# BI278 Lab 1 Kirsten Pastore

1.1 Connect to the BI278 Unix Environment

connect to the course environment

#secure shell (ssh) allow us to connect to remote computing environment 
ssh klpast23@bi278

1.2 Navigate and find your Colby home

working directory is denoted as:
[klpast23@vcacbi278 ~]$

begin navigating directories:

#pwd (print working directory)
pwd 
#returns /home/students/k/klpast23

#ls (list of all subdirectories in cwd)
ls 
#returns colby.cshrc colby.login colby.logout colby.profile 

# -1h flag which asks for a more detailed list of directory contents
ls -lh 
#returns file permissions, file size, and date created

navigate to the courses fileserver

cd /courses/bi278/klpast23

note: ~ = /home/colbyid

1.3 Organize your files

*note: don't use spaces in file / directory names

#navigate to bi278 home directory 
cd ~ 

#make two new directories 
mkdir lab_01a lab_01b

#copy over the entire contents of the first lab folder 
cp /courses/bi278/Course_Materials/lab_01a/* ./lab01a

commands:

#make a directory named name
mkdir name 

#remove a spec. directory (only works if it is empty, must use rm -r if not empty)
rmdir name 

#copy file a to b; an be used to change location and filename 
cp a b 

#move a filed from a to b, used for renaming files 
mv a b

#remove a file - cannot be reversed 
rm filename 

#concatenate, or print to screen the entire contents of a file as long as it is a text file 
cat filename 

#display the contents of a file one screen length at a time, exit by typing q 
less filename 

#print to screen the top 10 lines of a file 
head filename 

#print to screen the bottom 10 lines of a file 
tail filename 

#manual for mst Unix commands 
man command 

Organizing / Moving Files

#made a directory for figures 
mkdir figures

#move all files starting with fig to figure
mv fig1_all_variation.eps figures

#did this for files starting with fig(s)

#made a directory for raw preference
mkdir raw_preference 

#to move all raw_preference files to raw_preferece folder
mv raw_preference_* raw_preference
mv *pref* raw_preference

#made a directory for achybrid files 
mkdir achybrid

#move all achybrid files to achybrid folder 
mv *achybrid* achybrid

Exercise 2. Collect Basic Genome Statistics for Multiple Genomes

2.1 Get Basic Information About Genomes

additional commands

#finds a specific pattern within a file 
grep pattern filename 

#counts words in a file, can be used to counts lines -1 or characters -c in a file 
wc filename 

#translate or delete sets of chars 
tr 

# > sends the results of the command that proceded it to a file that you specify after it 
some command > filename 

1. Navigate to lab_01b and find what kind of sequences are listed in each file

#performed for each file in the folder lab_01b
grep ">" /courses/bi278/Course_Materials/lab_01b/GCF_00756045.1_ASM75604v1_genomic.fna 
#counted headers to find contigs

2. fill out table

| Organism | Strain | Contig Count | Genome Size | GC% |
| ------------- | ------------ | ------------ | --- | --- |
| P.agricolaris | baqs159 | 2 | 8721420 | 61.6% |
| P. bonniea | bbqs859 | 2 | 4098182 | 58.7% |
| P. bonniea | bbqs395 | 2 | 4009285 | 58.8% |
| P. bonniea | bbqs433 | 2 | 4013203 | 58.8% |
| P. fungorum | ATCC BAA-463 | 4 | 9058983 | 61.8% |
| P. hayleyella | bhqs11 | 2 | 4125700 | 59.2% |
| P. hayleyella | bhqs155 | 2 | 4118676 | 59.2% |
| P. hayleyella | bhqs21 | 35 | 4088512 | 59.2% |
| P. hayleyella | bhqs22 | 45 | 4084312 | 59.2% |
| P. hayleyella | bhqs23 | 36 |4090401 | 59.2% |
| P. hayleyella | bhqs171 | 35 | 4088457 | 59.2% |
| P. hayleyella | bhqs530 | 2 | 4118722 | 59.2% |
| P. hayleyella | bhqs69 | 2 | 4125852 | 59.2% |
| P. sprentiae | WSM5005 | 5 | 7829542 | 63.2% |
| P. terrae | DSM 17804 | 4 | 10062489 | 61.9% |
| P. xenovorans | LB400 | 3 | 9702951 | 62.6% |

3. answer questions for test.fa

wc test.fa 

#returns 411 because it counts >test chars and end of line chars

What is your GC%

grep ">" test.fa 
#returns >test

grep -v ">" test.fa
#returns bases (all text that doesnt include the ">" as a line )

grep -v ">" test.fa | tr -d -c GCgc
#deletes or truncates sets of characters, -d deletes chars in SET1, -c finds the complement 

grep -v ">" test.fa | tr -d -c GCgc | wc -c
returns 253

awk 'BEGIN {print(453/400) }'
returns 0.6325

2.2 Write and Run a UNIX Script to Automate Your Collection of Genome Stats

# open nano 
nano 

#tell Unix that this is a bash shell script 
#!/bin/bash 

write a script that finds the total number of BP and the total number of GC

#this tells me which strain the file refers too 
grep ">" $1
#tells me how many total base pairs there are 
grep -v ">" $1 | tr -d -c GCAT | wc -c
#tells me how many GCs there are 
grep -v ">" $1 | tr -d -c GCgc | wc -c

named the file BPCounter.sh

run the file with the fasta filename:

sh BPCounter.sh fasta_filename 

Ran the script for each genome to complete the table above