Hidden word quest
This exercise was modifed from an original idea by Kristian Rother, see www.academis.eu.
The goal of this exercice is to use and test what you have learned today about interacting with the command line on Unix/Linux.
You will have to:
- Navigate directories and files
- Edit text files
- Copy and remove files
- Process text data
Before starting, the hidden_word_exercise.zip file with the exercise material must be downloaded to a Linux computer, and unpacked in your home directory. Use unzip on the command line to extract it:
unzip hidden_word_exercise.zip
This will create the folder unix_tutorial_modified
In this exercise, you will be searching for 12 characters making two words. All characters are hidden in the exercises below. All exercises should be solved using the Unix command line only. Write down the letters you acquire!
NOTE: In these exercises, you will run several small Perl scripts. If you are curious, don't hesitate to open them and try to understand what they do.
The first character is hidden in a file somewhere in the exercise1 directory. Use the commands cd and ls to find the directory with the name solution_1.1. If you went to a wrong directory, you can always type cd .. to go back one level, or cd to go back to the beginning.
1.2 Show a hidden file
Some files are not visible immediately but are instead hidden. Hidden files are recognized by the . in front of their name. To see hidden files, you need to issue the ls -a command. This will allow you to find the second character, hidden in the same directory as the first character.
Go back to the directory exercise_1/directoryB/. When listing its contents, you should see a Perl program. To find the next character, you need to execute the program. You can do this with the command perl <program_name> and the character should appear on your Terminal window.
Go now to exercise_1/directoryC/. To find the fourth character, you first need to find out how big the text file in the directory is. This is done with the command ls -l. This will produce a long format list, where you can see the file size (in bytes), the file's owner, permissions to read and modify it, and the date/time of the last modification. To obtain the fourth character, execute the Perl program file_size_check.pl - the program will ask you to enter the size of the file.
HINT: When typing names of directories or files, try typing the first three characters, and press <TAB>. Unix will try to guess what you are typing.
To find out more letters, navigate to the directory exercise_2.
In the directory exercise_2/, you will find the text file solution_2.1.txt. The fifth character is inside that file. By now you should know at least one way of viewing files.
To find character number six, you will need to create a text file in the exercise_2 directory. On Linux and MacOS, you can do this using for example the editor nano. You can start this program by typing the name of the program followed by the name of the file you want to create (we will name this file solution_2.2.txt):
nano solution_2.2.txt
Add now the exact text Please give me solution 2.2, then save and quit nano. To save a file in nano, press Ctrl+o, to quit Ctrl+x. Afterwards, run the Perl program text_file_check.pl.
Please go to the directory exercise_3.
To find the next two characters, you will have to create a subdirectory named solution in exercise_3 and copy the file codes.txt to it. Use the command mkdir to make directories . For copying files, you can use the command cp <filename from> <filename to>. Use the command ls solution/ afterwards to verify that the file codes.txt is there. Finally, run the Perl program check_code.pl to find the characters.
In the same directory, there is a file junk.txt that does not contain anything useful, and we would like to delete it. To delete it, use the rm <filename> command. Also, there are more files to be deleted in the data directory. To remove more than one file at once, you can use the wildcard *, for example from the directory exercise_3:
rm data/junk*
will remove all the files in data/ at once.
WARNING: On the command line, it is not possible to recover files once deleted. Use the rm command wisely!
To get characters number nine and ten, run the Perl program check_junk.pl after removing all the files.
To find the last 2 characters, move to the directory exercise_4.
exercise_4 contains a text file, which corresponds to the Wikipedia page for Bioinformatics. Have a look at the content of this file with less. As you can
see, it is a rather long file with 269 lines (you can run the command wc -l text.txt to convince yourself). You can also use the command grep to search this file, for example grep bioinformatics text.txt will output to your Terminal all the lines that contain the word bioinformatics.
To discover the last 2 hidden characters, you need to run the Perl program get_last2char.pl, which requires as argument on the command line the number of lines in text.txt that contain the word bioinformatics. Combine grep and wc to help you find this number (hint: the | symbol can be used to combine commands).
Now you should have all the letters you need to make out the hidden word. Show it the assistants to be done with this exercise.
Voilà! This is the end of this tutorial.