Perl Tutorial For Bioinformatics

Speaker: Ping-lun Liao

pinglunliao@gmail.com

What is Perl?Perl is an acronym that stands for Practical Extraction and Reporting Language.HistoryWritten by Larry Wall.The three chief virtues of a Perl programmer:LazinessImpatienceHubris

Purpose of PerlWorld Wide Web Programming (CGI)Internet Server Application Programming Interface extensionActiveX script languageSystem Administration choresObject Linking Embedded AutomationNetwork ProgrammingGraphics User Interface

Perl's BenefitsEase of ProgrammingRapid PrototypingPortabilitySpeedProgram Maintenance

SoftwareInterpreterWindowsActivePerlStrawberryPerlLinuxActivePerlperlMac OS XActivePerlPerl Download

IDEPadreEclipse + EPICPerl ExpressOpen Perl IDE

Hello Perl#!/usr/bin/perl# This line is commentprint "Hello Perl";

Save this file as hello.plType perl hello.pl from the MS command line

Hello Perl

perl cmdperl h: print summary of options"perl c: test01.pl": check syntax without running programperl v: version and patch-level of perl"perl W test01.pl": prints warnings about possible bad constructs

perl cmd

User Inputprint "Who are you?\n";$name = ;chomp $name;print "Hello, $name!\n";

name.pl

Data Type(scalars)$variableName(array)@variableName(hash)%variableName

Scalars Perl Perl Perl

-> ++ -- ** ()! ~ \ =~ !~ * / % x + - . >

< > = lt gt le ge

== != eq ne cmp

& AND| OR^ XOR&& AND()|| OR ().. ? : ($a > $b) ? $a : $b;

= +=-=*= , => not NOTand ANDor ORxor XOR

Perl (stringDemo.pl)

(escapes)

stringDemo.pl

Perl Perl $ _

scalarDemo.pl

scalarWithStrDemo.pl

0 '0'"0" ''"" "0" undef

randomDemo.pl

Data Type

Perl (list)()(0 )

("Mmm", "NNN", "Jjj", "Kkk", "Xxx") qw ( Perl )

Perl @ @oklist index index 0 index $#oklist $oklist[0] $oklist[1] $oklist[2] $oklist[$#oklist]

@oklist=(1, 2, 4, 6);@oklist 4 $oklist[0], $oklist[1], $oklist[2], $oklist[3]

$#oklist 3 $oklist[$#oklist] 6@tiny=(); #

arrayDemo1.pl

arrayDemo2.pl

arrayDemo3.pl

for loop: arrayDemo4.pl

foreach: arrayDemo5.pl

poppushshiftunshift

pop:arrayDemo6.pl

push:arrayDemo7.pl

push:arrayDemo8.pl

shift:arrayDemo9.pl

unshift:arrayDemo10.pl

unshift:arrayDemo11.pl

arrayDemo12.pl

arrayDemo13.pl

ASCII:arrayDemo14.pl

arrayDemo15.pl

:arrayDemo16.pl

:arrayDemo17.pl

(key)(value) "/"

${}

%all=("t111222333", "", "s444555666", "", "k333111555", "");

:HashDemo1.pl

reverse //

keys values each /exists delete

keys:HashDemo2.pl

keys:HashDemo3.pl

values:HashDemo4.pl

each/:HashDemo5.pl

exists:HashDemo6.pl

exists:HashDemo7.pl

delete/:HashDemo8.pl

/HashDemo9.pl

my VariableScope.pl

VariableCheck.pl

Flow Control

if if : IfDemo.pl

if if :IfDemo.pl

unlessunless ,:UnlessDemo.pl

until():UntilDemo.pl

untilUntilDemo.pl

forForDemo.pl

whileWhileDemo.pl

foreachForeachDemo.pl

LastDemo.pl

LastDemo.pl

NextDemo.pl

RedoDemo.pl

Subroutine

Subroutines v.s FunctionsSubroutines are chunk of code you defines.Functions are provided by Perl.

Functions

Subroutine

SubMaxDemo.pl

my $a $b

SubMaxDemo.pl

return return Perl

SubGetTimeDemo.pl

Regular Express

(Regular Express)([\w\-])+@([\w\-])+(\.[\w\-])+(Pattern) Perl

BasicPatterns.pl$str =~ /like it/ $str "like it" ()

Perl

BasicPatterns.pl

BasicPatterns.pl

BasicPatterns.pl

BasicPatterns.pl

!~

BasicPatterns.pl

SpecialCharacters.pl$& $` $'

SubstitutingDemo.pl

SubstitutingDemo.pl

SubstitutingDemo.pl

TransformDemo.pl

TransformDemo.pl

TransformDemo.pl

References Perl@Taiwanhttp://www.cyut.edu.tw/~ckhung/b/pl/ by Online Ebook http://www.unix.com.ua/orelly/perl/index.htmPerl