# BI278 lab 1 – Unix, genome files, and shell scripts

1.1 Connect to bi Unix environment

ssh cgsnow25@bi278
exit

1.2 Navigate and find colby home
when you log in, letters should say

[cgsnow25@vcacbi278 ~]$

'~' changes as you move around directory structure

pwd

Print working directory, pwd brings to /home/cgsnow25 - so cd ~, pwd brings you home

ls
ls ~
ls /home/students/d/cgsnow25
ls .

This command asks for a list of all of the files and directories (folders)

ls -lh

This command asks for more detailed list of directory contents

ls colbyhome
ls /personal/cgsnow25

This is a link to your personal irectory on Colby's fileserver Filer
You can mount a folder to your desktop by going to Mac desktop and typing [command K] and enter smb://filer.colby.edu and use your Mac's finger to navigate the folder

ls /courses/bi278

Allows you to access the Courses filesaver

cd

'Change directory to'

cd colbyhome
cd /personal/cgsnow25

Will take you to colbyhome, you can type in the "ls" command to find files
Once you're in colbyhome, it won't be a visible destination from your current location, but you can navigate the directory structure using cd

cd ..
pwd

Will allow you to move up a directory or go to a parent directory. '.' is the current directory, so

cd .
pwd

will put you in the same place

1.3 Organize your files
*Don't use spaces in directory or file names. Example: My Documents would be typed in Unix like

ls My\ Documents

You should instead use an underscore or period to type

my_documents
my.documents
myDocuments

Example: make two directories adn copy over entire contents of the lab folder/directory

mkdir lab_01a lab_01b
cp /courses/bi278/Course_Materials/lab_01a/* ./lab_01a

Go to the directory

cd lab_01a
ls

Organize directory

mkdir name #Make a directory named whatever you list after this command
rmdir name #To remove specific directory
rm -r #if directory is not empty
cp a b #Copy file a to b, changes location and file name
mv a b #move a file from a to b, both must be specified
rm filename #rm (remove) whatever you list after it, irreversable
cat filename #concatenate, or print to screen the entire contents of a file
less filename #display contents of a file one screenlength at a time
head filename #print to screen the top 10 lines of a file
tail filename #print to screen the ottom 10 lines of a file
man comand #manual for most Unix commands, shows how the command works
command --help #access usage information

Useful shortcuts:
. (current location)
. . (one directory above)
~ (home)
*(a wildcard that will match any string of characters)

You can find most recent commands by using up arrow key, you can see recent commands by typing in 'history'

Autocomplete saves time, if you start typing in a command or filename and click tab, the Unix shell will complete the name for you.

Example: moving all eps files into a folder

ls *eps #finds all eps files
mkdir eps_files #creates new directory
mv *eps eps_files #moves all files containing eps into the new directory

2. Collect basic genome statistics for multiple genomes

Don't copy over files from folder, refer to them by specifying where the file is (its PATH)

grep pattern filename #find a specific pattern within a file, use ('') to contain the pattern
wc filename #count the words in a file; can be used to count lines (-1) or characters (-c)
tr #translate or delete sets of characters

In Unix, '>' sends the results of the command that preceded it into a file that you specify after it so use qua=otes if you want to use '>' as a pattern

grep ">" /courses/bi278/Course_Materials/lab_01b/filename

Run command for a given geome to see what kinds of sequences are in each file (example: to see all GCF files, you would type in GCF* for filename)

GCF file will tell you how many chromosomes, preceded by the header (the line that starts with >), will tell you which organism and the strain

Other files have the organism and strain identity in file name but not the header

| Organism | Strain | Contig count | Genome size (bp) | GC % |
| -------------- | ------- | ------------ | ---------------- | ---- |
| P. agricolaris | baqs159 | 2 | 8721420 | 5375334 |
| P. bonniea | bbqs859 | 2 | 4098182 | 2406657 |
| P. bonniea | bbqs395 | 2 | 9058983 | 5593928 |
| P. bonniea | bbqs433 | 2 | 7829542 | 4948909 |
| P. fungorum | ATCC BAA-463 | 4 | 9058983 | 5593928 |
| P. hayleyella | bbqs155 | 2 | 10062489 | 6230535 |
| P. hayleyella | bhqs171 | 35 | 4088457 | 2421259 |
| P. hayleyella | bhqs21 | 35 | 4088512 | 2421281 |
| P. hayleyella | bhqs22 | 45 | 4084312 | 2418627 |
| P. hayleyella | bhqs23 | 36 | 4090401 | 2422298 |
| P. hayleyella | bhqs530 | 2 | 4118722 | 2439957 |
| P. hayleyella | bhqs69 | 2 | 4125852 | 2444184 |
| P. Terrae | DSM17804 | 4 | 10062489 | 6230535 |
| P. xenovorans | LB400 | 3 | 9702951 | 6077288 |
| P. sprentiae | WSM505 | 5 | 7829542 | 4948909 |
| P. hayleyella | bhqs11 | 2 | 4125700 | 2444079 |

What is the size of your genome (how many total bases?)

grep -v ">" PATH/test.fa | tr -d -d ATGCatgc | wc -c

What is your GC%?

awk 'BEGIN {print (253/400)}'

Commands that help:

grep "v" PATH/test.fa #test
grep -v ">" PATH/test.fa #genetic code
grep -v ">" PATH/test.fa | tr -d -c GCgc #only Gs and Cs
grep -v ">" PATH/test.fa | tr -d -c GCgc | wc -c #G and C count": 258
awk 'BEGIN {print (253/400)}' #GC%, 0.6325

Write and run a unix script to automate your collection of genome statistics

To bundle commands together
To open up editor within unix shell type

nano

You can use control X to exit back to the normal terminator

#!/bin/bash

Then type commands

grep -v ">" /courses/bi278/Course_Materials/lab_01b/test.fa |tr -d -c ATGCatgc | wc -c
grep -v ">" /courses/bi278/Course_Materials/lab_01b/test.fa |tr -d -c GCgc | wc -c
#awk 'BEGIN {print (253/400)}'

Type in filename (GC%_genomesize.sh)
To save, you want to save it to folder lab_01b

~/lab_01b/

To excecute:

sh GC%_genomesize.sh #only if you're in the directory with ~/lab_01b

Change filename into a variable that can be designated at excecution

nano GC%_genomesize.sh #to go back and edit

Change filename in each line (test.fa) to $1 and exit while saving

grep -v ">" /courses/bi278/Course_Materials/lab_01b/$1 |tr -d -c ATGCatgc | wc -c
grep -v ">" /courses/bi278/Course_Materials/lab_01b/$1 |tr -d -c GCgc | wc -c
#awk 'BEGIN {print (253/400)}'

To excecute and get the numbers to calculate %GC, type as prompt:

sh GC%_genomesize.sh fasta_filename

When done working in bi278 type

exit