Things covered here:
Redirectors and wildcards
To be sure we are still working in the same place, let’s run:
When we are talking about “redirectors” here, we are referring to things that change where the output of something is going. The first we’re going to look at is called a “pipe” (
A pipe (
|) is used to connect multiple commands. It takes the output from the previous command and “pipes” it into the input of the following command.
Let’s look at an example. Remember we used
wc -l to count how many lines were in a file:
wc -l example.txt
ls lists the files and directories in our current working directory:
If we “pipe” (
ls command into the
wc -l command, instead of printing the output from
ls to the screen as usual, it will go into
wc -l which will print out how many items there are:
ls | wc -l
For another example, let’s look at what’s in the subdirectory, “data/all_samples/”:
That prints out a lot of stuff, let’s see how many things are in that directory:
ls data/all_samples/ | wc -l
We’ll get back to making sense of that when we get to wildcards in the next section.
Another important character is the greater than sign,
>. This tells the command line to redirect the output to a file, rather than just printing it to the screen as we’ve seen so far.
For an example of this we will write the output of
ls to a new file called “directory_contents.txt”:
ls ls > directory_contents.txt
Notice that when we redirect the output with the
>, nothing printed to the screen. And we’ve just created a file called “directory_contents.txt”:
ls head directory_contents.txt
It’s important to remember that the
> redirector will overwrite the file we are pointing to if it already exists.
ls experiment/ > directory_contents.txt head directory_contents.txt
If we want to append an output to a file, rather than overwrite it, we can use two of them instead,
ls >> directory_contents.txt head directory_contents.txt
Wildcards as used at the command line are special characters that enable us to specify multiple items very easily. The
?are probably the most commonly used, so let’s try them out!
The asterisk (*)
As we’ve seen,
ls lists the contents of the current working directory, and by default it assumes we want everything:
But we can be more specific about what we’re interested in by giving it a positional argument that narrows things down. Let’s say we only want to look for files that end with the extension “.txt”. The
* wildcard can help us with that.
Here’s an example:
What this is saying is that no matter what comes before, if it ends with “.txt” we want it.
At the command line, the
*means any character, any number of times (including 0 times).
For a more practical example, let’s change directories into that messy subdirectory we saw earlier:
cd data/all_samples/ ls ls | wc -l
So there are 900 files here, and it looks like there are 3 different extensions: “.txt”; “.tsv”, and “.fq” (a common extension for the “fastq” format, which holds sequences and their quality information).
ls *.txt | wc -lAh good, it's nice when things make sense 🙂
ls *.tsv | wc -l
ls *.fq | wc -l
So far we’ve just been using the
* wildcard with the
ls command. But wildcards can be used with many of the common Unix commands we’ve seen so far.
For example, we can use it with the
mv command to move all 300 of the “.fq” files into their own directory at once:
ls | wc -l mkdir fastq_files ls fastq_files/ ls *.fq mv *.fq fastq_files/ ls fastq_files/ ls | wc -l
Note: When using wildcards, running
lsfirst like done in the above example (
ls *.fq) is good practice before actually running a command. It is a way of checking that we are specifying exactly what we think we are specifying.
BONUS ROUND: History!
The shell also keeps track of our previous commands for us. There are a few different ways we can take advantage of this, one is by using the
history command. But that alone will print all of it to the screen. It can be more practical to “pipe” (
|) that into something else like
tail to see the last few commands:
history | tail
less so we can scroll through our previous commands:
history | less
To get out of
less, press the
We can also use the up and down arrows at the command line to scroll through previous commands. This is useful for finding commands, but it’s also useful for making sure we are acting on the files we want to act on when using wildcards. As mentioned above, we can check first with
ls *.fq, press
return to see we are acting on the files we want, and then press the up arrow to bring up the previous command, and change it to what we want without altering the “*.fq” part of the command – as we already know it’s correct. Any time we can remove the chance of human error, we should 🙂
mkdir text_files ls *.txt mv *.txt text_files mkdir tsv_files ls *.tsv mv *.tsv tsv_files lsIt doesn't matter what the directories are named, but at the end they should be the only 3 things in the working directory 🙂
The question mark (?)
At the command line, the
?wildcard represents any character that appears only one time.
To see how this can be needed at times when the
* won’t do, let’s change into the “fastq_file” subdirectory:
And let’s say we wanted only the “.fq” files for samples 10-19. If we tried to grab those with the
*, we’d get more than we wanted:
* allows for any character any number of times, it is also grabbing those in the 100s. But if we use the
? wildcard, which only allows any character one time, we get only the samples we want:
They may seem a little abstract at first, but redirectors and wildcards are two fundamental concepts of working at the command line that help make it a very powerful environment to work in. Just knowing they exist and generally what they do means that we can learn more about them when needed 🙂
Special characters introduced:
||a “pipe” allows stringing together multiple commands|
||sends output to a file (overwrites target file)|
||sends output to a file (appends to target file)|
||represents any character appearing any number of times|
||represents any character appearing only once|