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Command line 2

General

General review (see also below)

  • whoami
  • pwd
  • clear (Ctrl+l)
  • ls (-l, -a, -G, -lh, -d, -d */, -1, -F); ls /Users/djb/Documents/data-shell

History and tab completion

Review

  • history (up and down arrows)
  • !580
  • !!
  • tab: 1) Filename completion, 2) Command completion
  • Editing the command line: Ctrl + a, Ctrl + e, Ctrl + u, Option + click (Mac only)
  • file /Users/djb/Documents/myfile.txt

And something new

  • !$: last word of last command
  • Ctrl+r: initiate (or continue) history search

Getting around the file system review

  • cd or cd ~: go to your home directory
  • cd -: go back to the directory you came from
  • cd .. go up one level
  • cd /Users/djb/Documents/data-shell: To to specified directory

Working with directories

  • mkdir: make directory
    • What’s a good name for a directory?
    • What’s a good directory structure for a project?
  • mkdir -p a/b/c: create intermediate directories
  • rmdir: remove empty directory
  • rm -rf: remove directory and its contents recursively (careful!)

Working with files

  • cp: copy
    • cp oldfile newfile copy a file
    • cp oldfile1 oldfile2 newdirectory: copy multiple files
    • cp -r olddirectory newdirectory copy directory recursively
  • mv: rename / move
    • Rename a file or directory
    • Move a file or directory to a different location (optionally rename)
  • rm: delete (careful—deletion is forever!)
  • rm -i: delete after asking permission
  • Editing and saving files (in your editor of choice)
    • Mac default is TextEdit
    • Or install BBEdit
    • Or use vim from the command line
    • What’s a good filename?
  • less /Users/djb/Documents/myfile.txt (space, b, q, /, ?, n, G , G1)

Wildcards (“globbing”; annoyingly different from regex)

Examples

  • *.xml (files ending in “.xml”)
  • *.x?l (files ending in “.x” followed by any single letter followed by “l”, e.g., XML [xml], XSLT [xsl], XProc [xpl] files)
  • *.x[ms]l (files ending in “.x” followed by “m” or “s” followed by “l”, e.g., XML and XSLT files, but not XProc)

Regex vs globbing

  • Regex: * and ? are repetition indicators for the preceding item
  • Globbing: * and ? are wildcards
  • Glob * = regex .*
  • Glob ? = regex .?

Practice with ls in data-shell/molecules

Reading from and writing to files

  • stdin, stdout, stderr
  • <: input from file
  • >: output to file (careful: overwrites existing files with the same name)
  • >>: append to file (creates file if it doesn’t already exist)
  • 2>: error messages to file (2> /dev/null)

Save file listings with ls, file contents with cat, or command-line text with echo.

Filters

About filters

  • Filters are programs that accept input on stdin and produce output on stdout.
  • Stdin defaults to the keyboard and stdout defaults to the screen, but both can be redirected to or from a file or a pipe.
  • Filters can be chained together to form computational pipelines.

First filters

  • cat (one or more files)
  • wc (-l lines, -w words, -c characters)

Redirect input, contrast wc file, wc < file

Filters and piping

  • | pipes output of process on the left into input of process on the right
  • head (-10, or any other number, or -n 10)
  • tail (-10, or any other number, or -n 10)
  • sort (-r reverse, -u unique, -n numeric); numeric vs alphabetic sorting
  • uniq (only on sorted input)

Practice

In data-shell/north-pacific-gyre/2012-07-03 (experimental results; imagine hundreds of files):

  • wc -l *.txt
  • wc -l *.txt | sort -n | head -n 5 (one is too short; bad data)
  • wc -l *.txt | sort -n | tail -n 5 (notice “Z”)
  • ls *Z.txt
  • ls *AB[].txt
  • ls *[^AB].txt