Practice on basic shell scripting

© 2024 Abdoallah Sharaf

basic shell scripting commands

• present directory

 pwd

• Make directory

mkdir FOO

• Navigate

cd FOO
pwd
cd ../
cd CL_data
ls
cd -
pwd

• Copy, paste and remove

cp CL_data/Ceratodon_purpureus.fasta FOO/
cp CL_data/* FOO/
rm FOO/Ceratodon_purpureus.fasta
rm FOO/
rm -r FOO/

• navigate files (cat, head,tail)

cd CL_data/
cat Dunaliella_salina.fasta
head Dunaliella_salina.fasta
cat Dunaliella_salina.fasta Ceratodon_purpureus.fasta Physcomitrium_patens.fasta
cat *.fasta >> merged_seq.faa
more Dunaliella_salina.fasta
Ctrl+c
less Dunaliella_salina.fasta

• select strings and edit (grep and sed)

grep '>' Dunaliella_salina.fasta
grep -c '>' Dunaliella_salina.fasta
grep -c '>' *.fasta
grep -v '>' Dunaliella_salina.fasta
grep '>' Dunaliella_salina.fasta|head
sed 's/>/</g' Dunaliella_salina.fasta
sed 's/>/</g' Dunaliella_salina.fasta > Dunaliella_salina.faa
sed -i 's/</>/g' Dunaliella_salina.faa
sed 's/Dunaliella_salina/Chlorophyta_core chlorophytes_Dunaliella_salina/g' Dunaliella_salina.fasta
sed '/^>/s/$/_Chlorophyta_core/g' Dunaliella_salina.fasta
sed '/^>/s/$/_Chlorophyta_core/g' Dunaliella_salina.fasta|grep '>'|head

• wc and cut commands

wc 1kP_Sample_List.csv
wc -l 1kP_Sample_List.csv
ls |wc -l
cut -f1 1kP_Sample_List.csv
cut -f1,3 1kP_Sample_List.csv

looping

mkdir loop
for i in `cat CL_data/sp_list.txt`; do cp $i.fasta loop/;done

create bash program

nano script.sh
vi script.sh
vim script.sh

#!/bin/bash
pwd
ls
mkdir test_data
cd test_data
pwd
cp /workspace/SequAna_course2024/CL_data/sp_list.txt ./

for i in `cat sp_list.txt`; 
do 
    cp /workspace/SequAna_course2024/CL_data/$i.fasta ./
    echo 'file is transferred';
done
rm Physcomitrium_patens.fasta
cd ../
ls 

echo 'THIS IS HOW WE DO IT'

chmod a+x script.sh
bash script.sh
./script.sh