Aritalab:Lecture/NGS/Unix commands/Examples

Set Operations

We assume two sets A and B whose elements are listed line by line.

• Set size: the number of elements in set A

wc -l A

• Set inclusion: whether an element k is in set A

$ grep -xc 'k' A

• Set equivalence between two sets A and B

$ diff -q <(sort A | uniq) <(sort B | uniq)

• Set union A ∪ B = C

$ cat A B | sort | uniq > C

• Set intersection A ∩ B = C

$ comm -12 <(sort A | uniq) <(sort B | uniq)

The 'comm -12' command outputs shared lines only. This command can be used to find the set inclusion (whether set A is a subset of B). The following option outputs lines only in the first file (set A), i.e., no output means that A is completely included B.

$ comm -23 <(sort A | uniq) <(sort B | uniq)

Arithmetics

• Simple arithmetic by the shell command echo "$(( ... ))" (no floating number)

echo "$((12345 + 23456))"

• Interactive mode of Perl

perl -E "say 123 / 1.5"