovingto

moving all files with certain feature in name (ex: all txt files) (wildcards) - mv *.txt directorymovingto

copying a file - cp docname.txt docname2.txt

rename - mv docname.txt newdocname.txt

removing files (gets rid of permanently!) - rm docname.txt

count number of lines in your file - wc -l summary_table.csv

look at a particular line - grep "term" summary_table.csv

• will give you every line that includes "term"

PIPES

| is the pipe symbol

Put it between commands to do more than one thing at a time

ex: grep "NonDynamic" summary_table.csv | wc -l

Write your grep to a new file - grep "term" summary_table.csv > newfile.csv

Append to already existing file - grep "term2" summary_table.csv >> newfile.csv

Looking at gene with largest increase in expression at any point

LOOPS

Listing all files of a particular type: wc -l *.txt

Now doing the same thing with a for loop…

for filename in 'ls data/'; do echo; $filename; done

Other commands

Finding stuff: if you know the file name: find . -name summary_table.csv

• dot tells it to search everywhere