Command Line Introduction: Excercises
=====================================
Excercise 1.1: Directory structure
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Tasks:
1. Navigate to your home directory
2. Create a new directory called "testdir" inside your home directory
3. navigate into the "testdir" directory
4. Create a new file called "example.txt" inside the "testdir" directory
Solution:
.. raw:: html
cd
mkdir testdir
cd testdir
touch example.txt
Excercise 1.2: Directory structure
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Tasks:
1. Use the ls command to display the file "example.txt" file using an absolute path
2. Use the ls command to display the file "example.txt" file using a relative path
3. Go one directory up (to your home directory) Use the ls command to display the file "example.txt" using a relative path
Solution:
.. raw:: html
ls /home/$USER/testdir/example.txt
cd testdir
ls example.txt
cd ..
ls testdir/example.txt
Excercise 2: Tab completion
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Tasks:
1. Navigate to your home directory
2. Create a new folder “testfolder” and a file “example.txt” in it
3. go to the root folder
4. Use tab completion to cd to the folder “testfolder” inside you home directory
5. Use tab completion in the testfolder to ls -l the file “example.txt”
Solution:
.. raw:: html
cd
mkdir testfolder
cd testfolder touch example.txt
cd /
use tab completion...
Excercise 3: Basic File Operations
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Tasks:
1. Change to your home directory
2. Create a file named ‘test.txt’ (and check if it is there)
3. Create a directory named ‘tutorial’
4. Copy ‘test.txt’ into the directory ‘tutorial’
5. Delete ‘test.txt’ (in your home)
6. Change to ‘tutorial’ and rename ‘test.txt’ to ‘file.txt’ and verify
7. Remove the directory ‘tutorial’ and its contents
8. Remove the directories `testfolder` and `testdir` and its contents
Solution:
.. raw:: html
cd
touch test.txt
ls -lrt
mkdir tutorial
cp test.txt tutorial/
rm test.txt
cd tutorial
mv test.txt file.txt
ls
rm file.txt
cd ..
rmdir tutorial
rmdir testfolder testdir
Excercise 4: Links
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Tasks:
1. change to /mnt/
2. Create a directory with the name “linux_intro” and give it to the user ubuntu
3. Go back to your home directory
4. Create a soft link called ‘linux_intro’ to /mnt/linux_intro
**Note:** this cannot be done using normal permission. Use sudo for operating with root privileges
Solution:
.. raw:: html
cd /mnt
sudo mkdir linux_intro
sudo chown ubuntu:ubuntu linux_intro
cd
ln -s /mnt/linux_intro
Excercise 5: Display File Content
---------------------------------
Before you can do the next excercise, you need to donwload the
sequencing data:
::
cd ~/linux_intro
wget https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/linuxcourse/seqs.fasta
Tasks:
1. Use head and tail to inspect the file
2. Print the first and last entry of the fasta file to the command line
3. Browse the file using less, search for start codons
Solution:
.. raw:: html
head seqs.fasta
tail seqs.fasta
head -n 2 seqs.fasta
tail -n 2 seqs.fasta
less seqs.fasta
Excercise 6: Wildcards
----------------------
For the next excercise, we will donwload more sequencing data:
::
wget https://openstack.cebitec.uni-bielefeld.de:8080/swift/v1/linuxcourse/linuxdata.tar.gz
tar -zxvf linuxdata.tar.gz
Tasks:
1. List all tools in /usr/local/bin/ starting with ‘blast’
2. List all tools in /usr/local/bin/ starting with ‘blast’ followed by one additional character
3. List all tools in /usr/local/bin/ starting with ‘a’ or ‘b’ and ending with ‘c’ or ‘d’
4. Copy all sequence files from the directory linuxdata to the linux_intro directory (except seqs.fasta)
Solution:
.. raw:: html
ls /usr/local/bin/blast*
ls /usr/local/bin/blast?
ls /usr/local/bin/[ab]*[cd]
cd ~/linux_intro
cp ~/linuxdata/sequences* ~/linux_intro/
cp ~/linuxdata/sequences_?.fasta ~/linux_intro/
cp ~/linuxdata/sequences_[1-4].fasta ~/linux_intro/
cp ~/linuxdata/sequences_{1..4}.fasta ~/linux_intro/
Excercise 7: grep and wc
------------------------
Tasks:
1. Copy the Araport11_genes.gff from the previously uncompressed ‘linuxdata.tar.gz’-archive into your linux_intro
2. Inspect the file using less
3. How many lines does the file contain?
4. How many entries are there for Chromosome 1?
5. Find all entries related to ‘Auxin’
6. Use the command “grep” to find a file inside the “linuxdata” directory that contains the words “Romeo and Juliet”
Solutoin:
.. raw:: html
cd ~/linux_intro
cp ~/linuxdata/Araport11_genes.gff .
less Araport11_genes.gff
wc -l Araport11_genes.gff
grep -c "^Chr1" Araport11_genes.gff
grep Auxin Araport11_genes.gff
grep -r "Romeo und Juliet" ~/linuxdata/
Excercise 8: Streams
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Tasks:
1. Use *cat* and wildcards to combine all sequence-files into a new file “sequences.fasta”
2. Use *head* and *tail* to get the *second* sequence from sequences.fasta
3. Use *grep* to store the sequence headers of sequences.fasta in a file
4. Use *grep*, *head* and *tail* to store headers 11-20 in a file
5. Append the headers 41-50 to the same (!) file
6. Also store the first 50 headers in a separate file. Do this in one command by using “tee” !
7. Use *grep* and *wc* to find out the number of bases in sequences.fasta
Solutoin:
.. raw:: html
cat sequences_[1-4].fasta > sequences.fasta
head -n 4 | tail -n 2 sequences.fasta
grep ">" sequences.fasta > headers.txt
grep ">" sequences.fasta | head -n 20 | tail -n 10 > headers_2.txt
grep ">" sequences.fasta | head -n 50 | tail -n 10 >> headers_2.txt
grep ">" sequences.fasta | head -n 50 | tee headers50.txt | tail -n 10 >> headers_2.txt
grep -v ">" sequences.fasta | wc
Excercise 9: Tabular Data
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Tasks:
1. How many features (CDS/mRNA/UTR…) are there for each type?
**Hint:** features are in row 3, sort and uniq might be useful
2. Create the same statistic for each chromosome
**Hint:** cut can select multiple columns
3. How many genes with a ‘kinase’ annotation are there per chromosome?
Solution:
.. raw:: html
cut -f 3 Araport11_genes.gff | sort | uniq -c | grep -v "#"
cut -f 1,3 Araport11_genes.gff | sort | uniq -c | grep -v "##"
grep kinase Araport11_genes.gff | cut -f 1,3 | grep gene | cut -f 1 | sort | uniq -c
Excercise 10: Shell scripts
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Tasks:
1. Write a shell script for the following task: Count the number of lines in file that is given as a parameter
2. Write a shell script for the following task: Search for a keyword given as the first parameter in a file that is given as the second parameter
Solution:
.. raw:: html
#!/bin/sh
wc –l $1
#!/bin/sh
grep $1 $2