Wildcards and pipes

Overview

Teaching: 45 min
Exercises: 10 min

Questions

How can I run a command on multiple files at once?

Is there an easy way of saving a command’s output?

Objectives

Redirect a command’s output to a file.

Process a file instead of keyboard input using redirection.

Construct command pipelines with two or more stages.

Explain what usually happens if a program or pipeline isn’t given any input to process.

Required files

If you didn’t get them in the last lesson, make sure to download the example files used in the next few sections:

Using wget — wget https://aniabrown.github.io/hpc-carpentry-shell-WHPC/files/bash-lesson.tar.gz

Using a web browser — https://aniabrown.github.io/hpc-carpentry-shell-WHPC/files/bash-lesson.tar.gz

Now that we know some of the basic UNIX commands, we are going to explore some more advanced features. The first of these features is the wildcard *. In our examples before, we’ve done things to files one at a time and otherwise had to specify things explicitly. The * character lets us speed things up and do things across multiple files.

Ever wanted to move, delete, or just do “something” to all files of a certain type in a directory? * lets you do that, by taking the place of one or more characters in a piece of text. So *.txt would be equivalent to all .txt files in a directory for instance. * by itself means all files. Let’s use our example data to see what I mean.

$ ls

bash-lesson.tar.gz                           SRR307024_2.fastq  SRR307028_1.fastq
dmel-all-r6.19.gtf                           SRR307025_1.fastq  SRR307028_2.fastq
dmel_unique_protein_isoforms_fb_2016_01.tsv  SRR307025_2.fastq  SRR307029_1.fastq
gene_association.fb                          SRR307026_1.fastq  SRR307029_2.fastq
SRR307023_1.fastq                            SRR307026_2.fastq  SRR307030_1.fastq
SRR307023_2.fastq                            SRR307027_1.fastq  SRR307030_2.fastq
SRR307024_1.fastq                            SRR307027_2.fastq

Now we have a whole bunch of example files in our directory. For this example we are going to learn a new command that tells us how long a file is: wc. wc -l file tells us the length of a file in lines.

$ wc -l dmel-all-r6.19.gtf

542048 dmel-all-r6.19.gtf

Interesting, there are over 540000 lines in our dmel-all-r6.19.gtf file. What if we wanted to run wc -l on every .fastq file? This is where * comes in really handy! *.fastq would match every file ending in .fastq.

$ wc -l *.fastq

SRR307023_1.fastq
SRR307023_2.fastq
SRR307024_1.fastq
SRR307024_2.fastq
SRR307025_1.fastq
SRR307025_2.fastq
SRR307026_1.fastq
SRR307026_2.fastq
SRR307027_1.fastq
SRR307027_2.fastq
SRR307028_1.fastq
SRR307028_2.fastq
SRR307029_1.fastq
SRR307029_2.fastq
SRR307030_1.fastq
SRR307030_2.fastq
320000 total

That was easy. What if we wanted to do the same command, except on every file in the directory? A nice trick to keep in mind is that * by itself matches every file.

$ wc -l *

bash-lesson.tar.gz
   542048 dmel-all-r6.19.gtf
dmel_unique_protein_isoforms_fb_2016_01.tsv
   106290 gene_association.fb
SRR307023_1.fastq
SRR307023_2.fastq
SRR307024_1.fastq
SRR307024_2.fastq
SRR307025_1.fastq
SRR307025_2.fastq
SRR307026_1.fastq
SRR307026_2.fastq
SRR307027_1.fastq
SRR307027_2.fastq
SRR307028_1.fastq
SRR307028_2.fastq
SRR307029_1.fastq
SRR307029_2.fastq
SRR307030_1.fastq
SRR307030_2.fastq
  1043504 total

Multiple wildcards

You can even use multiple *s at a time. How would you run wc -l on every file with “fb” in it?
Solution
wc -l *fb*
i.e. anything or nothing then fb then anything or nothing

Using other commands

Now let’s try cleaning up our working directory a bit. Create a folder called “fastq” and move all of our .fastq files there in one mv command.
Solution
mkdir fastq
mv *.fastq fastq/

Redirecting output

Each of the commands we’ve used so far does only a very small amount of work. However, we can chain these small UNIX commands together to perform otherwise complicated actions!

For our first foray into piping, or redirecting output, we are going to use the > operator to write output to a file. When using >, whatever is on the left of the > is written to the filename you specify on the right of the arrow. The actual syntax looks like command > filename.

Let’s try several basic usages of >. echo simply prints back, or echoes whatever you type after it.

$ echo "this is a test"
$ echo "this is a test" > test.txt
$ ls
$ cat test.txt

this is a test

bash-lesson.tar.gz                           fastq
dmel-all-r6.19.gtf                           gene_association.fb
dmel_unique_protein_isoforms_fb_2016_01.tsv  test.txt

this is a test

Awesome, let’s try that with a more complicated command, like wc -l.

$ wc -l * > word_counts.txt
$ cat word_counts.txt

wc: fastq: Is a directory

    53037 bash-lesson.tar.gz
   542048 dmel-all-r6.19.gtf
    22129 dmel_unique_protein_isoforms_fb_2016_01.tsv
        0 fastq
   106290 gene_association.fb
        1 test.txt
   723505 total

Notice how we still got some output to the console even though we “piped” the output to a file? Our expected output still went to the file, but how did the error message get skipped and not go to the file?

This phenomena is an artefact of how UNIX systems are built. There are 3 input/output streams for every UNIX program you will run: stdin, stdout, and stderr.

Let’s dissect these three streams of input/output in the command we just ran: wc -l * > word_counts.txt

stdin is the input to a program. In the command we just ran, stdin is represented by *, which is simply every filename in our current directory.
stdout contains the actual, expected output. In this case, > redirected stdout to the file word_counts.txt.
stderr typically contains error messages and other information that doesn’t quite fit into the category of “output”. If we insist on redirecting both stdout and stderr to the same file we would use &> instead of >. (We can redirect just stderr using 2>.)

Knowing what we know now, let’s try re-running the command, and send all of the output (including the error message) to the same word_counts.txt files as before.

$ wc -l * &> word_counts.txt

Notice how there was no output to the console that time. Let’s check that the error message went to the file like we specified.

$ cat word_counts.txt

    53037 bash-lesson.tar.gz
   542048 dmel-all-r6.19.gtf
    22129 dmel_unique_protein_isoforms_fb_2016_01.tsv
wc: fastq: Is a directory
        0 fastq
   106290 gene_association.fb
        1 test.txt
        7 word_counts.txt
   723512 total

Success! The wc: fastq: Is a directory error message was written to the file. Also, note how the file was silently overwritten by directing output to the same place as before. Sometimes this is not the behaviour we want. How do we append (add) to a file instead of overwriting it?

Appending to a file is done the same was as redirecting output. However, instead of >, we will use >>.

$ echo "We want to add this sentence to the end of our file" >> word_counts.txt
$ cat word_counts.txt

  22129 dmel_unique_protein_isoforms_fb_2016_01.tsv
 471308 Drosophila_melanogaster.BDGP5.77.gtf
      0 fastq
1304914 fb_synonym_fb_2016_01.tsv
 106290 gene_association.fb
      1 test.txt
1904642 total
We want to add this sentence to the end of our file

Chaining commands together

We now know how to redirect stdout and stderr to files. We can actually take this a step further and redirect output (stdout) from one command to serve as the input (stdin) for the next. To do this, we use the | (pipe) operator.

grep is an extremely useful command. It finds things for us within files. Basic usage (there are a lot of options for more clever things, see the man page) uses the syntax grep whatToFind fileToSearch. Let’s use grep to find all of the entries pertaining to the Act5C gene in Drosophila melanogaster.

$ grep Act5C dmel-all-r6.19.gtf

The output is nearly unintelligible since there is so much of it. Let’s send the output of that grep command to head so we can just take a peek at the first line. The | operator lets us send output from one command to the next:

$ grep Act5C dmel-all-r6.19.gtf | head -n 1

X	FlyBase	gene	5900861	5905399	.	+	.	gene_id "FBgn0000042"; gene_symbol "Act5C";

Nice work, we sent the output of grep to head. Let’s try counting the number of entries for Act5C with wc -l. We can do the same trick to send grep’s output to wc -l:

$ grep Act5C dmel-all-r6.19.gtf | wc -l

Note that this is just the same as redirecting output to a file, then reading the number of lines from that file.

Writing commands using pipes

How many files are there in the “fastq” directory we made earlier? (Use the shell to do this.)
Solution
ls fastq/ | wc -l
Output of ls is one line per item so counting lines gives the number of files.

Reading from compressed files

Let’s compress one of our files using gzip.
$ gzip gene_association.fb
zcat acts like cat, except that it can read information from .gz (compressed) files. Using zcat, can you write a command to take a look at the top few lines of the gene_association.fb.gz file (without decompressing the file itself)?
Solution
zcat gene_association.fb.gz | head
The head command without any options shows the first 10 lines of a file

Key Points

The * wildcard is used as a placeholder to match any text that follows a pattern.

Redirect a commands output to a file with >.

Commands can be chained with |

previous episode

HPC Carpentry part 1 - Using the shell

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Wildcards and pipes

Overview

Required files

Multiple wildcards

Solution

Using other commands

Solution

Redirecting output

Chaining commands together

Writing commands using pipes

Solution

Reading from compressed files

Solution

Key Points

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