PERL : Practical Extraction Reporting Language

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PERL : Practical Extraction Reporting Language

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Title: PERL : Practical Extraction Reporting Language

1
PERL Practical Extraction Reporting Language

Neha Barve
Lecturer
Bioinformatics
Devi Ahilya University

Perl stands for Practical Extraction and Report
Language.
Perl is known as a high-level, interpreted,
general-purpose and dynamic programming language.
Perl was invented by Larry Wall, a linguist
working as a systems administrator at NASA in
1987.
Perl run well on UNIX and Windows systems. If you
develop Perl for UNIX system, it can be portable
to Windows system as well.

3
What is programming?

Telling a computer what you want it to do.
The only thing Is to give instructions in a way,
the computer can understand.
Usually use a language that a computer can
understand.

Difference in Human learning and machine
learning?
The most important thing is that you never going
to express a task to computer if you cant express
it to urself.

5
Source code/Code

The instruction that we give to the computer are
collectively called as Source Code.

6
Difference between compiler aNd interpreter
7
Perl compiler or Interpreter

Compiler convert source code into bytecode
(machine code) and than interpreter (denoted by
p) convert it into real code.
Hence PERL is not a strictly compiled language or
Interpreted one.

8
Is PERL a Scritping language

Yes it is
Some people say it scripting language that is
interpreted language.
Perl run well on UNIX and Windows systems. If you
develop Perl for UNIX system, it can be portable
to Windows system as well.

9
Some key features of PERL

Keywords There are certain instructions that
PERL recognizes and understand.
Statement and statement blocks
The statement in PERL ends with .
Blocks are used to divide coding into several
parts to separate each statement from
surroundings.
This shows that how you are passing argument to
certain functions.

ASCII and UNICODE
Escape sequences Escape helps to introduce the
characters which can be types.
White spaces
name we give to Tabs, New lines and Spaces.

11
Writing your first program

! C/Perl/usr/bin/perl
! C/perl/bin/perl
! C/strawberry/Perl/usr/bin/perl
! usr/bin/perl
Print hello world
The first line is called shebang line (use either
of one.)
Which gives path to Perl compiler.

12
Data types in PERL

Scalars
Arrays (lists)
Associative arrays (hashes)

13
Scalars

Scalar variables are used to store single values
- for example, a number or a string. They are
preceded by the dollar sign ().
sigil A symbol. In Perl a sigil refers to the
symbol in front of a variable.
A number can be integer or float.
num10
num10.5
numhello all how r u?

14
autovivication

!usr/bin/perl -w
use strict
use warnings
my diameter4
my circumference
my pie
print "hello world"
print ( circumferencediameterpie)
Something which is not defined and perl consider
it as zero

15
Print function

Statement is ended by using .
There are more than one ways to do a thing.
How to write statement in PERL
!perl/bin/perl
Print hello world
Print q/hello world/
Print q/hello world/
The output will be
hello world
hello world
hello world

stringq(hi all)
string1qhi all
string2qlthi allgt
string3qhi all
string3qhi all
string3qhi all
print "string\n"
print "string1\n"
print "string2\n"
print "string3\n"
The output will be
hi all
hi all
hi all
hi all

Alternative delimiters
17

Print (hello, all, how), are, you
The output would be
Helloallhow (without space)
Some important points
U can use print or printf function
Using Escape characters (text formatting)
New line
Tb
backspace

18
Here documents

End of File

19
Single quote vs double quote (for windows)

There is no processing is done under single
quoted string.
Single quote treat every argument as plain text.
Double quoted string will have its escape
(backslash)sequences processed eg scalars
interpolation.
Backslash are used to turn off special effect of
any character. (overwhacking)

20
Few examples

Print C\\win\\bun\\perl\\
Print C\\win\\bun\\perl\\
Now what the heck is that?

21
Number system

We can express numbers as binary, hexadecimal,
and octal.
Hex are denoted by 0X
Octal are denoted by 0
Binary are denoted by 0b

Some examples are
Print 255
Print 0378
Print 0b11111111
Print 0xFF
Question what are Barewords (series of
characters that perl doesnt recognize)

Related errors Illegal octal digit Illegal
binary digit
23
Converting numbers (use of printf or sprintf)

Finding a octal number
num42
printf("o", num) (output 52)
Finding hexadecimal value (small and capital)
Printf (x, num)
Converting octal to decimal
Print oct(num)
Converting hexadecimal to decimal
Print hex(num)

Converting decimal to binary
Printf(b, 10) (output 1010)
Converting binary to decimal
iosprintf ("b",10)
hhoct("0b". io)
print hh

25
ltSTDINgt INPUT function

print "gimme some number"
oneltSTDINgt
chomp one
print oct(one)

concatenation
String concatenation uses the period character
".
my fullname 'mud' . "bath"
Print fullname

27
CGI-PERL

Neha Barve
Lecturer Bioinformatics
DAVV

28
Introduction to CGI

CGI stands for Common Gateway Interface.
CGI is a standard programming interface to Web
servers that gives us a way to make our sites
dynamic and interactive.
CGI is not a programming language. It is just a
set of standards (protocols.)
CGI can be implemented in an interpreted language
such as PERL or in a compiled language such as C.
CGI is one method by which a web server can
obtain data from (or send data to) databases,
documents, and other programs, and present that
data to viewers via the web. More simply, a CGI
is a program intended to be run on the web.

29
Introduction to CGI(continued)

CGI programs work as follows
STEP 1 (On the client side) Get Information from
the user (using HTML forms, SSI, Java Applet,
,etc).
STEP 2 (On the server side) Process the data,
connect to DATABASE, search for PATTERNS, ,etc.
STEP 3 (On the server side) Send the result of
computation back to the client.

30
Static Pages
Request file
Retrieve file
Send file
31
Dynamic Pages
Request service
Do Computation Generate HTML page with
results of computation
Return dynamically generated HTML file
32
CGI Web Application
Request service
Run CGI program print result
HEADERS BODY
33
What do u need?

A text editor
A web server
Perl interpreter

34
Basics of CGI program

A CGI is simply a program that is called by the
webserver, in response to some action by a web
visitor (user)
if you're writing a CGI that's going to generate
an HTML page, you must include this statement
somewhere in the program before you print out
anything else.
print "Content-type text/html\n\n"

35
Imp note

This is a content-type header that tells the
receiving web browser what sort of data it is
about to receive in this case, an HTML
document. If we forget to include it, or if you
print something else before printing this header,
you'll get an "Internal Server Error" when you
try to access the CGI program

36
Our first CGI program

!/usr/bin/perl -wT
print "Content-type text/html\n\n"
print "Hello, world!\n"
Save this file to ur CGI-BIN folder.
Run the web server, and run the file by typing
the URL.
Eg http//localhost/cgi-bin/first.cgi

What happened in above program when u run it.

38
Now write ur second program

!/usr/bin/perl -wT
print "Content-type text/html\n\n"
print "lthtmlgtltheadgtlttitlegtHelloWorldlt/titlegtlt/head
gt\n"
print "ltbodygt\n"
print "lth2gtHello, world!lt/h2gt\n"
print "lt/bodygtlt/htmlgt\n"
(This program shows you tht how u combine HTML,
PERL and CGI)

39
Lets try our third CGI program

!/usr/bin/perl -w
print "Content-type text/html\n\n"
print ltltEndOfHTML
lthtmlgtltheadgtlttitlegtTest Pagelt/titlegtlt/headgt
ltbodygt lth2gtHello, world!lt/h2gt lt/bodygtlt/htmlgt
EndOfHTML

40
CGI-PERL module

These are collections of pre-written code that
can be used to do all kinds of tasks.
You can save yourself the time and trouble of
reinventing the wheel by using these modules.
standard library modules
Some modules are included as part of the Perl
distribution these are called standard library
modules and don't have to be installed. If you
have Perl, you already have the standard library
modules.

41
Comprehensive Perl Archive Network (CPAN)

These are modules available that are not part of
the standard library.
The CGI.pm Module The CGI.pm module is part of
the standard library, and has been since Perl
version 5.004.

42
How to include modules in CGI program

First include the module via the use command.
This goes after the
!/usr/bin/perl line and before any other code
The .pm is implied in the use statement
The qw(standard) part of this line indicates
that we're importing the "standard" set of
functions from CGI.pm.

use CGI qw(standard)
43
CGI functions

A function is a piece of code that performs a
specific task it may also be called a subroutine
or a method.
Functions may accept optional arguments (also
called parameters), which are values (strings,
numbers, and other variables) passed into the
function for it to use

The CGI.pm module has many functions for now
we'll start by using these three
header
start_html
end_html

45
The header function

The header function prints out the "Content-type"
header. With no arguments, the type is assumed to
be "text/html".
E.g.
! C/perl/bin/perl
Use CGI qw(standard)
Print header

46
The start_html function

start_html prints out the lthtmlgt, ltheadgt, lttitlegt
and ltbodygt tags. It also accepts optional
arguments. If you call start_html with only a
single string argument, it's assumed to be the
page title.
! C/perl/bin/perl
Use CGI qw(standard)
Print header
Print start_html(hello world)

47
The output will be (in CMD)

lthtmlgt ltheadgt lttitlegtHello Worldlt/titlegt ltheadgt
ltbodygt
Giving arguments in Start_html function
! C/perl/bin/perl
Use CGI qw(standard)
Print header
Print start_html(-titlegt page, -bgcolorgt
cccffg, -textgt ggghhh backgroundgt
xyz.jpg)

48
The end_html function

The end_html function prints out the closing HTML
tags
lt/bodygt lt/htmlgt

49
A final program

!/usr/bin/perl -w
use CGI qw(standard)
print header
print start_html("Hello World")
print "lth2gtHello, world!lt/h2gt\n"
print end_html
(u can also include all line in one print
function)

50
USING SCALARS IN CGI-PERL

!perl/usr/bin/perl
Use CGI qw(standard)
Use CGIcarp qw(warningsToBrowser
fatalsToBrowser)
Use strict
my emailxyz_at_gmail.com
my domainwww.xyz.com
Print start_html(scakars)
Print ltltendofhtml
lth2gtthese are scalarslt/h2gt
ltpgt My e-mail address is email, and my web url
is lta href"url"gturllt/agt. lt/pgt
Endofhtml
Print end_html

Use CGIcarp qw(warningsToBrowser
fatalsToBrowser)
The CGICarp module causes all warnings and
fatal error messages to be echoed in your browser
window
Use strict (it is optional)
This is a standard Perl module that requires us
to declare all variables.

52
OPERATORS

The numeric operator take at least one number as
an argument and return another number.
These operators are of three types
ARITHMATIC OPERATOR
BITWISE OPERATOR
LOGIC OPERATOR

53
ARITHMATIC OPERATOR

Adding
Dividing
multiplying
Subtracting
Exponentiation
Remainder (modulus)
Etc

54
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55
Precedence

The order in which PERL do calculations.
Multiply and divide have higher precedence than
addition and subtraction.
The outcome should be 108

For lower precedence
Use brackets.
But it would give you error.
Sowrite like this ..

57
Exponentiation

Which raises one number to the power of another.
Denoted by
The output will be 16, 243, -16
Here in the last output precedence would be
and -.

58
Remainder

This calculates remainder when one number divides
another.

59
Perl assignment operators

Write a program using simple numeric operator.
Write program in which perl show precedence

60
BITWISE OPERATOR

Binary for 51
Binary for 170
Binary for 85
The and operator compare bits and gives the
output written as .
The output will be 17 (it compare one bit at a
time)

The or operator compare any of the bit is
one. Denoted by .
Eg if either of the bit is one we produce one
otherwise 0.
As a rule of thumb X Y will always be smaller
or equal to the smallest value of X and Y. And X
Y will be bigger than or equal to the largest
value of X or Y

The exclusive or operator
Denoted by .
The nor operator
Denoted by .
Eg 85.
The output would be

63
COMPARING NUMBER FOR EQUALITY

Denoted by .
If true it gives one otherwise nothing.

COMPARING NUMBER FOR NOT EQUALITY
64
COMPARING NUMBER FOR INEQUALITY
65
Some other operators

It does not return true or false value
Instead 0 if values are same, -1 if right
hand side is bigger, 1 if left hand side is
bigger.
Denoted by lt gt.

66
LOGIC OPERATOR(BOOLEAN OPERATOR)

AND ()
OR ()
NOT (!)
XOR

67
Lazy evaluation of perl
68
String operators

Concatenation operator
Repetition operator
Repitition has higher precedence than
concatenation

69
SOME OTHER EXAMPLES

Now what happens here

70
String comparison

Getting ASCII value of characters.
Generally PERL compares by ASCII values of each
character.
To find out the ASCII value
Use ORD function
E.g.
!perl/bin/perl w
Print here is the ASCII value of , ord()

But for comparing whole string (it would be
tedius)
So perl uses some comparison operators
Greater than gt
Less than lt
Equal to eq
Not equal ne

72
example
73
Autoincrement/ autodecrement operator

These are the operators which increment or
decrement value according to their position.
When they precedes variable they act before
everything else.
When they come after a variable they act after
everything else.

74
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75
SCOPE of variable

Global and local variable

76
Variable interpolation

Single and double quote.

77
Currency conversion

!/xampp/usr/bin/perl w
Use strict
My dol 50
Print one dollar equals to , 1dol, \n
Using standard input
Print Please enter ur value
valltstdingt
Print one dollar equals to , 50val, rs.

78
Write a program

Write a program which convert a hexadecimal
number to decimal number and a octal number to
decimal number.
Write a program which ask for a decimal number
which is less than 256 and convert it to binary.
Write a program to find out the answer of the
following

79
list

Giving any argument to print function is an
example of list
E.g
Print (one , two, three, four)

80
Accessing list value

Print ((one, two, three) 2))
Another way to do it
If you use qw u can separate the words using
whitspace , tabs and new lines.

81
List slices

print (('one', 'two', 'three','four','five')1,3)
Another way to do it

82
Ranges

print (('one', 'two', 'three','four','five')0..3
)
Perl can count reverse too.
print (('one', 'two', 'three','four','five')-1..2
)
The first ouput would be one, two three four.
The second output would be five, one, two, three

Few eaasy examples
print "counting up" , (1.. 6), "\n"
print "counting down" , (6 .. 1),"\n"
print "counting up" , (-1.. 6),"\n"
print "counting up" , reverse(1... 6),"\n"
print "alphabates ", ('a' .. 'm')

84
Combining ranges and slices

Three examples to do it

85
Arrays

Started with _at_ sign.

86
Two ways to right an array

_at_arr(one, two, three, four)
or
_at_arrqw(one two three four)

87
Examples of declaring arrays
88
Wanna count array

Assign it to a variable..
E.g.
My count _at_arr
Print count
Or u can just write
Print scalar _at_arr

89
List context and scalar context

Operations which want list are list context
Operations which want single value are scalar
context
The value of an array in list context is list of
elements
The value in scalar context is its number.

90
Array variable interpolation

_at_arr qw(1 2 3 4 5 6)
Print _at_arr
Print _at_arr
The output will be
123456
1 2 3 4 5 6

91
Accessing values in array

my _at_arrqw(one two three four)
Print arr0
Print arr1
Print arr2
Print arr3

92
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93
Running through array
Here introduces concept of iterator variable or
loop variable
We can also do it by using _ special variable
94
Another easy way to write it

!/strawberry/perl/bon/perl -w
use strict
my _at_questions qw(java perl C)
my _at_ans qw(good best no)
for (0..questions)
print "the questions_"
print "is ans_"

is shows the last element or highest element
95
If u want to reverse ur array values

my _at_rev(1..5)
for (reverse(_at_rev))
print "_...., \n"
print "blast off"

96
Pushing and poping of array

Push is the operator tht add an element to the
end of the array.
Pop is the operator which remove top element

97
example

my _at_listqw(neha dhiraj sonu monu)
print "here is list _at_list"
my one pop_at_list
print "i m picking one","\n"
my twopop _at_list
print "now i m picking two", "\n"
print "_at_list", "\n"
my _at_list1push (_at_list, one)
print "_at_list", "\n"
my _at_list1push (_at_list, two)
print "_at_list"

98
Unshift/shift

my _at_shi()
unshift (_at_shi, "first")
print "_at_shi", "\n"
unshift (_at_shi, "second", "third")
unshift (_at_shi, "forth", "fifth")
print "_at_shi","\n"
shift _at_shi
print _at_shi

99
Sorting data (alphabetically and numerically)

my _at_listtqw(java perl python)
my _at_listt1 sort_at_listt
print _at_listt1
Numeric comparison
my _at_listtqw(1 56 78 3 5 67)
my _at_listt1 sort (_at_listt)
print _at_listt1

100
hashes

Hashes are like a dictionary in which all entries
are stored unordered manner.
In hash the data is totally unsorted and there is
no intrinsic order
A hash contains pairs of data with no particular
order and all scattered.

101
Writing a hash

There are two ways to write hahses
The first way is
The second way is

102

In the above example we used gt operator.
It acts like quoting comma,
It is essentially a comma but whatever appear on
the left side of it , treated as double quoted
string.
See the first value Garry gt dallas
The value at the lest side of the operator is key
and the key at the right side is its value.
We use keys to retrieve the value.
Hashes keys must be unique, u can not have more
than one entry for the same name., other wise it
will be over written.

103
Converting values between arrays and hashes

my _at_name qw (neha barve dheeraj kumar kshama
masihi vibha maltare shradha gavshinde)
print "_at_name", "\n"
my name1 _at_name
print name1kshama
my _at_newarray name1
print "_at_newarray"
Output
1st output neha barve dheeraj kumar kshama
masihi vibha maltare shradha gavshinde.
2nd output masihi
3rd output shradha gavshinde vibha maltare
kshama masihi dheeraj kumar neha barve

104
Flipping the hashes

If you want to retrieve ur hash by using value,
use reverse function.
my name (neha gt"barve", dheeraj gt
"kumar", kshamagt "masihi", vibhagt
"maltare", shradhagt "gavshinde")
My rev reverse name
This will interchange the hash keys into values.

105
Adding changing and taking value away from hashes

Adding value
phn aabha "sharma"
print "aabhas last name is phnaabha", "\n"
my _at_assign phn
print _at_assign ", "\n"
Changing value
phn aabha joshi"
print "aabhas last name is phnaabha", "\n"
my _at_assign phn
print _at_assign ", "\n"

106
Removing entry from hash

my name (neha gt"barve", dheeraj gt
"kumar", kshamagt "masihi", vibhagt
"maltare", shradhagt "gavshinde")
Delete namekshama

107
Accessing multiple values

Using for loop
my name (neha gt"barve", dheeraj gt
"kumar", kshamagt "masihi", vibhagt
"maltare", shradhagt "gavshinde")
For (keys name)
Print _ \last name is name_, \n
You can also use Keys for counting an hash.

108

Store your phn numbers in hash. Write a program
to look up numbers by the persons name.

109
Loops and Decision

Control structure which regulate flow of
execution.

110
The if statement

Lets have this example
!/strawberry/perl/bin/perl -w
use strict
my (from, to, value, rate)
my rates qw(pounds 1 dollars 1.6
marks 3.0 french 10 yen 174.8 swiss 2.43 euro
1.5)
print "enter the currency name u want to
convert"
to ltSTDINgt
print "enter the currency name u want to convert
into"
from ltSTDINgt
print "enter ur value"
valueltSTDINgt
chomp (from, value, to)
rate ratesfrom/ratesto
print "value of value in from is",
valuerate,"\n"

111

But what if value entered by user doesnt exist
in hashes
Here we use if loop

112

Lets have this example
!/strawberry/perl/bin/perl -w
use strict
my (from, to, value, rate)
my rates qw(pounds 1 dollars 1.6
marks 3.0 french 10 yen 174.8 swiss 2.43 euro
1.5 rs 50)
print "enter the currency name u want to convert
into"
from ltSTDINgt
print "enter the currency name u want to
convert"
to ltSTDINgt
print "enter ur value"
valueltSTDINgt
chomp (from, value, to)
if (not exists ratesto) die "worng entry
to"
if (not exists ratesfrom) die "wrong
enrtry from"
rate ratesfrom/ratesto
print "value of value in to is",
valuerate,"\n"

113
Actual if is like tht

if (not exists ratesto)
die "wrong entry to"
if (not exists ratesfrom)
die "wrong enrtry from"

114
How it works

By using IF statement we check that If the
currencies are valid entries in the hash.
Die is a way of making perl print out an error
message and finish the program.
The part in bracket (not exists ratesto) is
known as condition, if this condition Is true we
do the action in braces and terminate the program.

115

Another program using operators

116

!/strawberry/perl/bin/perl -w
use strict
my target 50
print "guess my number \n"
print "enter ur guess"
my guessltSTDINgt
if (targetguess)
print "here u r\, u guessed correctly"
if (targetgtguess)
print "nop ur number is smaller than me."
if (targetltguess)
print "nop ur number is bigger than me."

117
Comparing string
118

!/strawberry/perl/bin/perl -w
use strict
my password"hi"
print "enter password"
my guesltSTDINgt
chomp gues
if (password eq gues)
print "hello my friend"
if (password ne gues)
print "go away"

119
If condition operator

Exists
Not exists
Defined (whether variable are defined or not..)

120

How will u make sure that user didnt leave
string empty. See the part of program
my target 50
print "guess my number \n"
print "enter ur guess"
my guessltSTDINgt
if (guess)
print please enter ur value"
if (targetguess)
print "here u r\, u guessed correctly"

121
Unless loop

Another way of saying if(not exists)

122

!/strawberry/perl/bin/perl -w
use strict
my (from, to, value, rate)
my rates qw(pounds 1 dollars 1.6 marks 3.0
french 10 yen 174.8 swiss 2.43 euro 1.5)
print "enter the currency name u want to convert
into"
from ltSTDINgt
print "enter the currency name u want to
convert"
to ltSTDINgt
print "enter ur value"
valueltSTDINgt
chomp (from,value,to)
unless (exists ratesto)
die "worng entry to"
unless (exists ratesfrom)
die "wrong enrtry from"

123

Write a program to design currency converter
using unless loop to check whether user has
entered correct information or not.

124
Statement modifier

We can write above coding like this
Die u have entered wrong value in to
Unless exists(ratesto)
Die u have entered wrong value in from
Unless exists(ratesfrom)
Or
Die u have entered wrong value
If not exists(ratesto)
Die u have entered wrong value
If not exists(ratesfrom)

125
If else loop

my password"hi"
print "enter password"
my guesltSTDINgt
chomp gues
if (password eq gues)
print "hello my friend"
else
print "go away"

126
ifelsif

!/strawberry/perl/bin/perl -w
use strict
print "how is whether out side\n"
my whetherltSTDINgt
print "what is temp outside"
my templtSTDINgt
chomp(whether, temp)
if (whether eq "snow")
print "well we can go"
elsif (whether eq "rainy")
print "make a plan for tomorrow"
elsif (temp gt 20)
print "this is good to go outside"
else
print "no way"

127
Using and operator

!/strawberry/perl/bin/perl -w
use strict
print "how is whether out side\n"
my whetherltSTDINgt
print "what is temp outside"
my templtSTDINgt
chomp(whether, temp)
if (whether eq "snow" temp lt 30)
print "well we can go"
else
print "no way"

128
For/foreach loop

A simple example
!/strawberry/perl/bin/perl -w
use strict
my _at_arraqw(1 2 3 4 5 6)
for my i(_at_arra)
print i
print "\n"

129
Selecting a iterator

It is variable which can be selected inside or
outside of the loop.
E.g i

130
Finite and indefinite loop

A finite loop will always iterate for each item
in the array. While indefinite loop check the
condition and do the action.
For loop is definite loop
While loop in indefinite

131
While loop

While check the condition and perform action if
it is true.
!/strawberry/perl/bin/perl -w
use strict
my count0
while(countlt5)
print "here i m \n".count
count

132
Backward translation using reverse function and
while loop

while(ltSTDINgt)
chomp
die not done!\n" unless _
my sdrawkcabreverse _
print "sdrawkcab\n"

133
Do while
134
Until loop

Opposite of while loop.
my count5
until(count0)
print "count count\n"
count--

135
Controlling loop flow

my stop0
until(stop)
_ltSTDINgt
chomp
if(_)
print my backreverse(_)
else
stop1
print "end\n"
(when _ becomes empty string, the if test fails
and the control is transferred to else, which set
flag to 1 and until loop stops.)

136
Making an array using flag

!/strawberry/perl/bin/perl -w
use strict
!usr/bin/perl -w
_at_arr()
my stop0
until(stop)
_ltSTDINgt
chomp
if(_)
push(_at_arr, _)
else
stop1
print "_at_arr"

137
Breaking out statement

!/strawberry/perl/bin/perl -w
use strict
my _at_array("red","green","stop","blue")
for (_at_array)
last if _ eq "stop"
print "today's colour is _\n"

138
Going onto next statement
139
Regular expressions

These are the expressions to find out patterns in
paragraph, in a sentences, or in whole file.
A simple program
!/strawberry/perl/bin/perl -w
use strict
my word"hello there, how are you "
if(word/people/)
print "yes i found it."
else
print "nop i cant"
The output will be nop I cant.

Some imp tips Regular exp are embedded in / /
slashes. And for comparing a value operator is
used
140
Patterns to use

If(_ //)
Unless(_//)
Or
If(_ !//)
RE are very sensitive they match string from
start to end they consider comma, white spaces,
capitals and the whole word until specified.

141
Few examples which are not considered
142
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143
Perl insensitivity

We can modify this sentense by putting I at the
end of closing slash.

144
Interpolation of RE

!/strawberry/perl/bin/perl -w
use strict
_"we all are students of bioinformatics"
print "enter ur word of choice"
my choiceltSTDINgt
chomp(choice)
if(/choice/)
print "here u typed choice"
else
print "sorry word not found"
here we didnt use but RE interpret it this
is called interpoation just like double quoted
string.

145
Metacharecters

Just like in double quote if u want to turn off
effect of special characters, use \.
Eg.
If u want to search in a string
Or some special charectors like , , - _at_ ,?
Etc.
By using escape sequence
\Q removes effect of all 14 special character.
Anything which follows \Q loses its meaning.
Opposite of \Q is \E.
Eg if(/\Qpattern\E/)

146
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147
ANCHORS

To match the character at the beginning of the
string and at the end of the string.
Two types of anchors
anf
appear at the beginning of the pattern and
match the beginning of the string.
appears at the end of the pattern and match
end of the string.
E.g
In PIR format the sequence should be ended with
.
So we can match the pattern like this.
\.

148
coding

! Xampp/perl/bin/perl w
Use strict
While(ltgt)
If (/\/)
Print correct sequence
else
Print please enter PIR format only

Here is my input format
A T C T
Save this document naming pir.txt.
Now on command prompt
Perl hello.pl pir.txt

149
Similarly for matching pattern at the beggining

! Xampp/perl/bin/perl w
Use strict
While(ltgt)
If (/gt/)
Print correct sequence
else
Print please enter Fasta format only

Here is my input format
gt A T C T
Save this document naming fasta.txt.
Now on command prompt
Perl hello.pl fasta.txt

150
Matching pattern from a file

If u want to match pattern in a file.
Use while loop
!/strawberry/perl/bin/perl -w
use strict
my word"ing"
while(ltgt)
print if /word/
( open it using try.txt file)

151
How it works

While (ltgt) opens a file specified in command
prompt and loops through it line one by one
feeding each one into special variable _.
perl RE ignore new line character in each
word.

152
Character classes

To find out the pattern which are pretty much
irregular, we use character classes.
We put character we consider acceptable inside
square bracket.
E.g. wordpeel of mango.
Print enter the word u want to find
The into can be like this peiel.
This means that the character in may be followed
by e or i.

153
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154
\w metacharacter

To find out exact word pattern in a string
wordno one can make u feel inferior without
your consent
(no to find whether the above line contain 4
letter word)
If(/\s\w\w\w\w\s/)
..
(but only \w\w\w\w is wrongly interpreted)

155
Perl boundary (\b)

\b it matches the point between smthing tht is
not a character.
It matches the word pattern which are
specifically embedded by certain punctuations.
Like( , )
wordno one can make u feel inferior without
your consent
If (/\b\w\w\b/)
..

156
. metacharacter

To give particular range to pattern.
wordno one can make u feel inferior without
your consent
If (/i..er/)
..

157
class character (negation of character class)

If we want that given sequence of character
should not be present in word.
E.g.
word the principal shared nice thought
Now
Print enter the word u do not want to match
This my be theo
The th word should by neither e nor o
Similarly

158
Hyphen character class(-)

To find out the range of certain pattern
E.g.
0-9 to find out numerals in the string literal
a-z to find out lower case letter.
0-9a-z digit followed by any alphabet.
a-z0-9 alphabet followed by any digit.
0-9A-F to find out any hexadecimal number.
0-9A-Fa-f hexadecimal with lower case.

159

!/strawberry/perl/bin/perl -w
use strict
my (from, to, value, rate)
my rates qw(pounds 1 dollars 1.6 marks 3.0
french 10 yen 174.8 swiss 2.43 euro 1.5)
print "enter the currency name u want to convert
into"
from ltSTDINgt
print "enter the currency name u want to
convert"
to ltSTDINgt
print "enter ur value"
valueltSTDINgt
chomp (from,value,to)
unless (exists ratesto)
die "worng entry to"
unless (exists ratesfrom)
die "wrong enrtry from"

160
Statement modifier

We can write above coding like this
Die u have entered wrong value
Unless exists(ratesto)
Die u have entered wrong value
Unless exists(ratesfrom)
Or
Die u have entered wrong value
If not exists(ratesto)
Die u have entered wrong value
If not exists(ratesfrom)

161
If else loop

my password"hi"
print "enter password"
my guesltSTDINgt
chomp gues
if (password eq gues)
print "hello my friend"
else
print "go away"

162
ifelsif

!/strawberry/perl/bin/perl -w
use strict
print "how is whether out side\n"
my whetherltSTDINgt
print "what is temp outside"
my templtSTDINgt
chomp(whether, temp)
if (whether eq "snow")
print "well we can go"
elsif (whether eq "rainy")
print "make a plan for tomorrow"
elsif (temp gt 20)
print "this is good to go outside"
else
print "no way"

163
Using and operator

!/strawberry/perl/bin/perl -w
use strict
print "how is whether out side\n"
my whetherltSTDINgt
print "what is temp outside"
my templtSTDINgt
chomp(whether, temp)
if (whether eq "snow" temp lt 30)
print "well we can go"
else
print "no way"

164
For/foreach loop

A simple example
!/strawberry/perl/bin/perl -w
use strict
my _at_arraqw(1 2 3 4 5 6)
for my i(_at_arra)
print i
print "\n"

165
Selecting a iterator

It is variable which can be selected inside or
outside of the loop.
E.g i

166
Finite and indefinite loop

A finite loop will always iterate for each item
in the array. While indefinite loop check the
condition and do the action.
For loop is definite loop
While loop in indefinite

167
While loop