07. Transliterating text tr

The tr command is used as a character-based search and replace function.

Simple Bioinformatics

If you're a bioinformaticist, you may find the need to replace all T characters from a DNA strand to U's to obtain the corresponding mRNA strand. We can do this in a one-liner with the tr command.

$ echo 'CATCGTAGCTAGTCACTG' | tr T U
CAUCGUAGCUAGUCACUG

In biology, each DNA strand has a corresponding strand. G's pair to C's and T's pair to A's. Can we use tr to find the corresponding strand?

$ echo 'CAGTCGTACGTACGT' | tr 'ATGC' 'TACG'
GTCAGCATGCATGCA

Lowercase to Uppercase

You can use this function to map lowercase letters to uppercase.

$ echo 'what is up world?' | tr a-z A-Z
WHAT IS UP WORLD?

From standard in and to standard out

You may also use redirection to direct an input file and write to some output.

$ cat fox.txt
The quick brown fox jumped over the lazy dog.
$ tr 'aeiou' 'AEIOU' < fox.txt
ThE qUIck brOwn fOx jUmpEd OvEr thE lAzy dOg.
$ tr 'aeiou' 'AEIOU' < fox.txt > vowelsCappedFox.txt
# Output to vowelsCappedFox.txt

Deleting specific characters

With the -d option, we can delete specific characters from a string.

$ echo 'Removing all vowels' | tr -d 'aeiou'
Rmvng ll vwls

Squeezing text

We can eliminate repeated instances of a letter with the squeeze option, -s. This removes all repeated characters that occur in sequence.

$ echo '1111112222233333344444' | tr -s 123
12344444

Generating a secret message

We can generate an amateur secret message by mapping our lowercase characters to their inverse correspondence.

$ cat fox.txt | tr a-z zyxwvutsrqponmlkjihgfedcba
Tsv jfrxp yildm ulc qfnkvw levi gsv ozab wlt.

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