Introduction to PERL and RegExp

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

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

• Client lt-gt Server lt-gt CGI
• Modules for cgi-bin
• CGI, CGI_Lite, example
• Regular Expressions
• Exercises

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Definitions

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

• CPA N
• Comprehensive Perl Archive Network

4
History

• Created by Larry Wall in 1987
• Last major release Perl5 in 1994
• 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

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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.perl.com/pub/q/functionlist

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

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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
• !

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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__

• Modules
• Huge amount of free modules in CPAN repository
• use mod_name
• require mod_name

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Client lt-gt Server lt-gt CGI
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Modules for cgi-bin

• CGI.pm
• use CGI
• cginew CGI
• my seqcgi-gtparam(sequence')
• my _at_databasecgi-gtparam('database')
• Carp.pm
• use CGICarp q(fatalsToBrowser)

• CGI_Lite.pm
• use CGI_Lite
• cginew CGI_Lite
• val cgi-gtparse_form_data
• my seqval(sequence')
• my _at_databasecgi-gtget_multiple_values
  (valdatabase')

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Example

• !/usr/local/bin/perl
• import modules
• use CGICarp q(fatalsToBrowser) makes
  debugging more easy
• use CGI
• read arguments
• cgiCGI-gtnew() create CGI instance
• my _at_interetscgi-gtparam('interets')
• my nomcgi-gtparam('nom')
• my passcgi-gtparam('motdepasse')
• my genrecgi-gtparam('sexe')
• my universitecgi-gtparam('universite')
• select(STDOUT) configure output stream... to
  possibly send error message
• 1 flush buffering to true
• start HTML output
• print "Content-type text/html \n\n"
  required line (HTTP)
• print "ltHTMLgtltHEADgtlt/HEADgtltBODY
  bgcolor'afeeee'gt\n"
• if (genre eq "homme") titre "Monsieur"
  else titre "Madame"
• print "lth2gtltpgtBonjour titre,\nlt/h2gt"
• print "ltpgtVotre nom est ltbgtnomlt/bgt et votre mot
  de passe est ltbgtpasslt/bgt\n"

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Regular Expressions (1)

• 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 !

• 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

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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/
• Modifiers //
• /i case insensitive
• /g global match
• Many other /s,/m,/o,/x...

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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 IP address
  123.456.789.012
• Create a regexp to recognize any email address
  Jean.Dupond_at_isrec.isb-sib.ch
• Create a regexp to change any HTML tag to another
  
• ltaddressgt -gt ltpregt
• On ludwig-sun2 use visual_regexp-1.2.tcl to
  check your regular expressions (requires
  X-windows)

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Exercises

• Exercises URL http//www.isrec.isb-sib.ch/DEA/m
  odule5/P2
• Login to ludwig-sun2
• In your home directory create a subdir called
   public_html 
• In this public_html subdir create another subdir
  called  cgi-bin 
• Place your pages here /home/username/public_html
  
• Place your scripts here /home/username/public_ht
  ml/cgi-bin
• View your pages with http//www.isrec.isb-sib.ch
  /username/mypage.html
• Call the scripts with http//www.isrec.isb-sib.c
  h/cgi-bin/dea/username/myscript.pl

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Exercises HTMLperl cgi-bin

• The goal of this exercise is to take an existing
  pair of files (hits_form.html and dea-hits.pl)
  and analyse how these two files work together.
• hits_form.html is a very simple form to allow the
  retrieval of protein sequences matching with a
  given profile (e.g., UBA, CARD or HECT). This
  form calls a cgi-bin perl script that makes use
  of the "hits" script to interrogate the Hits
  database.
• Modify these two files to allow multiple database
  selection
• Try to modify the perl script to allow
  hyperlinking of the results with the  get_doc 
  script
• Syntax
• http//www.isrec.isb-sib.ch/cgi-bin/get_doc?format
  textdbyyyentryxxx
• xxx entry AC number
• yyy database code (sp, trembl, trest or trgen)

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Exercise interface analyse_seq

• The goal of this exercise is to take an existing
  pair of files (freak.html and freak.pl) and
  analyse how these two files work together, then
  create another pair of files to interface the
  analyse_seq program.
• freak.html is a very simple form to interface the
  EMBOSS program freak, that calculates the gc
  percentage of a DNA sequence and displays it in a
  table or graphically, very similarly to your
  analyse_seq
• (see http//www.uk.embnet.org/Software/EMBOSS/App
  s/freak.html)
• This form calls a cgi-bin perl script (freak.pl )
  that performs the command line action and
  displays the results in a new page.
• Modify these two files to interface your
  analyse_seq instead of freak.
• Textual output of the table is OK.
• Try to modify the perl script to allow a
  graphical output of the results using GNUPLOT
• Check if the user want a graphic output and which
  type
• Create a gnuplot command file and execute it
• Display the gif or pdf output (use  ps2pdf  to
  convert the postscript file to a pdf file).

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Exercises

• Exercises URL http//192.33.215.131/teacher
• Login to your account
• Copy a tar file into
• your home directory cp ../teacher/exdea.tar .
• Untar the file tar xvf exdea.tar
• In your home directory it creates a subdir
  called  public_html 
• Place your pages here /home/username/public_html
  
• Place your scripts here /home/username/public_ht
  ml
• View your pages with http//192.33.215.131/user
  name/mypage.html
• Call the scripts with http//192.33.215.131/use
  rname/myscript.cgi