The programming language "Perl" for Biologists

Contents

1. Introduction (Quick start)

2. Variables and Data Formatting
Scalar variable
New line
Tab
Uppercase
Lowercase

3. Arithmetic Operations and Standard Input
Addition
Subtraction
Multiply
Division
Remainder
Exponent
Autoincrement
Autodecrement
Add assign
Subtract assign

4. Arrays
Quote word
Push
Pop
Unshift
Shift
Splice
Reverse
Sort
Join

5. Associative Arrays
Keys
Values
Each
Delete

6. Comparison Operators and Choices
Equal to
Not equal to
Greater than
Greater than or equal to
Less than
Less than or equal to
if
if-else
if-elsif-else
Boolean operators
AND
OR
NOT

7. Loops
For
While
Foreach

8. Regular Expressions
Match operator
Substitute operator
Translate operator

9. Functions for Strings
Index
Substr
Length
Reverse
Split

10. References
Dereferencing
Anonymous array
Anonymous associative array
Two dimensional array

11. Subroutines
Arguments
Scalar as an argument
Array as an argument
Associative array as an argument
Return

12. File and Directory Handling
Read
Write
Append
Open
File handle
Opendir
Directory handle
Readdir
Close

13. Modules and Packages

Reusable code

Namespace

About the book

This book is designed to be useful in theory and practical classes of UG and PG bioinformatics students. Moreover, it will be beneficial to other persons who wish to learn Perl programming language. To explain the Perl jargon, program based approach is used throughout the book. Important points are provided at the end of each chapter along with questions to test the skills. Solutions of find errors are provided at the end of the book. All the programs are tested on Windows 7 with Perl v5.18.1.

The book is divided into thirteen chapters which gradually take a reader from basic to advanced Perl. Although the book has been drafted with utmost care, it is quite possible that some errors/misprints might have crept in the book. I request the readers for their valuable suggestions and comments for further improvement of the book.

Acknowledgements

To my teachers, students, family, friends, and The Architect of Universe.

Preface

The interdisciplinary field of bioinformatics establishes itself as an indispensible branch of science. It is impossible to conduct the high throughput biological studies without the involvement of bioinformatics. Even it is difficult to imagine large scale biological projects which do not use any bioinformatics tool. To fulfill this requirement bioinformaticians have developed several tools that can help in the study of genomics, proteomics, metabolomics and other areas of biological sciences. Apart from this a large number of biological databases have also been developed which are sometimes a byproduct of high throughput research. Programming languages play a very important role in these developments.

Practical Extraction and Report Language (PERL) proved to be one of the most useful programming languages in such projects including the human genome sequencing project. The pattern matching and parsing capabilities of Perl suits the tasks required in biological science research which makes it a choice of bio-programmers. Researchers and academicians are extensively using Perl in devising programming solutions for problems related to biological data. Ever since Perl is one of the most important programming languages for a bioinformatician, therefore, throughout the country Perl is included as a core component in the syllabi of UG and PG courses in bioinformatics. During my teaching experience I found that students of diverse backgrounds opt for bioinformatics courses. Among them the students with biological background face lots of difficulty in learning programming languages. This prompted me to undertake this exciting, challenging project and put my several years of teaching and research experience in it. Perl for Biologists: Solutions for Beginners has been written keeping in view the requirements of Perl readers and incorporating the syllabi of the UG and PG bioinformatics courses of various Indian universities. I tried to express Perl in an easy, understandable language through lots of programming solutions which can be comfortably grasped by the learners. The layout of the book ensures that the readers can easily understand the given concepts without having prior knowledge of programming languages. I hope this book comes out as a useful publication. Enjoy Programming!!!

List of Perl Programs

Chapter 1 Introduction (Quick start)

Program 1.1 Test program

Chapter 2 Variables and Data Formatting

Program 2.1 Program to check case sensitivity of variables name

Program 2.2 Program to show interpolation

Program 2.3 Program to assign values to scalar variable

Program 2.4 Program to use \n and \t

Program 2.5 Program to convert characters in uppercase

Program 2.6 Program to convert characters in lowercase

Chapter 3 Arithmetic Operations and Standard Input

Program 3.1 Program to add numbers

Program 3.2 Program to subtract numbers

Program 3.3 Program to multiply numbers

Program 3.4 Program for division

Program 3.5 Program to get remainder of division

Program 3.6 Program to get exponent

Program 3.7 Program to autoincrement a number

Program 3.8 Program to autodecrement a number

Program 3.9 Program for addition and assignment

Program 3.10 Program for subtraction and assignment

Program 3.11 Program to get input using keyboard

Program 3.12 Program to get input using keyboard in interactive manner

Program 3.13 Program to get input using keyboard and display the entered value

Program 3.14 Program to get input using keyboard and check hidden new line character

Program 3.15 Program to get input using keyboard and remove new line character

Program 3.16 Program to get strings from keyboard

Program 3.17 Program to get strings from keyboard and remove new line using chop

Program 3.18 Program to check the effect of chomp on a string

Program 3.19 Program to check the effect of chop on a string

Chapter 4 Arrays

Program 4.1 Program to create an array of strings

Program 4.2 Program to create an array of numbers

Program 4.3 Program to create an array of strings and numbers

Program 4.4 Program to assign array using quote word function

Program 4.5 Program to use quote word function in interpolation mode

Program 4.6 Program to assign array using scalar variables

Program 4.7 Program to assign one array to another array

Program 4.8 Program to merge multiple array into one array

Program 4.9 Program to assign values to specific index of an array

Program 4.10 Program to check the size of array

Program 4.11 Program to empty an array

Program 4.12 Program to check the size of array without scalar function

Program 4.13 Program to check the last index of array

Program 4.14 Program to check the size of array using last index

Program 4.15 Program to check the last index of array using array size

Program 4.16 Program to print value stored in last index of array

Program 4.17 Program to add array element at the end

Program 4.18 Program to remove array element from end

Program 4.19 Program to remove array element from end and print the value

Program 4.20 Program to add array element in the beginning

Program 4.21 Program to remove array element from beginning

Program 4.22 Program to remove array element from beginning and print the value

Program 4.23 Program to remove array element from beginning and add it at the end

Program 4.24 Program to check the size of array after array manipulation

Program 4.25 Program to check the last index of array after array manipulation

Program 4.26 Program to insert elements in-between array indexes by replacing other elements

Program 4.27 Program to insert elements in-between array indexes without replacing other elements

Program 4.28 Program to remove element from in-between array indexes without adding new elements

Program 4.29 Program to empty an array from specific index

Program 4.30 Program to empty an array from specific index and check array size

Program 4.31 Program to reverse array

Program 4.32 Program to sort array

Program 4.33 Program to join array elements

Program 4.34 Program to check the effect of chop on array

Chapter 5 Associative Arrays

Program 5.1 Program to create associative array

Program 5.2 Program to check effect of double quotes on associative array

Program 5.3 Program to assign value to a specific key

Program 5.4 Program to print value of a key

Program 5.5 Program to retrieve keys

Program 5.6 Program to retrieve values

Program 5.7 Program to empty associative array

Program 5.8 Program to undefine a value associated with a key

Program 5.9 Program to delete a key-value pair

Program 5.10 Program to check the effect of chop on associative array

Chapter 6 Comparison Operators and Choices

Program 6.1 Program to check the equality of two numbers

Program 6.2 Program to check the non-equality of two numbers

Program 6.3 Program to check which number is greater

Program 6.4 Program to check whether number is greater than or equal

Program 6.5 Program to check which number is lesser

Program 6.6 Program to check whether number is less than or equal

Program 6.7 Program to check the logical error

Program 6.8 Program to use if-else

Program 6.9 Program to use if-elsif-else

Program 6.10 Program to check equality of strings

Program 6.11 Program to check non-equality of strings

Program 6.12 Program to check which string is greater

Program 6.13 Program to check whether string is greater or equal

Program 6.14 Program to check which string is lesser

Program 6.15 Program to check whether string is lesser or equal

Program 6.16 Program to check whether a key in associative array contains a defined value

Program 6.17 Program to check defined value of a key

Program 6.18 Program to check whether key a exists in associative array

Program 6.19 Program to check whether a key exists in associative arrays using nested if

Program 6.20 Program to check whether a key exists in associative arrays using AND operator

Program 6.21 Program to check whether a key exists in any one of two associative arrays using OR operator

Program 6.22 Program to use NOT operator

Chapter 7 Loops

Program 7.1 Program to print a series of numbers from 0-9 using for loop

Program 7.2 Program to print a series of numbers from 0-9 using while loop

Program 7.3 Program to print elements of array using foreach loop

Program 7.4 Program to print elements of array using for loop

Program 7.5 Program to print elements of array using while loop

Program 7.6 Program to print each key-value pair of associative array in new line using foreach

Program 7.7 Program to print each key-value pair of associative array in new line using while loop

Program 7.8 Program to print values of associative array in new line using for loop

Program 7.9 Program to print key-value pair of associative array using each function

Program 7.10 Program to skip iteration of loop using next

Program 7.11 Program to terminate the loop using last

Chapter 8 Regular Expressions

Program 8.1 Program to find a pattern using match operator

Program 8.2 Program to find a pattern

Program 8.3 Program to find a pattern and count number of occurrences

Program 8.4 Program to perform case sensitive search of a pattern

Program 8.5 Program to perform case insensitive search of a pattern

Program 8.6 Program to substitute a pattern using substitute operator

Program 8.7 Program to substitute all occurrences of a pattern using substitute operator

Program 8.8 Program to substitute pattern in case insensitive mode

Program 8.9 Program to generate complementary sequence using tr operator

Program 8.10 Program to replace ambiguous characters from DNA sequence

Program 8.11 Program to count characters in a sequence

Program 8.12 Program to count characters in a sequence and replace them

Program 8.13 Program to replace ambiguous characters from DNA sequence and count them

Program 8.14 Program to replace ambiguous characters from DNA sequence and squeeze the gaps

Program 8.15 Program to replace ambiguous characters from DNA sequence and delete the gaps

Program 8.16 Program to find patterns like GAA, GTA, GCA, GGA

Program 8.17 Program to find patterns with specific choices

Program 8.18 Program to find sequence accession number in fasta comment line

Program 8.19 Program to find sequence accession number using quantifiers

Program 8.20

Program to use backslash escaped characters to find sequence accession number

Program 8.21

Program to find a pattern using quantifier symbol ?

Program 8.22

Program to find a pattern 0 or 1 times

Program 8.23

Program to find a pattern using quantifier symbol +

Program 8.24

Program to find a pattern 1 or more times

Program 8.25

Program to find a pattern using quantifier symbol *

Program 8.26

Program to find a pattern 0 or more times

Program 8.27

Program to find a pattern exactly 3 times

Program 8.28

Program to find a pattern exactly 3 or more times

Program 8.29

Program to find a pattern with minimum 3 and maximum 5 occurrences

Chapter 9 Functions for Strings

Program 9.1

Program to check length of a string

Program 9.2

Program to reverse a string

Program 9.3

Program to break a string from desired character

Program 9.4

Program to break a string from individual characters

Program 9.5

Program to find the index of a substring

Program 9.6

Program to find all positions of a substring

Program 9.7

Program to retrieve a substring from a string

Chapter 10 References

Program 10.1

Program to create reference to scalar variable

Program 10.2

Program to dereference a reference

Program 10.3

Program to create reference to array and dereference it

Program 10.4

Program to retrieve value of an array index using reference

Program 10.5

Program to create anonymous array

Program 10.6

Program to create reference to associative array and dereference it

Program 10.7

Program to retrieve value associated with a key using reference

Program 10.8

Program to create anonymous associative array

Program 10.9

Program to create a reference of reference

Program 10.10

Program to check type of referent

Program 10.11

Program to create two dimensional array

Chapter 11 Subroutines

Program 11.1

Program to add two numbers using subroutine

Program 11.2

Program to add two numbers using subroutine and return the value

Program 11.3

Program to pass array to subroutine

Program 11.4

Program to pass two arrays to subroutine

Program 11.5

Program to pass two arrays to subroutine as reference

Program 11.6

Program to pass associative array to subroutine

Program 11.7

Program to pass two associative arrays to subroutine

Program 11.8

Program to pass two associative arrays to subroutine as reference

Chapter 12 File and Directory Handling

Program 12.1

Program to open a file and read the contents

Program 12.2

Program to open a file and read the contents line by line

Program 12.3

Program to open a file stored in another directory

Program 12.4

Program to open a file and write its contents in new file

Program 12.5

Program to open a file and write its contents in existing file

Program 12.6

Program to open a directory and get the file names

Program 12.7

Program to open a directory and get the relevant file names

Program 12.8

Program to open a directory and read the contents of all files one by one

Chapter 13 Modules and Packages

Program 13.1

Program to generate complementary DNA

Program 13.2

Program to generate complementary DNA using module stored in a directory

Program 13.3

Program to generate complementary DNA and RNA sequence using same subroutine name

Advice Before You Start

- Have patience.
- Carefully read the warnings and error messages.

Chapter 1

Introduction (Quick start)

- PERL is an acronym of Practical Extraction and Report Language developed by Larry Wall in 1987.
- Perl is freely available as a part of various operating system distributions (Linux, Mac etc.) and can be easily installed on Windows OS.
- To check the version of Perl installed on your system type perl –v followed by enter on command prompt (Start à Accessories à Command Prompt) and it will show you the installed version, if any.

Abbildung in dieser Leseprobe nicht enthalten.

- It is a case-sensitive, interpreter based, procedural programming language but can also be used to write programs in object oriented programming paradigm.
- Perl works with the motto that "There's more than one way to do it."
- To start with Perl open a text editor (Notepad in Windows and vim in Linux) and type following lines

print "Hello there";

save the file with filename “first_ program.pl”. To execute this Perl program type perl first_ program.pl on command prompt

Abbildung in dieser Leseprobe nicht enthalten.

- It is good to write comments in your program. A # sign is used to write comment in Perl and interpreter skips the text written after this sign.
- In this program the print function has been used to display the string (Hello there) on standard output (monitor).
- Almost all statements in Perl end with a semicolon (;).
- Windows users take care if Perl is not in the system path then save the program in Perl/bin folder where the interpreter will be present. Perl folder will be present in the directory where Perl has been installed.
- It is a good practice to save Perl programs with .pl extension and the program name must be related to the problem for which program is written. For example, substring.pl is a suitable name for a program that can be used to retrieve a substring from a string.

Points to remember

- Usually beginners do mistake by not remembering the location of program where it is saved. When program has been executed from any other location where it is not stored, an error message similar to “Can't open Perl script "ProgramName.pl": No such file or directory” appears on the command prompt.
- Always remember the location of the stored program. After opening the command prompt navigate to the same location where the program is stored then execute it.
- Type the program name correctly. Incorrect name leads to error message.
- Check whether Perl is present in system path. If not, ask system administrator to include it in the system path, otherwise save the program in Perl/bin folder and execute.

Test Yourself

1. Write a program to print your name.
2. Write a program to print your class.
3. Write a program to print the name of your institute.
4. Write a program to print your age.

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