29: Miscellaneous Unix power commands

  Wurm lab

The following examples introduce some other Unix commands, and show how they could be used to work on a fictional file called file.txt. Remember, you can always learn more about these Unix commands from their respective man pages with the man command. These are not all real world cases, but rather show the diversity of Unix command-line tools:

  • View the penultimate 10 lines of a file (using head and tail commands):
tail -n 20 file.txt | head
  • Show lines of a file that begin with a start codon (ATG) (the ^ matches patterns at the start of a line):
grep "^ATG" file.txt
  • Cut out the 3rd column of a tab-delimited text file and sort it to only show unique lines (i.e. remove duplicates):
cut -f 3 file.txt | sort -u
  • Count how many lines in a file contain the words ‘cat’ or ‘bat’ (-c option of grep counts lines):
grep -c '[bc]at' file.txt
  • Turn lower-case text into upper-case (using tr command to ‘transliterate’):
tr 'a-z' 'A-Z' < file.txt
  • Change all occurences of ‘Chr1’ to ‘Chromosome 1’ and write changed output to a new file (using sed command):
sed 's/Chr1/Chromosome 1/g' file.txt > file2.txt