:!: Page under costruction

Command Line: first commands

Today we will use a first set of commands.

General rules

  • :!: Read carefully each paragraph before typing commands.
  • :!: Use the TAB completion. Always.
  • :!: Strictly follow the instructions using the suggest filenames: creativity is not a positive quality for Bash beginners ;)

Enter in your VM, and restore your screen.

If you need help, see:

The general syntax is: ls [options] [files]. Both the options and the files are optional, and files can be files of directories. Now we introduce some of the options:

Option Description
-a Also show hidden files
-l Long format, will show one file per line, with size, owner, date…
-h Used with -l, will display file size in human readable format (e.g. 2.3Mb instead of 2298011 )
-d Show directories as files, without listing their content

The options can be combined together, the following two commands are identical:

ls -l -h -a
ls -lha

If we want to list the files present at the root, we don't need to move there, but simply ask ls which path to scan for you:

ls /

Here another example:

ls /homes/qib/examples/

You can type as many paths (files or directories) as needed in a single ls command:

ls -l ~/.bashrc ~/.screenrc /homes/qib/examples/

Using the "shell expansion": wildcards to select multiple files

As we noticed, ls can receive more than one file. Usually, though, we don't type each single item to be listed, but rather we use wildcards, then the shell will expand our shortcuts into a list of paths. There are wildcards, ranges and lists to be used.

Symbol Meaning Example
* Any set of characters (any length) *.fasta: all files ending with “.fasta”
? A single character A???.txt: files starting with A, followed by exactly 3 chars, endin by “.txt”
[a-z] Range: any single lowercase letters file1[a-c].txt: files called file1a, file1b and file1c, ending with “.txt”
[0-9] Range, any single digit reads_R[1-2].fastq: reads_R1.fastq and reads_R2.fastq
 {a,b} Comma separated list of words photo_{andrea,john}.jpg: photo_andrea.jpg and photo_john.jpg

There is a directory with some example files. First we will copy it to our home using the cp (copy) command and the -r (recursive) switch, since we want also the content of the directory1):

cp -r /homes/qib/examples/ ~ 

We should be in our home directory. Check with pwd, in case type cd to quickly return to your home directory.

To enter the new directory, type (remember the TAB):

cd examples

Now, using cd and ls try figuring out:

  • How many directories are inside the examples directory2)
  • The content of each directory3)

Creating a directory, coping some files

Create a directory called copies inside the examples directory. There are many ways: if you are already inside “examples”, just:

mkdir copies

Otherwise you have to craft the proper relative or absolute path.

Let's try again to copy some files. In particular we want a selection of files inside the phage directory:

# If we are not inside the examples directory:
cd ~/examples/
# Copy some files
cp -v phage/*.f?? copies/

In this case we use a new switch, -v (verbose) that will print all the files copied (useful when we want to see the progress). Using both * and ? wildcards we select all the files having an extension of three chars, the first being “f” (e.g. fna, faa).

:!: This feature has been removed

This server has a sort of cinema, to play recorded screencasts directly at the command line. The command is playdemo followed by the name of the film you want to see (type “playdemo” alone to see some titles). Example:

# See a small cinema on "find"
playdemo find

The find command can print all the files from a starting path, including directories and subdirectories.

Some examples:

# Print all files and directories in my home
find ~
# Print all files and directories in a specific path
find /usr/lib/ssl
# Print only directories / files
find ~ -type d
find ~ -type f
# Print files in a home with a specific extension
find ~ -name "*.txt"

The simples command is cat (concatenate), that can print the content of one or more files. Example:

cat ~/examples/files/wine.csv

Can you type it using a relative path?

When a file is very large, it's very convenient to have a look at a fraction of it. The commands head and tail allows to print only the first (or last) lines of a file. By default 10 lines, but you can change this with -n:

head ~/examples/files/wine.csv
head -n 3 ~/examples/files/wine.csv
tail -n 5 ~/examples/files/wine.csv

Do you remember man? Good, as we can now use a new command to interactively view text files that will behave as man:

# Run it, then press 'q' to exit:
less ~/examples/phage/vir_genomic.gff
# To disable wordwrap and see clearly the lines:
less -S ~/examples/phage/vir_genomic.gff

Counting the number of lines of a file is a common task. The wc (wordcount) command can do this, and something more.

# Count lines, words, characters of a file:
wc ~/examples/files/introduction.txt
# Count only lines:
wc -l ~/examples/files/introduction.txt
# Also on multiple files
wc -l ~/examples/phage/*.*

grep is a powerful command to extract lines containing a pattern. The simples use is “grep wordtosearch file”:

grep ">" ~/examples/phage/vir_protein.faa

In this case the word we looked for is simply the > character, that is, we extracted all the lines containing it. We are not going to expand this, but you can perform complex searches using a language called regular expressions.

Some switches: -c to count the number of matching lines, -i to perform a case insensitive search, -v to print the lines not containing the pattern.

So far every command we issues gave us some text lines that we inspected, but we never saved them for long term storage. Consider the following command:

find ~/examples -type d

If we want to save the output in a new file, the shell offer us a redirection symbol:

find ~/examples -type d > ~/examples/directories.txt

With this command we created a new file, called ~/examples/directories.txt, where the output of find was stored. Note that if the file was already present, it would have been overwritten!

Our commands print two type of text

We explained the behaviour of most commands as a set of characters printed on our screen. This is a simplification: the characters printed can be either real output or user messages (technically called standard output and standard error). The '>' sign will redirect the standard output (or STDOUT), but sometimes we are interested in the standard error (or STDERR). Try:

weather.pl > ~/weather.out

What can you note?

weather.pl 2> ~/weather.err

Now you know how to redirect the standard error (i.e. using 2>).

Let's make a real world example: when we align short reads against the reference we expect the output to be the alignments (in SAM/BAM format), but the program can be interested in printing some user information (e.g. alignment progress, how many unmapped reads…), so will use the standard error.

Go to your home directory. Try counting the lines from two files you choose inside your home, plus /etc/passwd. 4)

Now count the lines of /etc/passwd, but using a relative path! 5)

Go to the ~/examples/scripts/ and try to list the files included in the ~/examples/scripts/files, using the relative path. 6)

Finally, always from the ~/examples/scripts/ directory. Save into a file called phage_files_lines.txt placed inside your home the number of lines of each file inside the examples/phage directory. Use only relative paths. 7)


there are 4 subdirs
archives contains 2 files, files 7, phage 17 and finally scripts 2
An example can be
wc -l examples/files/introduction.txt  examples/phage/md5checksums.txt  /etc/passwd
Something like
wc -l ../../../etc/passwd
ls -l ../files/
wc -l ../phage/*.* > ../../phage_files_lines.txt