Bash and Linux - Text Tools (grep, cut, sort, uniq, tr)

Before you begin, take a few minutes to check what you already know and how confident you feel. You will see the same questions again at the end of the module — this helps both you and us measure what you have learned. Click an option for every question and confidence rating, then click Next to continue.

Most of what you will do at a Linux terminal is text wrangling - finding lines, picking columns, sorting, counting. These five commands are the workhorses. Each does one tiny job; the magic happens when you chain them with pipes. By the end, the question "how do I extract X from this file?" will have an obvious shape: pick a tool per stage, glue with |.

• grep - find lines that match a pattern.
• cut - pick columns or character ranges from each line.
• sort - sort lines alphabetically or numerically.
• uniq - squash adjacent duplicate lines (often paired with sort).
• tr - translate or delete individual characters.

grep prints every line of its input that contains a given pattern. Simplest form: grep PATTERN FILE.

$ grep P-002 diagnoses.csv
P-002,61,M,172,88,152,95

Here are some useful flags that can make grep more useful.

• -i - case insensitive ("hypertension" or "Hypertension" both match).
• -v - INVERT - show lines that do NOT match.
• -c - just count matching lines.
• -n - prefix each match with its line number.
• -r - recursive: search every file under a folder.
• -l - list only the FILENAMES that have a match.
• -w - whole word match (so "F" does not match "Female").
• -E - extended regular expressions (alternation with |, +, etc.).

The PATTERN is a regular expression, not a literal string. This is where characters like . * [ ] have special meaning. For a literal dot, escape with \. or use grep -F (fixed strings).

$ grep '@nus.edu.sg' emails.txt # dots are regex "any character"
$ grep -F '@nus.edu.sg' emails.txt # literal match

$ echo -e 'hypertension
diabetes
Hypertension' > dx.txt
$ grep h dx.txt
$ grep -i h dx.txt
$ grep -v h dx.txt

$ grep ,M, cohort_2026.csv | head -n 3
$ grep -c ,F, cohort_2026.csv
$ grep -c ,M, cohort_2026.csv

cut pulls out part of each line. The most common shape is "columns from a delimited file": say what the separator is with -d and which fields (columns) with -f.

$ cat cohort_2026.csv
patient_id,age,sex,height_cm,weight_kg,systolic,diastolic
P-001,54,F,168,72,138,84
P-002,61,M,172,88,152,95
$ cut -d, -f1 cohort_2026.csv
patient_id
P-001
P-002
$ cut -d, -f1,6 cohort_2026.csv
patient_id,systolic
P-001,138
P-002,152

Field numbers start at 1, not 0. Pick a range with -f2-4 or open-ended -f2- (column 2 to the end). For TSV files use -d$'\t' (the dollar-sign quoting tells bash to interpret \t as a real tab).

$ cut -d, -f3 cohort_2026.csv
$ cut -d, -f6,7 cohort_2026.csv

The sort command is essential for rearranging lines in text files.

$ cat dx.txt
hypertension
diabetes
asthma
$ sort dx.txt
asthma
diabetes
hypertension

By default, it sorts alphabetically, but it becomes incredibly powerful when combined with various flags.

• sort -n - numeric sort (3 comes before 11; default would put 11 first).
• sort -r - reverse order.
• sort -k2 - sort by the SECOND whitespace-separated column.
• sort -t, -k6 - sort by column 6 in a comma-separated file.
• sort -u - dedupe as you sort (same as sort | uniq).

$ sort -t, -k6 -n cohort_2026.csv

uniq removes duplicate lines that are right next to each other. It does not find duplicates anywhere in the file - they have to be adjacent. That is why you almost always pipe sort | uniq.

$ cat sex_column.txt
F
F
M
F
$ sort sex_column.txt | uniq
F
M
$ sort sex_column.txt | uniq -c
  3 F
  1 M

uniq -c (count) is by far the most useful form. Combined with sort -rn it gives you "top items by frequency" in one pipeline: sort | uniq -c | sort -rn.

# Top ages in the cohort, most frequent first
tail -n +2 cohort_2026.csv |
  cut -d, -f2 |
  sort | uniq -c | sort -rn |
  head

tr works one character at a time. Two main forms: replace each character in set A with the matching character in set B, or delete every character in set A.

$ echo 'Hello World' | tr 'a-z' 'A-Z'
HELLO WORLD
$ echo 'P-001 P-002 P-003' | tr ' ' ','
P-001,P-002,P-003
$ echo 'BMI=28.4' | tr -d 'A-Z='
28.4

tr only reads from stdin - it does NOT take a filename. Pipe a file in with cat or <:

$ tr 'a-z' 'A-Z' < notes.txt > NOTES_LOUD.txt

$ cat notes.txt | tr 'a-z' 'A-Z'
$ head -n 2 cohort_2026.csv | tr ',' ' '

You have reached the end of the module. Try the same questions again — your answers here, paired with your pre-test answers, are how we measure what the module taught you. Answer every question and confidence rating, then click Submit and see results to view your score.

Here is how your post-test answers compare with your pre-test answers. The pre/post pairing is the most reliable way to see what this module actually taught you.