print "Hello World!\n";
#[This example does not provide the UNIX file directory path #which is usr/bin. The \n is also used in C and Java; without it #the prompt would remain on the same line]
#ActivePerl from ActiveState is probably now the most the #industry-standard, commercial-grade Perl distribution,
#available for Solaris, AIX and HP-UX or indeed the Enterprise #Edition. I would actually rely on ActivePerl to protect my #infrastructure and stay competitive with quality-assured #business solutions. Since it is compatible with the reference #distribution of Perl, the Code tested will run on any Perl #installation that has the extensions installed.
#Perl adapts the syntax of the C language including the use of semicolons at
the end of each statement and the use of curly brackets to identify a block of
commands.$Name = “James “ . “Snyder”;
#the concatenation operator takes the string “James “ and combines it with the second string “Snyder” to create a single
string that contains “James Snyder”.# In Perl 5.8, the default sorting algorithm is merge sort.
#In earlier versions of Perl, the default sorting algorithm was quick sort.
if $x > 5
{
command1;
command2;
}#To identify a block of commands in Perl, use curly brackets
$myVar
#Perl allows variables to hold any data types.
variable names begin with the dollar sign symbol
Perl is case-sensitive, so the Perl variable $myVar is considered completely different from $MYVar
== # The relational operator in Perl is two equal sign symbols (==) whereas the relational operator in other programming languages is just a single equal sign symbol (=).
(
#this is a unique comparison with signed result operator (< = >)
#this compares two values
#this returns 0 (if the two values are equal),
#thias returns 1 (if the first value is greater than the second)
#this returns –1 (if the first value is less than the second)
&&
# This Logical operator compares two Boolean values
# compares (True [1] or False [0]) and return a single True or False value to a truth table
+=
#Addition assignment operator
-=
# Subtraction assignment operator
#branching statement
#The simplest branching statement is an IF statement that only runs one or more commands if a Boolean condition is True. #In Perl, the IF statement uses curly brackets to enclose one or more commands
#make the computer choose between two mutually exclusive sets of commands
#use an IF-ELSE statement in Perl
#The IF-ELSE statement only offers two choices.
#If you want to offer multiple choices, use the IF-ELSEIF statement
#IF-ELSEIF uses two or more Boolean conditions to choose which of two or more groups of commands to run.
#use the ELSIF keyword
# In Perl, every subprogram is a function that can return a value.
# This is the format of a typical Perl function
#When you pass parameters to a Perl function,
#that function can access parameters with the foreach keyword and the @_ array
@arrayname = (element1, element2, element3);
# Perl offers three data structures: arrays, hash arrays, and references
#. An array stores multiple items, identified by an index number.
#A hash array stores multiple items, identified by a key, which can be a number or a string.
@numberarray = (1, 2, 3, 4, 5);
# you can list each number individually if you want to create an array that contains a range of numbers
@numberarray = (1..5);
# use the range operator (..) to define the lower and upper bounds of a range
# use the dollar sign ($) symbol in front of the array name to access the individual elements stored in an array
push(@arrayname, item2add);
#use arrays to mimic a stack data structure with Perl’s push and pop commands.
# use the push command to push a new item onto an array.
$variablename = pop(@arrayname);
# use the pop command to pop an item off the array
# This is a Perl hash array
# A second way to define a hash array
$variable = $hasharray (“key1”);
# you need to know the key associated with that value
#identify the hash array name by using the $ symbol
# Perl is a true object-oriented programming language.
# create and use objects in your programs.
# define a class to create an object
# This is a typical class definition
my $variablename = classname->new();
# After i define a class, i can create an object from that class by declaringconstructor method commonly called "new"
# use the @ISA variable inside a new class to use inheritance in Perl
# concatenation is the simplest form of string manipulation
#concatenation joins multiple strings into one.“key1” into the $variable.ACTGTTGTGTACCT
# This is what this simple program will print
$DNA3 = “$DNA1$DNA2”;#
The first method to concatenate two strings is to smash two strings together
$DNA3 = $DNA1 . $DNA2;
# The second way to concatenate the same two strings uses this dot operator.
< = >
#a Perl only relational operator that compares two values and returns a True or False value== # The relational operator in Perl is two equal sign symbols (==) whereas the relational operator in other programming languages is just a single equal sign symbol (=).
(
#this is a unique comparison with signed result operator (< = >)
#this compares two values
#this returns 0 (if the two values are equal),
#thias returns 1 (if the first value is greater than the second)
#this returns –1 (if the first value is less than the second)
&&
# This Logical operator compares two Boolean values
# compares (True [1] or False [0]) and return a single True or False value to a truth table
++
#Perl has a special increment (++) operator, which simply adds to a variable
--
#Perl has a special decrement (--) operator, which simply subtracts 1 to a variable
#Addition assignment operator
-=
# Subtraction assignment operator
if (condition) {
Command1;
Command2;
}#branching statement
#The simplest branching statement is an IF statement that only runs one or more commands if a Boolean condition is True. #In Perl, the IF statement uses curly brackets to enclose one or more commands
if (condition) {
Command;
Command;
}
else {
Command;
Command;
}#make the computer choose between two mutually exclusive sets of commands
#use an IF-ELSE statement in Perl
if (condition1) {
Command;
Command;
}
elsif (condition2) {
Command;
Command;
}
elsif (condition3) {
Command;
Command;
}#The IF-ELSE statement only offers two choices.
#If you want to offer multiple choices, use the IF-ELSEIF statement
#IF-ELSEIF uses two or more Boolean conditions to choose which of two or more groups of commands to run.
#use the ELSIF keyword
SWITCH
#Perl does not provide a SWITCH statement.
sub functionname {
Commands;
return $value;
}# In Perl, every subprogram is a function that can return a value.
# This is the format of a typical Perl function
sub functionname {
foreach $variablename (@_) {
Commands;
}
return $value;
}#When you pass parameters to a Perl function,
#that function can access parameters with the foreach keyword and the @_ array
@arrayname = (element1, element2, element3);
# Perl offers three data structures: arrays, hash arrays, and references
#. An array stores multiple items, identified by an index number.
#A hash array stores multiple items, identified by a key, which can be a number or a string.
#Perl arrays are zero-based, so the first element of an array is considered 0, the second is 1, and so on.
#,you must name that array with the @ symbol when you create a Perl array .
#You can define the elements of an array at the time you create the array
# you can list each number individually if you want to create an array that contains a range of numbers
@numberarray = (1..5);
# use the range operator (..) to define the lower and upper bounds of a range
@numberarray = (1..10);
$thisone = $numberarray[0];# use the dollar sign ($) symbol in front of the array name to access the individual elements stored in an array
#The value stored in the $thisone variable is the first element of the @numberarray, which is 1.
#use arrays to mimic a stack data structure with Perl’s push and pop commands.
# use the push command to push a new item onto an array.
$variablename = pop(@arrayname);
# use the pop command to pop an item off the array
%hasharray = (
key1 => value1,
key2 => value2,
key3 => value3,
);# This is a Perl hash array
# A hash array stores an item along with a key.
#there are two ways to store values and keys; this is the first way
# hash arrays are identified by the percentage (%) symbol.
%hasharray = (“key1”, value1, “key2”, value2, “key3”,
value3);# A second way to define a hash array
$variable = $hasharray (“key1”);
# you need to know the key associated with that value
#identify the hash array name by using the $ symbol
#This command would store the value associated with
package className;
sub new {
my $objectname = {
Data;
Data;
};
bless $objectname, $className;
return $objectname;
sub methodname{
Commands;
Commands;
};# Perl is a true object-oriented programming language.
# create and use objects in your programs.
# define a class to create an object
# This is a typical class definition
my $variablename = classname->new();
# After i define a class, i can create an object from that class by declaringconstructor method commonly called "new"
a variable as a new class type.
# I create an object by creating a
package newobject;
use class2inheritfrom;
@ISA = qw(class2inheritfrom);# use the @ISA variable inside a new class to use inheritance in Perl
$DNA1 = ‘ACTGTTG’;
$DNA2 = ‘TGTACCT’;
$DNA3 = “$DNA1$DNA2”;
print $DNA3;# concatenation is the simplest form of string manipulation
#concatenation joins multiple strings into one.“key1” into the $variable.ACTGTTGTGTACCT
# This is what this simple program will print
$DNA = ‘ACTGTTG’;
$compDNA = tr/ACGT/TGCA/;# The
# The tr/ACGT/TGCA/; command tells Perl to translate every A into a T, every C into a G, every G into a C, and every A into a T all at once.# The two strands of DNA are complimentary sequences.
use a simple program that replaces every A with a T, every C with a G, every T with
an A, and every G with a C.
# This is to calculate a complimentary sequence by knowing only one of the sequences
tr command simply tells Perl to translate or swap one character for another. use a simple program that replaces every A with a T, every C with a G, every T with
an A, and every G with a C.
# This is to calculate a complimentary sequence by knowing only one of the sequences
$DNA = ‘ACTGTTG’;
$compDNA = tr/ACGT/TGCA/;
$revDNA = reverse $compDNA;# The second step in determining a complimentary sequence is to reverse the
order of that sequence.
# sequences are always written a specific way
# sequences start with the end of the sequence known as 5’ phosphoryl (also
known as 5 prime or 5’) and ending with 3’ hydroxyl (known as 3 prime or
3’).
# reverse it using this Perl command to display the complimentary sequence correctly
The first method to concatenate two strings is to smash two strings together
$DNA3 = $DNA1 . $DNA2;
# The second way to concatenate the same two strings uses this dot operator.
