Goal: Introduce how to pipe the output of one command into the input of another, and how to redirect the output of a command into a file.
Output Redirection and Pipes
Redirection of output: > vs >>
A redirect sends a channel of output to a file.
A channel refers to standard input/output as well as standard error (not covered here).
You can redirect a file as input to a command using
<and<<(not covered here).
Using pipe “|’
A pipe passes standard output as the standard input to another command
Examples of the form:
View a text file and pipe to grep.
Cat a list and sort by line.
Sort and then find unique items.
View folder contents and look for a specifically named name.
Redirection of output: > vs >>
Remember we can use grep to search a file for some text.
This output is written to the command-line
[intro_to_linux]$ grep -i bayes software.csv
Redirect this output to a file:
[intro_to_linux]$ grep -i bayes software.csv > apps.txt [intro_to_linux]$ ls apps.txt clusters data software.csv [intro_to_linux]$ cat apps.txt
Using a single > will overwrite any existing file of the same name.
[intro_to_linux]$ grep -i IPA software.csv > apps.txt [intro_to_linux]$ cat apps.txt
The apps.txt file now contains the results from the second call.
Using a double >> will append to any existing file of the same name.
[intro_to_linux]$ grep -i bayes software.csv > apps.txt # Appends to the existing file. [intro_to_linux]$ grep -i IPA software.csv >> apps.txt
Example: Using pipe “|” from a file
Over the next set of examples we will pipe together a series of commands that will “generate a file that contains a sorted list of unique terms that include the sub string berry”.
[intro_to_linux]$ cat fruits.txt Gooseberry Apple Apricot Avocado Strawberry ... [intro_to_linux]$ cat fruits.txt | wc -l 97
We could use the wc command as it is normally intended, and confirm the file contains 97 lines.
[intro_to_linux]$ wc -l fruits.txt 97 fruits.txt
Example continued
First step, find all the terms that contain the sub string berry.
# The order of items is the same as listed within the fruits.txt file. [intro_to_linux]$ cat fruits.txt | grep berry Gooseberry Strawberry Bilberry Blackberry Marionberry Blueberry Boysenberry Gooseberry Cloudberry Elderberry Goji berry Honeyberry Juniper berry Cranberry Cranberry Marionberry Gooseberry Mulberry Salmonberry Huckleberry Raspberry Salal berry
Example continued
Second step, sort this list of berry terms into alphabetical order.
# Notice the duplicates. [intro_to_linux]$ cat fruits.txt | grep berry | sort Bilberry Blackberry Blueberry Boysenberry Cloudberry Cranberry Cranberry Elderberry Goji berry Gooseberry Gooseberry Gooseberry Honeyberry Huckleberry Juniper berry Marionberry Marionberry Mulberry Raspberry Salal berry Salmonberry Strawberry
Example continued
Third step, take the sorted list and find unique terms i.e. remove any duplicates.
The way that the uniq command works, you must provide it with a sorted list.
# Duplicates have been removed leaving only the unique names. [intro_to_linux]$ cat fruits.txt | grep berry | sort | uniq Bilberry Blackberry Blueberry Boysenberry Cloudberry Cranberry Elderberry Goji berry Gooseberry Honeyberry Huckleberry Juniper berry Marionberry Mulberry Raspberry Salal berry Salmonberry Strawberry [intro_to_linux]$ cat fruits.txt | grep berry | sort | uniq | wc –l 18
We could pipe this unique list into the wc command to count how many unique terms we have.
Example continued
Fourth step, redirect this output into a file called berries.txt
[intro_to_linux]$ cat fruits.txt | grep berry | sort | uniq > berries.txt [intro_to_linux]$ cat berries.txt Bilberry Blackberry Blueberry Boysenberry Cloudberry Cranberry Elderberry Goji berry Gooseberry Honeyberry Huckleberry Juniper berry Marionberry Mulberry Raspberry Salal berry Salmonberry Strawberry [intro_to_linux]$ cat berries.txt | wc -l 18
Although a simple example, it demonstrates the principle of piping four commands into a single call.
Without using the pipe command you would have had to create intermediate files, to store results, after each command.
As you get more confident, you can create more elaborate pipelines of commands.
Example: Pipe from ls command
This example demonstrates piping the output for a recursive ls call and then finding all the folders/files that contain the Feb string.
[intro_to_linux]$ ls -R [intro_to_linux]$ ls -R | grep "Feb" February ./data/2022/February: Feb ./data/2023/Feb: # Ignore case. [intro_to_linux]$ ls -R | grep -i "Feb" feb ./data/2021/feb: february_01_2021.tx February ./data/2022/February: Feb ./data/2023/Feb:
Exercises: Pipeline
Questions:
How does the
wccommand work? What are its options?How does the
sortcommand work? What are its options?How does the
uniqcommand work? What are its options?How many unique varieties of beans are there in the
vegetables.txtfile?
Answers
4. How many unique varieties of beans are there in the vegetables.txt file?
How do you deal with “soy beans” vs “Soy Beans”?
[intro_to_linux]$ cat vegatables.txt | grep -i beans | sort | uniq -i | wc -l 12
Make sure you are use the commands and options as you intend and understand and be able to describe and explain/justify.
Notice the difference between:
[salexan5@mblog1 intro_to_linux]$ cat vegatables.txt | grep beans | sort ... kidney beans ... soy beans
and
[salexan5@mblog1 intro_to_linux]$ cat vegatables.txt | grep -i beans | sort ... kidney beans kidney BEANS ... soy beans Soy Beans
What happens if you use
beaninstead ofbeans?What does the
uniq -ioption do?
Again: Explore and understand how commands work, and the order they are run in. For example, in your own time, understand if there is a difference between sort | uniq versus uniq | sort?
Previous | Workshop Home | Next |