1. The Scripting Programming Language
PERL
The Scripting Programming Language

2. Perl is a programming language.
#!/usr/bin/perl 1
WHAT IS PERL ?
Perl is a programming language.
Unlike programming languages such as C and Fortran, Perl programs are scripts which direct the execution of the program “perl”.
Perl execution is similar in form to shell script execution.
Look at the introduction:

3. Perl is quick and easy to write. Perl is versatile:
#!/usr/bin/perl 2
WHY USE PERL ?
Perl is quick and easy to write.
Perl is versatile:
File/Sequence Management
Command Line Execution
Database
GUI
Webpage
Easy manipulation of sequences in genetic sequence analysis

4. The script “Example.pl” is:
#!/usr/bin/perl 3
BASIC SCRIPT
The script “Example.pl” is:
#!/usr/bin/perl
$x = 1;
$y = 1;
$z = $x + $y;
print “$x + $y = $z”;
The execution of Example.pl is:
> chmod +x Example.pl
> ./Example.pl
1 + 1 = 2

5. WHAT ARE PERL VARIABLES ?
#!/usr/bin/perl 4
WHAT ARE PERL VARIABLES ?
Three main perl variables:
Scalar : $name
Array
Hash : %name

6. Scalar variables are common and versatile.
#!/usr/bin/perl 5
PERL SCALAR
Scalar variables are common and versatile.
Scalar variables hold either numbers or strings
$number = 12.4;
$string = “Value is: “;
print “$string$number\n”;
$string = $string . “number 12”;
print “$string\n”;
Generates:
Value is: 12.4
Value is: number 12

7. Array holds a list of values
#!/usr/bin/perl 6
PERL ARRAY
Array holds a list of values
$value = “there”;
@array = (“Hello”,$value,1);
print “$arr[0] $arr[1] number $arr[2]\n”;
$array[2] = 2;
$array[3] = “again”;
print “$arr[0] $arr[3] number “, $arr[2] – 1, “\n”;
$size
print “Array has size $size\n”;
Generates:
Hello there number 1
Hello again number 1
Array has size 4

8. Hash holds references to values
#!/usr/bin/perl 7
PERL HASH
Hash holds references to values
%hash = ( “number” => 1, 34 => “Hello there” );
print $hash{34}, “ number “, $hash{“number”}, “\n”;
@array = keys %hash;
foreach $ref
print “Key: $ref = $hash{$ref}\n”; }
Generates:
Hello there number 1
Key number = 1
Key 34 = Hello there

9. Perl controls line execution with
#!/usr/bin/perl 8
LINE CONTROL
Perl controls line execution with
if – elsif – else
while
for
foreach
With comparisons:
For numbers:
< (less than), > (greater than)
<= (less than or equal), >= (greater than or equal)
== (equal)
For strings:
eq (equal strings)
ne (not equal strings)

10. IF – ELSIF - ELSE For example: #!/usr/bin/perl 9 if( $val < 2 ){
print “Value is less than 2\n”; }
elsif( $val == 2 ){
print “Value is equal to 2\n”;
else{
print “Value is greater than 2\n”;
if( $stringA eq $stringB ){
print “Both strings are the same\n”;
print “Both strings are different\n”;

11. WHILE, FOR LOOPS For example: #!/usr/bin/perl 10 # while( condition )
while( $i < 20 ){
print “The value $i is less than 20\n”;
$i++; }
# for( initial operation; condition; loop action )
for( $i = 0; $i < 20; $i++ ){
print “The value $i is greater or equal to 0\n”;

12. FOREACH LOOP For example:
#!/usr/bin/perl 11
FOREACH LOOP
For example:
# foreach $value )
foreach $value ){
print “The value $value is in the array\n”; }
foreach $value ( keys %hash ){
print “$value has value $hash{$value}\n”;
Note that foreach loops traverse the array from low index to high index.

13. Array @ARGV holds command line arguments To open and read in a file:
#!/usr/bin/perl 12
READING IN DATA
holds command line arguments
To open and read in a file:
open(IN,”$fileName”);
$firstLine = <IN>;
while(<IN>){
print $_; }
close(IN);
To write to a file:
open(OUT,”> $fileName”);
print OUT “Write this into $fileName\n”;
close(OUT);

14. To read standard input:
#!/usr/bin/perl 13
STANDARD STREAMS
To read standard input:
print “Write something: “;
$value = <STDIN>;
print “User wrote $value\n”;
To write to standard output:
print STDOUT “You see this on the command line\n”;
To write to standard error:
print STDERR “This is written as an error\n”;

15. The basic evaluation of regular expression are written as:
#!/usr/bin/perl 14
REGULAR EXPRESIONS
Regular expressions are a powerful tool for locating and modifying data
The basic evaluation of regular expression are written as:
$variable =~ /regular expression/
which returns true if the variable holds to the regular expression and false otherwise.

16. REG EXP EXAMPLES Example: #!/usr/bin/perl 15
if( $string =~ /Jonathan/ ){
print “The string contains Jonathan”;
print “as a substring.\n”; }
if( $string !~ /Myers/ ){
print “The string does not contain”;
print “Myers as a substring”;

17. Basic elements in regular expressions:
#!/usr/bin/perl 16
REG EXP Variables
Basic elements in regular expressions:
/./ = Any single character
/\w/ = Any character a-z, A-Z, 0-9, and ‘_’
/\d/ = Any digit 0-9
/\s/ = space, tab, or enter
/\./ = The character ‘.’
/\\/ = The character ‘\’
Definition of groups:
/[xyz]/ = Occurrence of either x, y or z
/[^xyz]/ = Occurrence of anything but x, y, or z
Location of occurrence:
/^x/ = Occurrence of x as the first character
/x$/ = Occurrence of x as the last character

18. Number of occurrences:
#!/usr/bin/perl 17
REG EXP Counts
Number of occurrences:
/x*/ = 0 or more copies of character ‘x’ in a row
/x+/ = 1 or more copies of character ‘x’ in a row
/x{3}/ = 3 copies of character ‘x’ in a row
/(str)*/ = 0 or more copies of string ‘str’ in a row
/$var*/ = 0 or more copies of the string $var in a row
Example:
$str = “a string with too much”;
if( $str =~ /o{2}/ ){
print “True!\n”; }
if( $str =~ /(crazy)*/ ){

19. #!/usr/bin/perl 18
Substitutions
Substitutions are regular expressions that define replacements within strings.
$str =~ s/(regular expression)/(replacement)/
Examples:
$str = “aabbccddeeff”;
$str =~ s/c/1/;
print “$str\n”;
$str =~ s/.$/2/;
$str =~ s/^\w{3}/start /;
Generates:
aabb1cddeeff
aabb1cddeef2
start b1cddeef2

20. Split function breaks a string into an array of strings
#!/usr/bin/perl 19
SPLIT FUNCTION
Split function breaks a string into an array of strings
@array = split(/(regular expression)/,$string)
Example:
$str = “A set of strings”;
@array = split(/\s+/,$str);
for( $i = 0; $i $i++ ){
print “$array[$i]\n”; }
Generates: A
set of
strings

21. REMEMBER PRACTICE!!!! We learn by doing !!!! Look at these sites!!!
#!/usr/bin/perl 20
REMEMBER PRACTICE!!!!
We learn by doing !!!!
Look at these sites!!!