Introduction to programming in Perl

What is Perl ?

Perl : Practical Extraction and Report Language by Larry Wall in 1987

• Text-processing language

• Glue language

• Very high level language

• perl is the language compiler/interpreter program

A first example#!/usr/bin/perl # shebang line # Pragmas use strict; # Restrict unsafe constructs use warnings; # Provide helpful diagnostics

# Assign 15 to $number1 my $number1 = 15;

# Assign 25 to $number2 my $number2 = 25;

# Assign 11 to $number3 my $number3 = 11;

$number1 = $number1 + $number2; # $number1 contains 40 $number1 = $number1 + $number3; # $number1 contains 51 print “My result is : $number1\n”; # Print the result on the terminal

Scalar Data Type

• $answer = 36; # an integer

• $pi = 3141659265 # a real number

• $avocados = 6.02e23; # scientific notation

• $language = “Perl”; # a string

• $sign1 = “$language is nice”; # string with interpolation

• $sign2 = ‘$language is nice’; # string without interpolation

Scalar = singular variable

$ --> S

Scalar Binary Operators$u = 17 $v = 3 $s = “Perl”

Name Example Result

Addition $u + $v 17 + 3 = 20

Subtraction $u -$v 17 -3 = 14

Multiplication $u * $v 17 * 3 = 51

Division $u / $v 17 / 3 = 5.66666666667

Modulus $u % $v 17 % 3 = 2

Exponentiation $u ** $v 17 ** 3 = 4913

Concatenation $s . $s “Perl”. “Perl”= “PerlPerl”

Repetition $s x n “Perl”x 3 = “PerlPerlPerl”

Context $u = “12”+ 5; $u = “12john”+5; $u = “john12”+ 5; use strict; $u = “john12”+ 5;Argument “john12”isn’t numeric in addition (+) at line 3 5

$u = “12”+ 5; 17

Array data type

$data[0] = 35; $data[1] = 12.4; $data[2] = “bye\n”; $data[3] = 1.7e23; $data[4] = ‘Hi’; @data = (35, 12.4, “bye\n”, 1.7e23,

‘Hi’) Array = plural variable @ -->a

35

12.4

“bye\n”i

1.7e23

‘Hi’

1

2

3

4

5

Array operators@let = (“J”, “ P ”, “ S ”, “ D ”, “ C ”);

pop $r=pop(@let) $r=“C” @let=(“ J ”, “P”, “ S ”, “ D ”)

push push(@let,”G”) @let=(“J”,”P”,”S”,”D”,”C”,”G”)

shift $r=shift(@let) $r=“J” @let=(“P”,”S”,”D”,”C”)

unshift unshift(@let,”G”) @let=(“G”,”j”,”P”,”S”,”D”,”C”)

splice @a=splice(@let,1,2) @a=(“P”,”S”) @let=(“J”,”D”,”C”)

join $r=join(‘:’,@let) $r=“J:P:S:D:C”

scalar $r=scalar(@let) $r=5

reverse @a=reverse(@let) @a=(“C”,”D”,”S”,”P”,”J”)

Search for a name #!/usr/bin/perl use strict; use warnings;my @names = (“John”, “Peter”, “Simon”, “Dave”, “Chris”); my $offset = int(rand(scalar(@names))); # random index in [0, ..., 4]

if ($names[$offset] eq”Simon”) { # block start for the if statement print “Simon is found\n”; print “Success!\n”;} # block end for the if statement else { # block start for the else statement print “Simon is not found\n”; print “Failed!\n”;

} # block end for the else statement

Comparison operators Comparison Numeric String Return Value

Equal == eq 1 if $a is equal to $b, otherwise “”

Not equal != ne 1 if $a is not equal to $b, otherwise “”

Less than < lt 1 if $ais less than $b, otherwise “”

Greater than > gt 1 if $a is greater than $b, otherwise “”

Less than or equal <= le 1 if $a is not greater than $b, otherwise “”

Greater than or equal >= ge 1if $ais not less than $b, otherwise “”

Comparison <=> cmp 0 if $a and $b are equal, 1 if is greater, -1 if $b is greater

“”is the empty string

Match =~ Not match !~

What is true or false?

･ Any number is true except for 0.

･ Any string is true except for “”and “0”.

･ Anything else converted to a true value string or a true value number is true.

･ Anything that is not true is false.

Logical operators Example Name Result

$a && $b AND $a if $a is false, $b otherwise

$a || $b OR $a if $ ais true, $b otherwise

! $a NOT True if $a is not true, false otherwise

$a and $b AND $a if $a is false, $b otherwise

$a or $b OR $a if $a is true, $b otherwise

not $a NOT True if $a is not true, false otherwise

$a xor $b XOR True if $a or $b is true, false if both are true

$xyz = $x || $y || $z is not the same as $xyz = $x or $y or $y ! Use parentheses !

Conditional statements

･ Simple

Statement if (Expression);

･ Compound

if (Expression) Block

if (Expression) Block else Block

if (Expression) Block elsif (Expression) Block else Block

Loop statements

･ Simple

Statement while (Expression);

･ Compound

while (Expression) Block

for (Initialization; Expression; Incrementing) Block

Loop statement

foreach localvar (listexpr){

statement_block;

}

Until (<expression>) {

<statement_block>

}

Reading from a file#!/usr/bin/perl

use strict; use warnings;

print “Enter the filename: ”; my $filename = <STDIN>; # Read Standard Input for a filename chomp($filename); # Remove the end of line character if (! (-e $filename)) { # Test whether the file exists print “File not found\n”; exit 1; }open(IN, $filename) || die “Could not open $filename\n”; my @names = <IN>; # Store the content of the file in an array close(IN);

print @names;

Input file

John

Peter

Simon

Dave

Chris

Input and output functions open Open FILEHANDLE, EXPR Open a file to referred

using FILEHANDLE

close Close FILEHANDLE Close the file associated with FILEHANDLE

print Print [FILEHANDLE] LIST Print each element of LIST to FILEHANDLE

open GENE, "< /picb/home40/zhouyao/snp/gene.txt"; #open file->gene list

open SNP, "> /picb/home40/zhouyao/snp/snpout.txt"; #save file

Packages #!/usr/bin/perl

BEGIN{push@INC,'/picb/home40/zhouyao/Library/perl/'};

open GENE, "< /picb/home40/zhouyao/snp/gene.txt"; #open file->gene list

open SNP, "> /picb/home40/zhouyao/snp/snpout.txt"; #save file

chomp(@gene = <GENE>);

$url = "http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?id_type=snp_id&id_val=&disease_category=dl0&disease_name=0&search_mode=gene&gene_name=$gene&chr=1&start_pos=&end_pos=";

use LWP::Simple;

#!/usr/bin/perl

use strict;

use warnings;

use MyTools;

my $filename1 = “data1.txt”;

my $filename2 = “data2.txt”;

my %data1 = MyTools::get_data($filename1);

my %data2 = MyTools::get_data($filename2);

$, = “”; # set the print separator

print keys %data1, “\n”, values %data1, “\n”;

print keys %data2, “\n”, values %data2, “\n”;

References

Recommend book: “Beginner Learning Perl”, 4th Edition

by Randal Schwartz, Tom Phoenix & Brian D Foy

Perl 中文教程： www.sun126.com/perl5/

Perl bbs:www. Perlchina.org

Thank you!