Master datatypes 2011

Data Types in Perl

Bioinformatics master course, ‘11/’12

Paolo Marcatili

Agenda
•  Perl Basics
•  Hello World
•  Scalars
•  Arrays
•  Hashes


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Task Today


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Parsing

Parse a ﬁle
Sort its words alphabetically
Sort its words by number of occurences


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Perl Basics


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PERL

Practical Extraction
and Reporting Language

ü  Handle text ﬁles
ü  Web (CGI)
ü  Small scripts

http://www.perltutorial.org/


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Install

Windows
http://www.activestate.com/activeperl/
Cygwin (linux emulation)

Linux / OS-X
Native


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Hello World!


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First script
Open an editor (e.g. gedit)

#!/usr/bin/perl -w
use strict;
use warnings;
print "Hello World!n";

Save as -> ﬁrst.pl


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How to run a script
Terminal -> move to the script folder

perl first.pl

or
chmod a+x first.pl <- now it is executable by

everyone
./first.pl <- ./ means ‘in this folder’


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Variable Overview


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Overview
Data types
Casting
Variable Scope
(De)referencing


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Data Types

(1,1,2,3,5,8)
Mamma:3381245671
5
Hello world!

ACCGACGACGCAGC
J
1.6e-4
6.28


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Overview
Scalars

arrays

hashes
5
(1,1,2,3,5,8)
Mamma:3381245671

Hello world!

J

ACCGACGACGCAGC

6.28

1.6e-4


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Scalars


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Scalars
my $scalar;
$scalar=5;
$scalar=$scalar+3;
$scalar= “scalar vale $scalarn”;
print $scalar;

> scalar vale 8


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Scalars - 2
ü  Scalar data can be number or string.
ü  In Perl, string and number can be used "
nearly interchangeable."

ü  Scalar variable is used to hold scalar data.
ü  Scalar variable starts with dollar sign ($) "
followed by Perl identiﬁer.
ü  Perl identiﬁer can contain "
alphanumeric and underscores.
ü  It is not allowed to start with a digit.


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Examples
#ﬂoating-point values
my $x = 3.14;
my $y = -2.78;

#integer values
my $a = 1000;
my $b = -2000;

my $s = "2000"; # similar to $s = 2000;

#strings
my $str = "this is a string in Perl".
my $str2 = 'this is also as string too'.


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Operations
my $x = 5 + 9; # Add 5 and 9, and then store the result in $x
$x = 30 - 4; # Subtract 4 from 30 and then store the result in $x
$x = 3 * 7; # Multiply 3 and 7 and then store the result in $x
$x = 6 / 2; # Divide 6 by 2
$x = 2 ** 8; # two to the power of 8
$x = 3 % 2; # Remainder of 3 divided by 2
$x++; # Increase $x by 1
$x--; # Decrease $x by 1

my $y = $x; # Assign $x to $y
$x += $y; # Add $y to $x
$x -= $y; # Subtract $y from $x
$x .= $y; # Append $y onto $x


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Operations - 2
my $x = 3;
my $c = "he ";
my $s = $c x $x; # $c repeated $x times
my $b = "bye";
print $s . "n"; #print s and start a new line
# similar to
print "$sn";
my $a = $s . $b; # Concatenate $s and $b
print $a;
# Interpolation
my $x = 10;
my $s = "you get $x";
print $s;


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Type Casting
(or
data
conversion,
or
coercion)
is
usually
silent
in
perl

my $x = “3”;
print $x + 4 .”n”;

Be careful!!

my $x = "3";
my $y = 1;
my $z = "uno";
print $x + $y."n";
print $x + $z."n";
print $x + 4 . 1 ."n";
print $x + 4.1 ."n";


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Arrays


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boxed scalars

Scalar
Array

Indices
are
sequen6al
integers
star6ng
from
0


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array - 1

("Perl","array","tutorial");
(5,7,9,10);
(5,7,9,"Perl","list");
(1..20);
();


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array - 2

my @str_array=("Perl","array","tutorial");
my @num_array=(5,7,9,10);
my @mixed_array=(5,7,9,"Perl","list");
my @rg_array=(1..20);
my @empty_array=();

print $str_array[1]; # 1st element is [0]


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operations
my @int =(1,3,5,2);
push(@int,10); #add 10 to @int
print "@intn";

my $last = pop(@int); #remove 10 from @int
print "@intn";

unshift(@int,0); #add 0 to @int
print "@intn";
my $start = shift(@int); # add 0 to @int
print "@intn";


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on array
my @int =(1,3,5,2);

foreach my $element (@int){
print “element is $elementn”;
}

my @sorted=sort(@int);
foreach my $element (@sorted){
print “element is $elementn”;
}


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Hashes


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Hashes
•  Hashes are like array, they store collections of scalars"
... but unlike arrays, indexing is by name (just like in
real life!!!)"

•  Two components to each hash entry:
–  Key

example : name
–  Value

example : phone number

•  Hashes denoted with %
–  Example : %phoneDirectory

•  Elements are accessed using {} (like [] in arrays)


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Hashes continued ...
•  Adding a new key-value pair
$phoneDirectory{“Shirly”} = 7267975

–  Note the $ to specify “scalar” context!
•  Each key can have only one value
$phoneDirectory{“Shirly”} = 7265797
# overwrites previous assignment

•  Multiple keys can have the same value

•  Accessing the value of a key
$phoneNumber =$phoneDirectory{“Shirly”};


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Hashes and Foreach
•  Foreach works in hashes as well!

foreach $person (keys (%phoneDirectory) )

{

print “$person: $phoneDirectory{$person}”;

}

•  Never depend on the order you put key/values
in the hash! Perl has its own magic to make
hashes amazingly fast!!


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Hashes and Sorting
•  The sort function works with hashes as well
•  Sorting on the keys
foreach $person (sort keys %phoneDirectory) {
print “$person : $directory{$person}n”;
}
–  This will print the phoneDirectory hash table in
alphabetical order based on the name of the person,
i.e. the key.


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Hash and Sorting cont...
•  Sorting by value

foreach $person (sort {$phoneDirectory{$a} <=>
$phoneDirectory{$b}} keys %phoneDirectory)

{

print “$person :

$phoneDirectory{$person}n”;

}

–  Prints the person and their phone number in the
order of their respective phone numbers, i.e. the
value.


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Exercise
•  Chose your own test or use wget "

•  Identify the 10 most frequent words

•  Sort the words alphabetically"

•  Sort the words by the number of
occurrences


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Counting Words
my %seen;
my $l=“Lorem ipsum”;
my @w=split (“ “, $l);# questa è una funzione nuova…
foreach my $word (@w){

$seen{$word}++;
}
print “Sorted by occurrencesn”;
foreach my $word (sort {$seen{$a}<=>$seen{$b}} keys %seen){

print “Word $word N: $seen{$word}n”;
}

print “Sorted alphabeticallyn”;
foreach my $word (sort ( keys %seen)){

print “Word $word N: $seen{$word}n”;
}


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Homeworks
Download the “Divina commedia”
(wget
http://www.gutenberg.org/cache/epub/1000/pg1000.txt )

For each word length, count the number of occurences (e.g.
123456 words of length 2, etc.)

Length of a string : length($a)


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Modalità
di
esame:

Diﬃcoltà:
febbraio
<
giugno
<
seBembre

Per
fare
l’esame
è
NECESSARIO

avermi
mandato
tuM
i
compi6

e
una
esercitazione


Paolo Marcatili

Master datatypes 2011

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