Introduction to PERL modules

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Introduction to PERL modules
 There is more than one way to do it 
Larry Wall
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Contents

• Subroutines
• Procedures vs functions
• Internal or external?
• Packages/Modules
• Namespace/Typeglob
• Import/Export
• Includes
• Objects?

• In-liners
• Examples
• Exercises

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Subroutines (procedure, function)

• defining subroutine
• sub myfunc
• my param shift(_at__)
• return result
• calling function
• calcul myfunc(value)

• defining subroutine
• sub myproc
• my param shift(_at__)
• return
• calling procedure
• myproc(value)

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Call internal code?

• Script 1

• Script 2

f(param) call
f(param) call
sub f
sub f
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Call external code!

• Script 1

• Module Mymod

use Mymod Mymodf(param) call

• Script 2

sub f
use Mymod Mymodf(param) call
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Create a module

• Structure of module Mymod.pm
• package Mymod
• sub f
• sub g
• 1

• Calling the functions in a script
• use Mymod
• Mymodf(param)
• a Mymodg()

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Namespace

• Symbol table
• Every variable, function, handler is stored in a
  table of symbols (namespace)
• use can pollute your namespace
• default package main

• Typeglob (or aliases)
• Possibility to import variables from one package
  to another
• OnePackdick \OtherPackrichard
• Thus dick function eq richard function
• dick \richard
• Thus dick eq richard, but _at_dick ne _at_richard !!

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Export symbols
two essential lines in a package require
Exporter our _at_ISA (Exporter) inherits
from Exporter export by default our _at_EXPORT
qw(cat canis carnivore) export on demand our
_at_EXPORT_OK qw(tiger)
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Import symbols
use Animals import all _at_EXPORT symbols use
Animals() import nothing use Animals qw(cat
tiger) import tiger and cat use Animals
qw(/ca/) import carnivore and cat use Animals
qw(/\/) import all scalars More generally,
use Animals LIST is equivalent to BEGIN
require Animals import Animals LIST
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Includes

• List of directories to search for modules
• _at_INC
• Modify with pragma lib before compilation
• use lib ENVHOME/libperl adds /libperl

• Once started the list of loaded modules is
  available in a hash
• INC

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Modules and Objects

• An object is a reference
• A class is a package
• A method is a function
• A class inherits through _at_ISA array

• The method new is the constructor
• Example
• use CGI
• cgi new CGI instantiate
• call an instance method
• nom cgi-gtparam(Nom)
• call a class method
• CGI-gtnph(1)

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PERL In-liners
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In-liners some options

• -a autosplit (only with -n or -p)
• -c check syntax
• -d debugger
• -e pass script lines
• -h help
• -i direct editing of a file
• -n loop without print
• -p loop with print
• -v version

• Example
• perl -e 'print qq(hello world\n)'

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In-liners -n and -p

• perl -pe s/\r/\n/g ltfilegt
• is equivalent to
• open READ, file
• while (ltREADgt)
• s/\r/\n/g
• print
• close(READ)

• perl -i -pe s/\r/\n/g ltfilegt
• The -i option modifies the file directly
• perl -ne is the same without the print

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In-liners -a (only with -n or -p)

• perl -ane print _at_F, \n ltfilegt
• is equivalent to
• open READ, file
• while (ltREADgt)
• _at_F split( )
• print _at_F, \n
• close(READ)

• Example
• hits -b 'sw' -o pff2 prfCARD perl -ane 'print
  join("\t", reverse(_at_F)),"\n"'

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In-liners -a (only with -n or -p)

• hits -b 'sw' -o pff2 prfCARD

• swICEA_XENLA 1 90 prfCARD 5
  -1 18.553
• swRIK2_MOUSE 435 513 prfCARD 5
  -11 15.058
• swCARC_HUMAN 1 88 prfCARD 6
  -1 15.395
• swNAL1_HUMAN 1380 1463 prfCARD 7
  -1 15.058
• swASC_HUMAN 113 195 prfCARD 7
  -2 15.374
• swCAR8_HUMAN 347 430 prfCARD 8
  -1 18.343
• swCARF_HUMAN 134 218 prfCARD 9
  -1 12.932

• hits -b 'sw' -o pff2 prfCARD perl -ane 'print
  join("\t", reverse(_at_F)),"\n"'

18.553 -1 5 prfCARD 90 1
swICEA_XENLA 15.058 -11 5
prfCARD 513 435
swRIK2_MOUSE 15.395 -1 6 prfCARD
88 1 swCARC_HUMAN 15.058 -1
7 prfCARD 1463 1380
swNAL1_HUMAN 15.374 -2 7 prfCARD
195 113 swASC_HUMAN 18.343 -1
8 prfCARD 430 347
swCAR8_HUMAN 12.932 -1 9 prfCARD
218 134 swCARF_HUMAN
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In-liners examples

• perl -e print int(rand(100)),"\n" for 1..100'
  perl -e 'x_1 while ltgtprint sort altgtb
  keys x'

• for(i0ilt100i)
• nb int(rand(100))
• hashnb 1
• print sort altgtb keys hash

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In-liners extract FASTA from SP

• open (READ, /db/proteome/ECOLI.dat) open
  file
• while (lineltREADgt) read line by line until
  the end
• if(line /ID (\w)/) print gt1\n
  print fasta header
• if(line / /)
• line s/ //g remove spaces
• print line print sequence line
• close(READ)

• cat /db/proteome/ECOLI.dat perl -ne if (/ID
  (\w)/) print"gt1\n" if(/ /) s/ //g print

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In-liners your turn

• Create an In-liner that extracts non-redundant
  FASTA format sequences from a redundant database
  in SwissProt format

• cat /db/proteome/ECOLI.dat perl -ne ' if (/ID
  (\w)/) print "gt1\n if(/ /) s/ //g
  print' perl -e 'while(ltgt) if (/gt/) i_
  xi"" xi._ print values x

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Exercises 4.1 and 4.2

• Create a Perl module MyHTML.pm containing 4
  functions
• htmlHeader prints the HTTP header and
  ltHTMLgtltBODYgt tags
• htmlFooter prints lt/BODYgt and lt/HTMLgt tags and
  close
• htmlError calls htmlHeader, prints an error
  message, calls htmlFooter
• addLink gets a string, check for links, add
  them, return modified string (see exercise 3.1)
• Modify script of Exercise 3.1 by removing the
  internal function calls and replace them by calls
  to the module MyHTML.pm.
• Create a Perl In-liner that reads a database in
  SwissProt format and creates a non-redundant list
  of all the keywords (from KW lines).
• Optional count each occurence of the same
  keyword...