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• cut -f <field_number(s)> extracts one or more fields (-f) from each line of its input
  • -d <delim> to change the field delimiter (Tab by default)
• sort sorts its input using an efficient algorithm
  • by default sorts each line lexically
    • one or more fields to sort can be specified with one or more -k <start_field_number>,<end_field_number> options
  • has options to sort numerically (-n), or numbers-inside-text (version sort -V)
  • -t <delim> to change the field delimiter (whitespace -- one or more spaces or Tabs – by default)
• uniq -c counts groupings of its input (which must be sorted) and reports the text and count for each group
  • use cut | sort | uniq -c for a quick-and-dirty histogram (see piping a histogram)

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  GREP GREP

  grep -P '<pattern>' searches for <pattern> in its input and outputs only lines containing it
  • always enclose <pattern> in single quotes to inhibit shell evaluation!
  • -P says use Perl patterns, which are much more powerful than standard grep patterns
  • -c says just return a count of line matches
  • -n says include the line number of the matching line
  • -v (inverse match) says return only lines not matching the pattern
  • -L says return only the names of files containing no pattern matches
  • -l says return only the names of files that do contain the mattern match
  • <pattern> can contain special match meta-characters and modifiers such as:
    • ^ – matches beginning of line
    • $ – matches end of line
    • .  – (period) matches any single character
    • * – modifier; place after an expression to match 0 or more occurrences
    • + – modifier, place after an expression to match 1 or more occurrences
    • \s – matches any whitespace (\S any non-whitespace)
    • \d – matches digits 0-9
    • \w – matches any word character: A-Z, a-z, 0-9 and _ (underscore)
    • \t matches Tab
    • \r matches Carriage return
    • \n matches Linefeed
    • [xyz123] – matches any single character (including special characters) among those listed between the brackets [ ]
      
      • this is called a character class.
      • use [^xyz123] to match any single character not listed in the class
    • (Xyz|Abc) – matches either Xyz or Abc or any text or expressions inside parentheses separated by | characters
      • note that parentheses ( ) may also be used to capture matched sub-expressions for later use
  • Regular expression modules are available in nearly every programming language (Perl, Python, Java, PHP, awk, even R)
    • each "flavor" is slightly different
    • even bash has multiple regex commands: grep, egrep, fgrep.
  • This Wiki page: Tips and tricks#Regularexpressionsingrep,sedandperl from another CBRS course has more on using regular expressions on the command line, in grep, sed (string editor) and perl.
  • There are many good online regular expression tutorials, but be sure to pick one tailored to the language you will use.
    • here's a great step-by-step intro tutorial: https://regexone.com/
    • this Ryan's tutorial is also excellent: https://ryanstutorials.net/linuxtutorial/
    • and another here's a good general one:   https://www.regular-expressions.info/
    • and a perl regex tutorial: http://perldoc.perl.org/perlretut.html
      • perl regular expressions are the "gold standard" used in most other languages

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  AWK_script AWK_script

  awk '<script>' a powerful scripting language that is easily invoked from the command line
  • <script> is applied to each line of input (generally piped in)
    • always enclose <script> in single quotes to inhibit shell evaluation
  • General structure of an awk script:
    • BEGIN{<expressions>}  –  use to initialize variables before any script body lines are executed
      • e.g. BEGIN{FS=":"; OFS="\t"; sum=0} says
        • use colon (:) as the input field separator (FS), and Tab (\t) as the output field separator (OFS)
          
          • the default input field separator (FS) is whitespace
            • one or more spaces or tabs
          • the default output field separator (OFS) is a single space
        • initialize the variable sum to 0
    • {<body expressions>}  – expressions to apply to each line of input
      • use $1, $2, etc. to pick out specific input fields
      • e.g. {print $3,$4} outputs fields 3 and 4 of the input, separated by the output field separator.
    • END{<expressions>} – executed after all input is complete (e.g. print a sum)
  • Here is an excellent awk tutorial, very detailed and in-depth
    •  take a look once you feel comfortable with the example scripts we've gone over in class.

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