1. Learn PERL
PERL - Practical Extraction and Reporting Language
1.
Where do we use PERL: ........................................................................................................................ 2
2.
What are the key features of PERL: ...................................................................................................... 2
3.
SCALAR Data: ........................................................................................................................................ 2
4.
USER IO: ................................................................................................................................................ 5
5.
STRING OPERATIONS: ........................................................................................................................... 5
6.
CHOMP: ................................................................................................................................................. 6
7.
LOOPS and CONDITIONS: ...................................................................................................................... 6
8.
ARRAYS: ............................................................................................................................................... 11
9.
Usage of $_ ......................................................................................................................................... 13
10.
Sub Routines: .................................................................................................................................. 16
11.
PERL DB ........................................................................................................................................... 17
12.
PERL FILE HANDLING ....................................................................................................................... 18
13.
PERL REGULAR EXPRESSION ........................................................................................................... 20
14.
PERL HASH....................................................................................................................................... 20
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2. Learn PERL
1. Where do we use PERL:
Quick and dirty programs (automating simple daily jobs)
System Administration
Web backend (CGI/Database access)
Configuration Management
QA
Biotechnology
Prototypes
2. What are the key features of PERL:
Text processing (pattern matching)
List processing
Database access
System language
To know if PERL is installed in your machine, you can try perl –v or perl –V
Sample PERL code: perl -e "print 1000" will print à1000
# is a comment.
perldoc provides documentation about any one command
3. SCALAR Data:
A single piece of data either a number or a string is called a 'scalar' in Perl.
PERL Takes care of data types on its own:
print 3+4;
#7
print 9-7;
#2
print 2*3;
#6
print 3/0;
# ERROR - Even Perl cannot divide by 0
Print 11 % 3; # 2 (modulus)
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3. Learn PERL
print 2 ** 3; # 8 (power of)
print "another 'string'"; # another 'string'
print "escape" this"; # ERROR
print "escape" this"; # escape" this
STRING Operators:
print "a" . "b"; # ab - concatenation
print "e" x 3; # eee - repetition
print "perl " x 3; # perl perl perl
print "-" x 80; # ------- (80 times)
SCALAR Variable declaration:
To save the values for later use in your program you need variables.
Rules:



Start with letter or underscore
Contains letters, underscores and digits
Case sensitive
** Same scalar variable can store integers and strings:
$x = 3;
$y = $x + 2;
$z = "hello world";
$z = 8;
String TO Number Conversion:
$x = "3 apples";
$y = "5 banana";
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4. Learn PERL
$total = $x + $y;
print $total; # 8
# Using a numerical operator forces the strings to be numbers
print "3a2" * 4; # 12
print "7683a2" * 1; # 7683
print "a2" * 4; # 0
print "010a2" + 4; # 14
print "3.1" + 0; # 3.1
print "3e+2x" + 0; # 300
Special Observation:
print "2" + 3; # 5 - (+) is a numerical operator
print "2" . 3; # 23 - (.) is a string operator
Variable Interpolation:
$c = 3;
$what = "apples";
$q = "$c $what";
print $q; # 3 apples
works in double quoted strings only
print '$c $what'; # $c $what
Variable name
$what = "banana";
$c = 3;
print "$c $what"; # 3 banana
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5. Learn PERL
print "$c $whats"; # 3 (warning)
print "$c ${what}sn"; # this works well
$c = 3;
$what = 'apple';
print "$c $what sn";
print $c . " " . $what . " sn";
print $c, " ", $what , " sn";
# all will result in '3 apple s' followed by a newline
4. USER IO:
$line = <STDIN>; # To Accept User inputs
if ($line eq "") {
print "Blank line";
}
print $line;
5. STRING OPERATIONS:
substr returns a substring of a big string
$part = substr($big, $index_of_first, $length);
Examples:
$big = "This is a big string";
print substr($big, 5,2); # is
print substr($big, 14); # string (till the end)
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6. Learn PERL
print substr($big, length($big)-2, 2); # ng (from the end of the string)
print substr($big, length($big)-2); # ng (from the end of the string)
print substr($big, -2); # ng (from the end of the string)
print substr($big, 5,2,"was"); # is (original 2 characters)
print $big;
# This was a big string
uc, lc, ucfirst, lcfirst turns character(s) to upper case or lower case
Examples:
$y = "aBcD";
$x = lc($y); # $x becomes abcd
$x = uc($y); # $x becomes ABCD
$x = lcfirst($y); # $x becomes aBcD
$x = ucfirst($y); # $x becomes ABcD
6. CHOMP:
Removes exactly one newline if there is one (or more) at the end of the string
$line = <STDIN>;
chomp($line);
if ($line eq "") {
print "Blank line";
}
7. LOOPS and CONDITIONS:
You have to use {} even if there is only one statement between them !
if ($some_result) { ... }
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7. Learn PERL
if ($age > 3) { ... }
if ($age > 3) {
...
}
else {
...
}
if ($age < 0) {
...
}
elsif ($age < 20) {
...
}
else {
...
}
UNLESS:
Sometimes you want to leave off the if part, and just do something in the else.
o
unless can do this for you:
unless ($num > 0) {
print “I said greater than 0n”;
}
WHILE:
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8. Learn PERL
while ($num<0) {
print “Not valid, try again!n”;
print “Enter a number greater than 0n”;
$num = <STDIN>;
}
DO-WHILE:
do {
print “Enter a number greater than 0n”;
$num = <STDIN>;
} while ($num <= 0);
<STDIN> returns the value undef when it reaches End-of-File.
o undef is FALSE
while ($line = <STDIN>) {
print $line;
}
OR, AND Operators:
print “Enter a number between 1 and 100n”;
$num=<STDIN>;
if ($num<1 || $num>100) {
print “Dummyn”;
} else {
print “Great job! you entered $numn”;
}
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9. Learn PERL
for ($j=0;$j<10;$j++) {
print “$jn”;
}
for ($x=100;$x>0;$x=$x-10) {
print “$xn”;
}
ForEach:
foreach iterates over the elements in an array (a list). A scalar variable assumes the
value of each element in the list (iteratively):
foreach $x (2,4,6) {
print “x is $xn”;
}
“$_”
$total=0;
while (<STDIN>) {
chop;
print “you entered”;
print;
$total = $total + $_;
}
print “the total is $_n”;
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10. Learn PERL
EXERCISE:
Exercise 1
Write a program that computes the area of a rectangular ($length * $width) and prints it. Use
two variables and hard code their values.
Exercise 2
Modify the previous program to prompt for the two values (on two separate lines)
Exercise 3
Script that gets two strings (on two separate lines) and prints the concatenated version.
Exercise 4
Modify the previous area-calculator program to print a warning if one of the values is negative
and make the area 0 sized.
Exercise 5
Basic calculator that gets 2 values and an operator (+,-,*,/) (on 3 separate lines) and prints out
the result.
Exercise 6
Implement the 4 parameter version of substr using the 3 parameter version. Use the
documentation to find out what is the 4 parameter version. That is, assume your substr
function is not capable to work with 4 paramters. Write some code that would do the same
job. (hint: read the documentation to find out what does substr do with 4 parameters)
Exercise 7
You get a mathematical expression of two numbers and an operator on a single line of input
(one or more spaces separate the operator from the numbers). Calculate the result of the
expression.
(Input an be "31 * 8" or "23 / 7" etc.)
Exercise 8
Write a perl program that reads in a number and prints that number 10 times.
Exercise 9
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11. Learn PERL
Write a perl program that reads in a number and prints an ASCII square of that size. For
example, if the number is 4, the program prints:
8. ARRAYS:
While a scalar is single value a list is a bunch of single values. A scalar value can be stored in a
scalar variable. A list can be stored in a list variable. It is called and array.
List Literals, list ranges
A list is an ordered set of scalar values.
Examples of lists:
(1, 5.2, "apple")
(1,2,3,)
# 3 values
# 3 values
(1,2,3,4,5,6,7,8,9,10)
(1..10)
# same as (1,2,3,4,5,6,7,8,9,10)
('a'..'z')
# all the lowercase letters
("joe", "peter", "mario", "cohen") # is the same as quote word
qw(joe peter mario cohen)
($a, $b, $c) = (2, 3, 7); # nearly the same as $a=2; $b=3; $c=7;
($a, $b) = (8, 1, 5); # ignore 5
($a, $b, $c) = (3, 4); # $c will be undef
An array is a variable that can hold a list, that is a list of scalars.
To get to the individual elements of the array you use the name of the array and the index of
the element.
The index can be ANY integer value, including negative numbers.
$name[0] = "Joe";
$name[1] = "Peter";
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12. Learn PERL
$name[3] = "Cohen";
print $name[1]; # Peter
print $name[2]; # undef
Array Assignment:
You can write the following, but it is a bit too much typing
($name[0], $name[1], $name[2], $name[3]) = qw(joe peter mario cohen);
Instead you can use @ to refer to the whole array:
@name = qw(joe peter mario cohen);
You can also mix the variables on the right side and if there are arrays on the right side the
whole thing becomes one flat array !
@name = ($myname, 'joe', @oldnames);
($a, @b) = (1, 2, 3, 4); # $a is 1; @b is (2, 3, 4)
($a, @b, @x) = (1, 2, 3, 4); # $a is 1; @b is (2, 3, 4) @x is empty: ()
@a = (1, 2);
@b = (3, 4);
@c = (@a, @b); # @c becomes (1, 2, 3, 4)
In Perl there are several ways to go over all the elements of a list or an array.
Probably the most frequently used one is foreach.
foreach SCALAR (LIST) BLOCK
Example:
# this will print the names of 3 fruits:
foreach $fruit (qw(apple banana peach)) {
print "$fruitn";
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13. Learn PERL
}
# Instead of lists you can use it with arrays:
@fruits = qw(apple banana peach);
foreach $fruit (@fruits) {
print "$fruitn";
}
9. Usage of $_
There is this strange scalar variable called $_
In Perl several functions and operators use this variable as a default variable in case no variable
is explicitely used. foreach and print are such functions. So here we can see a shorter version of
the previous script:
@fruits = qw(apple banana peach);
foreach $fruit (@fruits) {
print $fruit;
}
foreach $_ (@fruits) {
print $_;
}
# but the real use of the variable is when it is not used explicitly:
foreach (@fruits) {
print ;
}
Print Arrays:
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14. Learn PERL
@a = qw(x y z);
print "pre ", @a, " postn";
# pre xyz post
# $, holds empty string
print "pre @a postn";
POP& PUSH, SHIFT and UNSHIFT
There are several functions working on arrays:
pop and push implement a LIFO stack.
pop fetches the last element of the array returns that value and the array becomes one shorter
if the array was empty pop returns undef
SCALAR = pop ARRAY;
Example:
@array = ('a', 'b', 'c');
$lastelem = pop(@array); # $lastelem gets 'c'
@array becomes ('a', 'b')
push is the opposite of pop it adds element(s) to the end of the array It returns number of
elements after the push.
PUSH ARRAY, SCALAR, ... (more SCALARs);
Example:
@array = ('a', 'b');
push(@array, 'd'); # @array becomes ('a', 'b', 'd')
push(@array, 'e', 'f'); # @array becomes ('a', 'b', 'd', 'e', 'f')
shift and unshift are working on the beginning (left side) of the array.
shift fetches the first element of an array.
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15. Learn PERL
It returns the fetched element and the whole array becomes one shorter and moved to the left.
Returns undef if the array was empty.
Example:
@array = ('a', 'b', 'c');
$f = shift @array; # $f gets 'a', @array becomes ('b', 'c')
unshift adds element(s) to the beginning of an array returns number of elements in the array
after the addition
Example:
@array = ('b', 'c');
unshift(@array, 'x', 'y') # @array becomes ('x', 'y', 'b', 'c')
Exercise 1
Implement pop,push,shift,unshift (only with @ $ and array index)
Example: pop is used like this:
$x = pop @a;
implementation:
$x = $a[$#a];
$#a = $#a - 1;
Exercise 2
Create a menu system where the user can select a fruit by giving the corresponding number (17) and you print the name of the fruit. (The list of the fruits is hard coded)
Exercise 3
Read in a few numbers, each one on a separate line till end-of-input and print out the min, max
and average. (End-of-input is ^D on linux and ^Z ENTER on windows.)
23
11
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16. Learn PERL
198
3
-70
1001
Exercise 4
Read in a few lines (till end-of-input) and print them in reverse order.
Exercise 5
Write a program that generates the first n Fibonacci numbers. (Definition: f(n) = f(n-1)+f(n-2),
f(0)=f(1)=1) The user supplies the value of n.
Example:
INPUT : 6
OUTPUT: 1 1 2 3 5 8
10.
Sub Routines:
sub foo {
"Hi Dave";
}
Calling Sub routines:
In the old days, the name of a subroutine started with '&' (doesn't have to any more).
These are all valid calls of the subroutine:
&foo; foo(1,2,3,4);
&foo("Hello"); foo 11.75;
** You can use the my keyword to declare a variable as private to the subroutine:
my($a,$b);
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17. Learn PERL
my($size) = 11;
my(@foo) = (1,3..11);
Sample Sub routine:
sub min {
my($a,$b) = @_;
if ($a < $b) {
$a;
} else {
$b;
}
}
11.
PERL DB
Sample 1:
use Win32::ODBC;
# Create a database object and make sure
# the database was found
$db = new Win32::ODBC("eiw");
if (! $db) {
print "Error - the eiw database could not be foundn");
...
}
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18. Learn PERL
Sample 2
use DBI;
$db=DBI->connect("dbi:ODBC:Flight32");
$a=$db->prepare("Select * from orders");
$a->execute;
@row=$a->fetchrow_array;
print @row;
12.
PERL FILE HANDLING
PERL reads files using various syntaxes :
open a file for reading, and link it to a filehandle:
open IN, “C:EHD.txt";
And then read lines from the filehandle, exactly like you would from <STDIN>:
$line = <IN>;
foreach $line (<IN>) ...
And don’t forget to close it:
close IN;
A nice way to check that the open didn’t fail (e.g. if the file doesn’t exists):
open IN, "$file" or die "can't open file $file";
PERL can also write into files:
open a file for writing, and link it to a filehandle:
open OUT, ">EHD.analysis";
(If a file by that name already exists it will be overwriten!)
Or, you can add lines at the end of an existing file (append):
open OUT, ">>EHD.analysis";
Print to a file:
print OUT "The mutation is in exon $exonNumbern";
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19. Learn PERL
PERL understands various representations of folders paths :
open IN, '<D:EyalPERLp53.fasta';
n
n
Always use a full path name, it is safer and clearer to read
Remember to use in double qoutes
open IN, "<D:EyalPERL$name.fasta";
n
You can also use / (usually…)
open IN, "<D:/Eyal/PERL/$name.fasta";
PERL also can work with foldersand files inside them:
Perl allows easy access to the files in a directory by “globbing”:
foreach $fileName (<D:/scripts/*.pl>) {
open IN, $fileName
or die "can't open file $fileName";
foreach $line (<IN>) {
do something...
}
}
More samples:
open OF, "<C:File1.txt";
foreach $l(<OF>)
{
print "$ln";
}
open WF, ">>C:File1.txt";
print WF "nThis is additional Line";
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20. Learn PERL
13.
PERL REGULAR EXPRESSION
Perl’s greatest capability is its regular expressions. It uses “/<expression> /” for applying regular
expression.
Sample:
print (" please enter your emailIDn");
$_=<STDIN>;
if (/[0-9].*@.*/)
{
print "It is a correct mail format";
}
else
{
print "it is a wrong mail format";
}
#Q> Write a text file with 10 mail ids (Valid and Invalid).
#Write a perl scrip which reads the file and copy all valid #emails to a new file.
14.
PERL HASH
What is a hash and why to use one?
 Unordered group of key/value pairs where
 key is a unique string and
 value is any scalar
Also called Associative Array Like an array but the 'index' is string instead of number.
Examples of use, some kind of mapping:
 phone book (name => phone number)
 worker list (ID number => name)
 DNS resolution (hostname => IP address)
 UNIX admin (username => UID)
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21. Learn PERL
 Windows (Netbios name of computer => Name of person using it)
 CGI: (fieldname => field value)
Sample1:
Accessing Individual Hash Elements
$phone{"Yossi Cohen"} = "03-672234";
# We create a hash called %phone and give value
to
print $phone{"Yossi Cohen"};
# one of its elements. then we can use that
element
$count_votes{"Bush"}++;
# in another hash we use the value as a number
$name = "Bush";
# We can use variables in place of the key
$count_votes{$name}--;
# The variable springs to existence.
# The original value is undef.
# before accessing a pair you should check if
if (exists $phone{"George"}) {
# the key exists at all
if (defined $phone{"George"}) {
# the value has been defined
print $phone{"George"};
}
}
# if you had enough from George
delete $phone{"George"};
# delete him from your phone book:
Sample 2
The whole hash
# The whole hash is called %phone
%phone = ("Yossi", 123, "Joe", 456, "Mary", 678);
%phone = (
# Maybe that is more readable like this
"Yossi", 123,
"Joe", 456,
"Mary", 678);
%phone = (
# or even better with the big arrow
"Yossi" => 123,
"Joe" => 456,
"Mary" => 678);
# If we get an array like this from somewhere, we can turn it to a hash but beware of the
change of meaning !
@array = ("Yossi", 123, "Joe", 456, "Mary", 678);
%phone = @array;
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