Week 3 working on sphinx server

#1
screen -S LAB_1

#2
mkdir Commandline_Lab

#3
cd Commandline_Lab/

#4
ls

#5 & 6
#this can be done using a variety of methods nano is easier in terminal but here i use echo for brevity
echo "Welcome to Applied Genome Analytics" > Text_1.txt

#7
mv Text_1.txt Myfile_1.txt

#8
scp [email protected]:/pickett_sphinx/projects/EPP531_AGA/reed_EPP531/Commandline_Lab/Myfile_1.txt .

#9
rm Myfile_1.txt

#10
scp ./Myfile_1.txt [email protected]:/pickett_sphinx/projects/EPP531_AGA/reed_EPP531/Commandline_Lab

#11
# Done!

#12
mv /<my_downloads_folder>/Data /home/mobaxterm/Desktop/EPP_531

#13
ls | wc -l

#14
more mgGenes.txt

#15
cat mgGenes.txt | grep "MG" | wc -l
# 525

#16
head mgGenes.txt
tail mgGenes.txt

#17
cat mgGenes.txt | grep "+" | wc -l
# 299

#18
cat mgGenes.txt | grep "-" | wc -l
# 227

#19
expr 299 + 227
# 526

#20
cut -f 5 mgGenes.txt | grep "-"
# rpmG-2
# polC-2

#21
nano mgGenes.txt
# Done replaced rpmG-2 with rpmG_2 and polC-2 with polC_2
expr $(cat mgGenes.txt | grep "+" | wc -l) + $(cat mgGenes.txt | grep "-" | wc -l)
# 525
# looks good!

#22
cut -f 1-4 mgGenes.txt | grep "+" > Plus_genes.txt

#23
cut -f 1-4 mgGenes.txt | grep "-" > Minus_genes.txt

#24
cat Plus_genes.txt | grep "MG" | wc -l
# 299
cat Minus_genes.txt | grep "MG" | wc -l 
# 226

#25
head -n 250 mgGenes.txt | tail -n 1
# MG_228  274653  275135  +       dhfR

#26
# Ctrl+q