Tapping the power of Unix

Wildcards, redirection to files, and pipes

Covered topics: working with multiple files using wildmasks, standard output redirection to a file, constructing complex commands with Unix pipes.

  1. open http://bit.ly/bashfile in your browser, it’ll download the file bfiles.zip
  2. unpack bfiles.zip to your home directory; you should see ~/data-shell
$ cd <parentDirectoryOf`data-shell`>
$ ls data-shell
$ cd data-shell/molecules
$ ls
$ ls p*   # this is a Unix wildcard; bash will expand it to 'ls pentane.pdb propane.pdb'
$ ls *.pdb      # another wildcard, will expand to "ls cubane.pdb ethane.pdb ...'
$ wc -l *.pdb   # list number of lines in each file
$ wc -l *.pdb > lengths.txt   # redirect the output of the last command into a file
$ more lengths.txt
$ sort -n lengths.txt   # sort numerically, i.e. 2 will go before 10, and 6 before 22
$ sort -n lengths.txt > sorted.txt
$ head -1 sorted.txt    # show the length of the shortest (number of lines) file
$ wc -l *.pdb | sort -n | head -1   # three commands can be shortened to one - this is called Unix pipe

Standard input of a process. Standard output of a process. Pipes connect the two.

Question 10

Running ls -F in ~/Desktop/Shell/Users/nelle/sugars results in:

analyzed/  glucose.dat  mannose.dat  sucrose.dat  fructose.dat  maltose.dat  raw/

What code would you use to move all the .dat files into the analyzed sub-directory?

Question 11

In a directory we want to find the 3 files that have the least number of lines. Which command would work for this?

  1. wc -l * > sort -n > head -3
  2. wc -l * | sort -n | head 1-3
  3. wc -l * | head -3 | sort -n
  4. wc -l * | sort -n | head -3
Question `ps` Use ps command to see how many processes you are running on the training cluster. Explore its flags.
Question 18 Using Unix pipes, write a one-line command to show the name of the longest .pdb file (by the number of lines). Paste your answer into the chat.
Question 19 Combine ls and head and/or tail into a one-line command to show three largest files (by the number of bytes) in a given directory. Paste your answer into the chat.
Question `echo with wildcards` What will the command echo directoryName/* do? Try answering without running it. How is this output different from ls directoryName and ls directoryName/*?
Question `redirection` Redirection 1> and 2> and /dev/null
Question `command separators` ; vs. && separators, e.g. mkdirr tmp; cd tmp

You can watch a video for this topic after the workshop.