Day 2 / Afternoon: Shell Basics:¶

A few commands used in the shell in the afternoon.

Useful commands:¶

Which user is logged on. In the virtual box you should see that you are software carpentry.

whoami
Unix for “print working directory”.

pwd
List directory

ls

ls -a #”list all”

ls -la # long all
Change directories:

cd mydir #change directories

cd .. # goes to directory one up from the working directory.
To make a new directory:

mkdir 2013-02-26
If we want to make a new directory not nested in the one we are in we can also do that

mkdir /users/newstuff/
Create a file in text editor nano:

nano Seattle.txt
Save by hitting Ctrl O and then Ctrl -X to exit.
Quick way to read file in shell

cat data.txt
Copying- Let’s say that we need to make a copy of this file. We will type the name of the file and then its new name’s. Let’s make a copy and call it something more descriptive. So in this case the command is “cp.” So first give it the name of the file you are trying to copy and then the new file name for the copy.

cp data.txt mammal_abundance_UW.txt
Moving files- if we want to move a file from one spot to another we can use the command mv. This is also how we rename files.

mv data.txt /Workshop

mv data.txt ..
To use mv to rename we can give the destination a new filename

mv data.txt data_current.txt
To delete something we can use rm-for remove. And just a note that there is no “trash” or “recycling” bin in the unix shell. Type rm file to remove a file or rmdir directory to remove a directory if it is empty.

rm data.txt

rmdir emptyfolder

To sort this by column from highest to lowest.

sort -k 2 -t, -n mammal_abundance_UW.txt
Lowest to highest:

sort -k 2 n -r mammal_abundance_UW.txt
We can find out many things about these unix commands on the internet, but also by going to the manual that comes with the programs.

man sort
Exit by pressing “q”.
Save this sorted file to a new file:

sort -k 1 mammal_abundance_UW.txt > sorted_mammal_abundance_UW.txt
Read first 10 lines of file:

head sorted_mammal_abundance_UW.txt
Top 2 lines:

head -2 sorted_mammal_abundance_UW.txt
Bottom 10 lines:

tail sorted_mammal_abundance_UW.txt
Bottom 2 lines:

tail -2 sorted_mammal_abundance_UW.txt
Pipes: send output from one command as input to another:

sort -k 2 n mammal_abundace_UW.txt | head -1
If we want to send the final output to a file we can also do that:

sort -k 2 n mammal_abundace_UW.txt | head -1 > most_abundant_mammal_UW.txt
Cut column from a file:

cut -d, -f 1 data.txt
Use word count wc to count the number of lines in a file

wc -l mammal_abundance_UW.txt
For multiple files:

wc -l mammal_abundance_UW.txt, mammal_abundance_UBC.txt

wc -l mammal_abundance_*.txt
See history of commands run in the shell session:

history
If we want we can send the print out of this command to a file. Good for our record keeping:

history > command_log_2013_02_26.txt
Find all lines in several files that contained “squirrels” and then aggregate these:

grep squirrels mammal_abundance_*.txt

for datafile in data_*

do

echo $datafile sort -k 2 -n $datafile

done

To make as a bash script save commands in a text editor as a .sh file and run in bash.

bash sorting_abundances.sh
What about another loop with numbers 1-4?

for number in {1,2,3,4}

do

echo $number

done
Even better would be:

for number in {1..4}

do

echo $number

done