Introduction to PERL and RegExp

1
Introduction to PERL and RegExp
 Perl is a language of getting your job done 
Larry Wall
2
Course overview

• Introduction to Perl language and Regular
  Expressions
• Introduction to HTML and cgi-bin
• Perl modules and in-liners
• Perl object and references

3
Contents

• Definitions
• PERL, CGI...
• History
• Language basics
• reserved words
• operators
• variables
• subroutines
• modules

• Data Structure
• Interpolation, quoting
• File handling
• Context
• Special variables
• Documents, help
• Regular Expressions
• Exercises

4
Definitions

• PERL
• Practical Extraction and Report Language
• CGI
• Common Gateway Interface

• CPA N
• Comprehensive Perl Archive Network

5
History

• Created by Larry Wall in 1987
• Last major release Perl5 in 1994 (currently Perl
  5.8)
• 1996 creation of the CPAN repository of Perl
  modules and documentation
• Today most cgi-bin behind web pages are perl
  scripts
• Good starting sites
• www.perl.org, www.perl.com, www.cpan.org
• history.perl.org

6
Language basics (1)

• Interpreted, JIT compiled
• Context dependent
• Object programming
• Reserved words
• Many!! E.g. if, else, until, while, for,
  foreach
• Large number of predefined functions
• See http//www.perldoc.com/perl5.8.0/pod/perlfunc.
  html

• In UNIX systems
• /usr/local/bin/perl
• /usr/bin/perl

7
Language basics (2)

• Variables
• Scalar
• var 12 car  abc 
• Array
• _at_var ( a , b , c , d )
• Hash
• var ( a ,first ,b,3)
• var (
•  a  gt  first ,
•  b  gt 3,
• )

• Operators
• - /
• ltlt gtgt
• ! and or not xor
• . x . x
• eq ! neq
• lt lt gt gt
• lt le gt ge
• ltgt cmp
• !

8
Language basics (3)

• Special variables (e.g.)
• _ default input
• process ID
• string of last match
• _at_ARGV cmd-line args
• ENV environment
• Functions
• sub funcname expr
• funcname(parameters)
• Get parameters by _at__

• Comments
• Start with
• End with \n
• Modules
• Huge amount of free modules in CPAN repository
• use mod_name
• require mod_name

9
Data structure

• Scalars
• Integer x 12345
• Float x 123.45
• Scientific x 12.34E5
• Octal x 0123
• Hexadec. x 0xffff
• Binary x 0b1100_1010
• Chains x petit texte

• Arrays / List
• _at_list (un, deux, trois)
• _at_list qw(un deux trois)
• list
• (a,b,c) (un, deux, trois)
• What if ???
• _at_list (un, deux, trois)
• list (un, deux, trois)
• size _at_list
• print list1

10
Data structure

• _at_clefs keys (hash)
• _at_valeurs values (hash)
• foreach k (keys hash)
• print hashk
• Warning the hash does not keep the order

• Hashes
• hash (rouge, 0xff0000, vert, 0x00ff00,
  bleu, 0x0000ff)
• hash (
• rouge gt 0xff0000,
• vert gt 0x00ff00,
• bleu gt 0x0000ff,
• )

11
Data structure

• References
• \ similar to in C
• refarray \_at_array
• What if ???
• refarray1 12
• refarray1 15
• refarray-gt1 18
• print array1

• Nested data structure
• Arrays of arrays
• Hashes of arrays
• Arrays of Hashes
• Hashes of hashes
• And more!

12
Data structure

• Global vs Local
• Lexicals
• my
• our
• Dynamics
• local

• What if ???
• our var A
• while (ltgt)
• var D
• local var B
• print var
• my var C
• print var
• last
• print var

13
Interpolation, quoting

• The quotes have different significations
• price 100
• print the price is price
• This is called interpolation

• Quoting (interpolated)
• q// (chain)
• qq// (chain)
• qx// (execute)
• ( ) qw// (word list)
• // m// (motif match)

14
File handling

• Opening a file
• open(LIRE, filename)
• Reading from a file
• line ltLIREgt
• Writing to a file
• open(ECRIRE, gtfilename)
• print ECRIRE line
• Closing a file
• close(LIRE) close(ECRIRE)

• Special handlers
• STDOUT, STDIN, STDERR
• Select(STDOUT)
• Piping
• open(PIPE, ls -1 )
• _at_filelist ltPIPEgt
• Other system calls
• system(command)
• exec(command, options, filename)

15
File testing

• File operators
• -rwxo
• -e exists
• -z empty
• -s not empty (return size)
• -f simple file
• -d directory
• -l symbolic link

• Example
• open (READ, filename) if -f filename
• What if ???
• foreach (_at_ARGV)
• next unless -f
• fsize -s _
• print("_ is fsize bytes long.\n")

16
Context

• Scalar
• a _at_b
• Boolean
• while (_at_a) shift _at_a
• List
• (a) _at_b
• Empty
• () f(a)
• Interpolation
• a b

17
Special variables

• INC hash of modules
• _at_INC list of lib directories
• ENV hash of env variables
• _at_ARGV list of arguments
• _at__ auto list
• _ auto var
• _at_F in liner -a option

• pid
• 0 program name
• autoflush
• string of last match
• / record delimiter
• V PERL version

18
Documents, help, debugging

• perl -h
• perldoc ltkeywordgt
• Web help
• www.perl.org
• www.perl.com
• Books
• OReilly

• Debugging?
• use strict
• use warnings or -w
• -d (debug mode)
• man perldebug

19
Calling perl

• perl file.pl
• or in an executable use shebang
• !/usr/bin/perl

• Check syntax
• perl -c file.pl

20
Exercises 1.1 and 1.2 on paper

• 1.1 Write a little Hello World application
• 1.2 Write a quadratic equation solver (polynomial
  of the 2nd degree)
• It should solve ax2bxc0 by taking a,b and c
  values on the command-line and print x1 and x2 or
  tell if the equation is not solvable (deltalt0)

21
Regular Expressions

• Idea powerful way to search for text patterns
• Literal (or normal characters)
• Alphanumeric
• abcABC0123...
• Punctuation
• -_ ,.()/ ?!\ltgt"_at_
• Metacharacters
• Ex ls .java
• Flavors
• awk, egrep, Emacs, grep, Perl, POSIX, Tcl,
  PROSITE !

22
Patterns are regular expressions

• Pattern ltA-x-ST(2)-x(0,1)-V
• Regexp A.ST2.?V
• Text The sequence must start with an alanine,
  followed by any amino acid, followed by a serine
  or a threonine, two times, followed by any amino
  acid or nothing, followed by any amino acid
  except a valine.
• Simply the syntax differ

23
Regular Expressions (1)

• In Perl
• Start and End of line
• start, end
• Match any of several
• ()
• Match 0, 1 or more
• . any, ? 0 or 1, 1 or more, 0 or more
• m,n range
• ! negation

• Examples
• Match every instance of a SwissProt AC
• m/OPQ0-9A-Z0-930-9/
• m/OPQ\dA-Z0-93\d/
• Match every instance of a SwissProt ID
• m/A-Z0-91,4_A-Z0-93,5/

24
Regular Expressions (2)

• Escape character or back reference
• \char or \num
• Shorthand
• \d digit 0-9
• \s whitespace space\f\n\r\t
• \w character a-zA-Z0-9_
• \D\S\W complement of \d\s\w
• Byte notation
• \num character in octal
• \xnum character in hexadecimal
• \cchar control character

• Match operator
• m//
• var m/colou?r/
• var ! m/colou?r/
• Substitution operator
• s///
• var s/colou?r/couleur/
• Translate operator
• tr///
• revcomp tr/ACGT/tgca/
• Modifiers //
• /i case insensitive
• /g global match
• Many other /s,/m,/o,/x...

25
Regular Expressions (3)

• Grouping
• External reference
• var s/sp\(\w\d5)/swissprot AC1/
• Internal reference
• var s/tr\(\w\d5)\\1/trembl AC1/
• Numbering
• 1 to 9
• 10 to more if needed...

• Exercises
• Create a regexp to recognize any pseudo IP
  address 123.456.789. 12
• Create a regexp to recognize any email address
  Jean.Dupond_at_isb-sib.ch
• Create a regexp to change any HTML tag to another
  
• ltaddressgt -gt ltpregt
• On sib-dea
• use visual_regexp-1.2.tcl to check your regular
  expressions (requires X-windows)

26
Regular Expressions (4)
27
Solution 1.1

• !/usr/local/bin/perl
• print "Hello World!\n"
• exit 0

28
Solution 1.2
!/usr/local/bin/perl my (a, b, c) _at_ARGV if
(a eq '' b eq '' c eq '') die ("missing
variable!") my delta bb - 4ac if
(delta 0) my x -b/2a
print "delta 0, one solution only x x\n"
elsif (delta gt 0) my x1
(-bsqrt(delta))/2a my x2
(-b-sqrt(delta))/2a print "delta gt
0, two solutions x1 x1, x2 x2\n"
else print "delta lt 0, no
solutions!!" exit 0
29
Solution RegExp

• /\d1,3\.3\d1,3/
• /\w\.\w\_at_\w\-\w\.a-z2,3/
• /\lt(\/?)address\gt/\lt1pre\gt/
• generalized
• address \w