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UNIX commands. Head More (press Q to exit) Cat Example cat file Example cat file1 file2 Grep Grep –v ‘expression’ Grep –A 1 ‘expression ’ Grep –B 2 ‘expression ’ Example: grep –v ‘#’ file.txt to remove comments Expression metacharacters $ end of line $ beginning of line
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UNIX commands • Head • More (press Q to exit) • Cat • Example cat file • Example cat file1 file2 • Grep • Grep –v ‘expression’ • Grep –A 1 ‘expression’ • Grep –B 2 ‘expression’ • Example: grep –v ‘#’ file.txt to remove comments • Expression metacharacters • $ end of line • $ beginning of line • [AB] A or B • * any character • Example: ‘CDKN*’ or ‘chr[1-7]’
UNIX commands • Cut • cut –f 1 • cut –f 3 –d ‘:’ • Sort • sort –n • sort –nr (or sort –n –r) • sort –k 2 • uniq • uniq • uniq -c • wc • wc –l file.txt • Example: cut –f 1 file | sort | uniq -c
UNIX commands • Sed • Sed ‘s/foo/bar/g’ file: find and replace • Awk • Awk ‘$3>2000’ file : select row with 3rd field>2000 • Awk ‘{if ($3>2000) print $1,$2}’ file only print first 2 columns • Awk ‘{sum+=$3} END {print sum}’ file print sum of column 3 • Awk ‘{sum+=$3} END {print sum/NR}’ file print average of column 3 • Join • join –j 1 sorted_file1 sorted_file2
