Perl Tutorial

Bioinformatics Orientation 2008

Eric Bishop

Adapted from slides found at:

www.csd.uoc.gr/~hy439/Perl.ppt
original author is not indicated 1
Why Perl?
 Perl is built around regular expressions
 REs are good for string processing
 Therefore Perl is a good scripting language
 Perl is especially popular for CGI scripts
 Perl makes full use of the power of UNIX
 Short Perl programs can be very short
 “Perl is designed to make the easy jobs easy,
without making the difficult jobs impossible.” --
Larry Wall, Programming Perl

2
Why not Perl?
 Perl is very UNIX-oriented
 Perl is available on other platforms...
 ...but isn’t always fully implemented there
 However, Perl is often the best way to get some
UNIX capabilities on less capable platforms
 Perl does not scale well to large programs
 Weak subroutines, heavy use of global variables
 Perl’s syntax is not particularly appealing

3
 Perl Example 1

#!/usr/bin/perl
#
# Program to do the obvious
#
print 'Hello world.'; # Print a message

4
Understanding “Hello World”
 Comments are # to end of line
 But the first line, #!/usr/local/bin/perl,
tells where to find the Perl compiler on your
system
 Perl statements end with semicolons
 Perl is case-sensitive

5
Running your program
 Two ways to run your program:
 perl hello.pl

 chmod 700 hello.pl

./hello.pl

6
 Scalar variables
 Scalar variables start with $
 Scalar variables hold strings or numbers, and
they are interchangeable
 When you first use (declare) a variable use the
my keyword to indicate the variable’s scope
 Not necessary but good programming practice
 Examples:
 my $priority = 9;
 my $priority = “A”;

7
 Arithmetic in Perl
$a = 1 + 2; # Add 1 and 2 and store in $a
$a = 3 - 4; # Subtract 4 from 3 and store in
$a
$a = 5 * 6; # Multiply 5 and 6
$a = 7 / 8; # Divide 7 by 8 to give 0.875
$a = 9 ** 10; # Nine to the power of 10, that
is, 910
$a = 5 % 2; # Remainder of 5 divided by 2
++$a; # Increment $a and then return
it
$a++; # Return $a and then increment
8
Arithmetic in Perl cont’d
 You sometimes may need to group
terms
 Use parentheses ()
 (5-6)*2 is not 5-(6*2)

9
 String and assignment
operators
$a = $b . $c; # Concatenate $b and
$c
$a = $b x $c; # $b repeated $c
times

$a = $b; # Assign $b to $a
$a += $b; # Add $b to $a
$a -= $b; # Subtract $b from $a
10
Single and double quotes
 $a = 'apples';
 $b = 'bananas';
 print $a . ' and ' . $b;
 prints: apples and bananas
 print '$a and $b';
 prints: $a and $b
 print "$a and $b";
 prints: apples and bananas
11
 Perl Example 2

#!/usr/bin/perl
# program to add two numbers

my $a = 3;
my $b = 5;
my $c = “the sum of $a and $b and 9 is: ”;
my $d = $a + $b + 9;
print “$c $d\n”;

12
Exercise 1
 Modify example 2 to print (12 -9 )*3
 (don’t do it in your head!)

13
 if statements

if ($a eq “”)
{
print "The string is empty\n";
}
else
{
print "The string is not empty\n";
}
14
Tests
 All of the following are false:
0, '0', "0", '', "”, “Zero”
 Anything not false is true
 Use == and != for numbers, eq and
ne for strings
 &&, ||, and ! are and, or, and not,
respectively.

15
 if - elsif statements

if ($a eq “”)
{ print "The string is empty\n"; }
elsif (length($a) == 1)
{ print "The string has one character\
n"; }
elsif (length($a) == 2)
{ print "The string has two characters\n";
}
else 16
 while loops
#!/usr/local/bin/perl

my $i = 5;
while ($i < 15)
{
print ”$i";
$i++;
}

17
 do..while loops
#!/usr/local/bin/perl
my $i = 5;
do
{
print ”$i\n";
$i++;
}
while ($i < 15” && $i != 5);
18
for loops

 for (my $i = 5; $i < 15; $i++)

{
print "$i\n";
}

19
last
 The last statement can be used to exit a loop before it
would otherwise end

for (my $i = 5; $i < 15; $i++)

{
print "$i,";
if($i == 10)
{
last;
}
}
print “\n”;
when run, this prints 5,6,7,8,9,10
20
next
 The next statement can be used to end the current loop iteration
early

for (my $i = 5; $i < 15; $i++)

{
if($i == 10)
{
next;
}
print "$i,";
}
print “\n”

when run, this prints 5,6,7,8,9,11,12,13,14

21
Standard I/O
 On the UNIX command line;
 < filename means to get input from this file
 > filename means to send output to this file
 STDIN is standard input
 To read a line from standard input use:
my $line = <STDIN>;
 STDOUT is standard output
 Print will output to STDOUT by default
 You can also use :
print STDOUT “my output goes here”;
22
 File I/O
 Often we want to read/write from specific files
 In perl, we use file handles to manipulate files
 The syntax to open a handle to read to a file for reading is
different than opening a handle for writing
 To open a file handle for reading:
open IN, “<fileName”;
 To open a file handle for writing:
open OUT, “>fileName”;

 File handles must be closed when we are finished

with them -- this syntax is the same for all file
handles
close IN; 23
File I/O cont’d
 Once a file handle is open, you may use
it just like you would use STDIN or
STDOUT
 To read from an open file handle:
 my $line = <IN>;
 To write to an open file handle:
 print OUT “my output data\n”;

24
 Perl Example 3
#!/usr/bin/perl
# singlespace.pl: remove blank lines from a file
# Usage: perl singlespace.pl < oldfile > newfile

while (my $line = <STDIN>)

{
if ($line eq "\n")
{
next;
}
print "$line";
}
25
Exercise 2
 Modify Example 3 so that blank lines
are removed ONLY if they occur in first
10 lines of original file

26
 Arrays
 my @food = ("apples", "bananas",
"cherries");
 But…
 print $food[1];
 prints "bananas"
 my @morefood = ("meat", @food);
 @morefood now contains:
("meat", "apples", "bananas", "cherries");

27
 push and pop
 push adds one or more things to the end of a
list
 push (@food, "eggs", "bread");
 push returns the new length of the list
 pop removes and returns the last element
 $sandwich = pop(@food);
 $len = @food; # $len gets length of
@food
 $#food # returns index of last element
28
@ARGV: a special array
 A special array, @ARGV, contains the
parameters you pass to a program on
the command line

 If you run “perl test.pl a b c”, then within

test.pl @ARGV will contain (“a”, “b”, “c”)

29
 foreach
# Visit each item in turn and call it
$morsel

foreach my $morsel (@food)

{
print "$morsel\n";
print "Yum yum\n";
}

30
Hashes / Associative arrays
 Associative arrays allow lookup by name rather than
by index
 Associative array names begin with %
 Example:
 my %fruit = ("apples”=>"red",
"bananas”=>"yellow", "cherries”=>"red");

 Now, $fruit{"bananas"} returns "yellow”

 To set value of a hash element:

$fruit{“bananas”} = “green”;

31
Hashes / Associative Arrays II
 To remove a hash element use delete
 delete $fruit{“bananas”};

 You cannot index an associative array, but you can use the
keys and values functions:

foreach my $f (keys %fruit)

{
print ("The color of $f is " . $fruit{$f} . "\n");
}

32
 Example 4
#!/usr/bin/perl

my @names = ( "bob", "sara", "joe" );

my %likesHash = ( "bob"=>"steak", "sara"=>"chocolate",
"joe"=>"rasberries" );

foreach my $name (@names)

{
my $nextLike = $likesHash{$name};
print "$name likes $nextLike\n";
}
33
 Exercise 3
 Modify Example 4 in the following way:
 Suppose we want to keep track of books
that these people like as well as food

Bob likes The Lord of the Rings

Sara likes Hitchhiker’s Guide to the Galaxy

Joe likes Thud!
 Modify Example 4 to print each person’s
book preference as well as food preference

34
Regular Expressions
 $sentence =~ /the/
 True if $sentence contains "the"
 $sentence = "The dog bites.";
if ($sentence =~ /the/) # is false
 …because Perl is case-sensitive
 !~ is "does not contain"

35
 RE special characters

. # Any single character except a

newline

^ # The beginning of the line or string

$ # The end of the line or string

* # Zero or more of the last character

+ # One or more of the last character 36

 RE examples

^.*$ # matches the entire string

hi.*bye # matches from "hi" to "bye"

inclusive

x +y # matches x, one or more blanks,

and y

^Dear # matches "Dear" only at

beginning 37
 Square brackets

[qjk] # Either q or j or k
[^qjk] # Neither q nor j nor k
[a-z] # Anything from a to z
inclusive
[^a-z] # No lower case letters
[a-zA-Z] # Any letter
[a-z]+ # Any non-zero sequence of38
 More examples
[aeiou]+ # matches one or more
vowels
[^aeiou]+ # matches one or more
nonvowels
[0-9]+ # matches an unsigned
integer
[0-9A-F] # matches a single hex digit
[a-zA-Z] # matches any letter 39
 More special characters
\n # A newline
\t # A tab
\w # Any alphanumeric; same as [a-zA-Z0-
9_]
\W # Any non-word char; same as [^a-zA-
Z0-9_]
\d # Any digit. The same as [0-9]
\D # Any non-digit. The same as [^0-9]
\s # Any whitespace character
\S # Any non-whitespace character 40
Quoting special characters

\| # Vertical bar
\[ # An open square bracket
\) # A closing parenthesis
\* # An asterisk
\^ # A carat symbol
\/ # A slash
\\ # A backslash
41
 Alternatives and parentheses

jelly|cream # Either jelly or cream

(eg|le)gs # Either eggs or legs

(da)+ # Either da or dada or

# dadada or...

42
The $_ variable
 Often we want to process one string
repeatedly
 The $_ variable holds the current string
 If a subject is omitted, $_ is assumed
 Hence, the following are equivalent:
 if ($sentence =~ /under/) …
 $_ = $sentence; if (/under/) ...

43
Case-insensitive substitutions
 s/london/London/i
 case-insensitive substitution; will replace
london, LONDON, London, LoNDoN,
etc.
 You can combine global substitution
with case-insensitive substitution
 s/london/London/gi

44
split
 split breaks a string into parts

 $info = "Caine:Michael:Actor:14,
Leafy Drive";
@personal = split(/:/, $info);
 @personal =
("Caine", "Michael", "Actor", "14,
Leafy Drive");
45
 Example 5
#!/usr/bin/perl

my @lines = ( "Boston is cold.",

"I like the Boston Red Sox.",
"Boston drivers make me see red!" );

foreach my $line (@lines)

{
if ($line =~ /Boston.*red/i )
{
print "$line\n";
}
} 46
Exercise 4
 Add the folowing to @lines in Example
5: “In Boston, there is a big Citgo sign
that is red and white.”
 Now modify Example 5 to print out only
the same two lines as before

47
Calling subroutines
 Assume you have a subroutine printargs
that just prints out its arguments
 Subroutine calls:

 printargs("perly", "king");

Prints: "perly king"

 printargs("frog", "and", "toad");


Prints: "frog and toad"

48
 Defining subroutines
 Here's the definition of printargs:
 sub printargs
{ print join(“ “, @_) . ”\n"; }

 Parameters for subroutines are in an array called @_

 The join() function is the opposite of split()


Joins the strings in an array together into one string

The string specified by first argument is put between
the strings in the arrray

49
 Returning a result
 The value of a subroutine is the value of the
last expression that was evaluated
sub maximum
{
if ($_[0] > $_[1])
{ $_[0]; }
else
{ $_[1]; }
}

$biggest = maximum(37, 24);

50
 Returning a result (cont’d)
 You can also use the “return” keyword to return a
value from a subroutine
 This is better programming practice

sub maximum
{
my $max = $_[0];
if ($_[1] > $_[0])
{ max = $_[1]; }
return $max;
}
$biggest = maximum(37, 24); 51
 Example 6
#!/usr/bin/perl

sub inside
{
my $a = shift @_;
my $b = shift @_;
$a =~ s/ //g;
$b =~ s/ //g;
return ($a =~ /$b/ || $b =~ /$a/);
}
if( inside("lemon", "dole money") )
{
print "\"lemon\" is in \"dole money\"\n";
}
52
 Exercise 5
 Create a new subroutine, doesnotstart
which, given 2 strings, tests that neither
string starts with the other one
 doesnotstart(abc, abcdef) will be false
 doesnotstart(doggy, dog) will be false
 doesnotstart(bad dog, dog) will be true

53
The End

54