Introduce to perl ebook

I recommend having one of these books around in case you need some help using the command line: • For students who haven’t done much UNIX: Sams Teach Yourself Unix in 24 Hours 4th Editio

Introduction to Perl

Matt Hudson

(with thanks to Stuart Brown of NYU, for some great examples and

teaching ideas)

• clustalw: align protein or DNA sequences

• fasta34: search a sequence using an older, slower, but sometimes more flexible algorithm

grep – my favorite

• Allows you to pick out lines of a text file that match a query, count them, and retrieve lines around the

match.

grep ‘Query=’ myblast.txt

What sequences did I BLAST?

grep –c ‘>’ testprotein.txt

How many sequences are in this file?

grep –A 10 ‘>’ testprotein.txt

Give me the first ten lines of each protein

ftp commands

• ftp ftp.ncbi.nih.gov go to the NCBI site

• open open a connection

• ls same as UNIX

• cd same as UNIX

• get get me this file

• mget get more than one file

• put put a file on the server

• lcd local cd

• ! local shell

• close close connection

• bye exit the ftp program

Test time

• OK You are now up and running with UNIX, and can use it to do some fairly sophisticated bioinformatics

• We’re going to concentrate on Perl

scripting from now on

UNIX books

• You might find that your UNIX skills need some refreshing from time to time I recommend having one of these books around in case you need some help using the command line:

• For students who haven’t done much UNIX:

Sams Teach Yourself Unix in 24 Hours (4th Edition) (Sams Teach Yourself in 24 Hours) (Paperback)

by Dave Taylor

For more advanced UNIX users:

UNIX System V: A Practical Guide (3rd Edition) (Paperback)

by Mark G Sobell

• Also, for those of you not so familiar with bioinformatics:

Bioinformatics for Dummies (Paperback)

by Jean-Michel Claverie , Cedric Notredame , Jean-Michel Claverie ,

Cedric Notredame

This I have heard good things about but not used much myself:

Beginning Perl, Second Edition (Paperback)

This is a classic but slow going if you know no programming:

Learning Perl, Fourth Edition (Paperback)

This is better if you have little programming experience, but not a textbook:

Perl for Dummies (Fourth Edition) (Paperback)

by Paul Hoffman

• Once you get started

Programming Perl, 3 rd edition,

Why use Perl?

• Interpreted language – quick to program

• Easy to learn compared to most

languages

• Designed for working with text files

• Free for all operating systems

• Most popular language in bioinformatics – many scripts available you can

“borrow”, also ready made modules

• Run the program

• Look at the output

• Correct the errors (debugging)

• Edit the script and try again.

All programming courses traditionally start with a

program that prints “Hello, world!” So in keeping with

that tradition:

Note:

No line numbers.

Each command line ends with a semicolon

Remember your program?

#!/usr/bin/perl

print “Hello, world\n”;

– Use \n in a text string to signify a newline.

– The \ character is called “backslash”.

– It is an “escape” – it changes the meaning of the character after it In this case it changes “n” to “newline” Other

examples are \t (tab) or \$ (= print an actual dollar sign,

normally a dollar sign has a special meaning).

Program details

• Perl programs on UNIX start with a line like:

#!/usr/bin/perl

• Perl ignores anything after a # (this is a

command not to Perl, but to the UNIX shell).

• Elsewhere in the program # is used for

comments to explain the code.

• Lines that are Perl commands end with a semicolon (;).

Run your Perl program

• In Perl, strings are very important They are just a series of any text characters – letters, numbers, ><?>:$%^&*, etc.

• In the statement

print “Hello, world\n”;

this is a

string Numbers, etc

• The other common type of data is a number.

• Perl can handle numbers in most common formats, without any complications:

456 5.6743 6.3E-26

• Arithmetic functions:

+ (add)

- (minus) / (divide)

* (multiply)

** (exponentiation)

A program using numbers

#!/usr/bin/perl

print “2+2\n”;

print 3*4 , “\n”;

print “8/2=” , 8/2 , “\n”;

Do you get it?

Numbers in quotes are part of a string.

Numbers outside quotes are numbers, and

• Up till now, we’ve been telling the

computer exactly what to print But in order for the program to generate what

is printed, we need to use variables

• A variable name starts with “$”

• It can be either a string or a number

Assigning values

In pretty much all programming languages, = means

“assign this value to this variable”.

The “my” command in Perl initializes the variable This is optional but highly recommended.

So, you assign values to a variable as follows:

my $number = 123;

A program with variables

• If you put a variable inside double quotes, Perl

interpolates the variable

print “The number is $number\n”

The number is 9

• If you use single quotes, no interpolation happens

print ‘The number is $number\n’

The number is $number\n

• A more flexible way to do this is to “escape” the $

print “The value of \$number is $number\n”;

Variables - summary

• A variable name starts with a $

• It contains a number or a text string

• Use my to define a variable

• Use = to assign a value

• Use \ to stop the variable being

interpolated

• Take care with variable names and with changing the contents of variables

Standard Input

• To make the program do something, we need to input data

expect input, by default from the keyboard – Usually this is assigned to a variable

print “Please type a number: ”;

my $num = <STDIN>;

print “Your number is $num\n”;

Perl evaluates the expression (1 == 1 )

Note TWO NOT ONE EQUALS SIGNS!

The if operator causes the command in curly

brackets to be executed ONLY IF the expression is true

• if evaluates some statement in

parentheses (must be true or false)

• Note: conditional block is indented,

using tabs

– Perl doesn’t care about indents, but it

makes your code more “human readable”

Comparing variables

if ($one == $two) {print “one equals two”;}

Note there are TWO equals signs in this expression If you remember, = means “assign this variable this value” So == actually means “equals” You can also use

> Greater than

< Less than

>= Greater than or equal to

<= Less than or equal to

!= Not equal to

What’s a block?

• In the case of an “if” statement:

• If the test is true, execute all the

command lines inside the {} brackets If not, then go on past the closing } to the statements below

• You can also do stuff in a block over and

over again using a loop – more later.

die, scum

• die kills your script safely and prints a

message

• It is often used to prevent you doing

something regrettable – e.g running your script on a file that doesn’t exist, or

overwriting an existing file

Exercising the Perl muscles

• Now let’s write a script to ask the user their age, and then deliver an insult

specific to the age bracket:

• Over 25 - old fogey

• Under 15 – callow youth

• 15-25 – (insert your own insult here)

Conditional Blocks, summary

• An if test can be used to control multiple lines of commands, as in this example *

print “Enter your age: ”;

$age = <STDIN>;

chomp $age;

if ($age < 15) { print “You are too young for this kind of work!\n”;

die “too young”;

}

if ($age > 25) {

print “You’re old enough to know better!”;

die “too old”;

}

• An array can store multiple pieces of data

• They are essential for the most useful

functions of Perl They can store data such as:

– the lines of a text file (e.g primer sequences) – a list of numbers (e.g BLAST e values)

• Arrays are designated with the symbol @

my @bases = (“A”, “C”, “G”, “T”);

Converting a variable to an array

split splits a variable into parts and puts them

in an array.

my $dnastring = "ACGTGCTA";

my @dnaarray = split //, $dnastring;

@dnaarray is now (A, C, G, T, G, C, T, A)

@dnaarray = split /T/, $dnastring;

@dnaarray is now (ACG, GC, A)

• join combines the elements of an array into a single scalar variable (a string)

$dnastring = join('', @dnaarray);

Converting an array to a variable

which array spacer

(empty here)

• A loop repeats a bunch of functions until it is done The functions are placed in a BLOCK – some code delimited with curly brackets {}

• Loops are really useful with arrays.

• The “foreach” loop is probably the most useful of all:

foreach my $base (@dnaarray) {

print "$base “;

}

• String comparison (is the text the same?)

• eq (equal )

• ne (not equal ) There are others but beware of them!

Comparing strings

Getting part of a string

• substr takes characters out of a

string

$letter = substr($dnastring, $position, 1)

which string where in

the string

how many letters to take

Combining strings

• Strings can be concatenated (joined)

• Use the dot . operator

Making Decisions - review

• The if operator is generally used together

with numerical or string comparison

operators, inside an (expression)

numerical: ==, !=, >, <, ≥, ≤

• You can make decisions on each member

of an array using a loop which puts each

part of the array through the test, one at a

More healthy exercise

• Write a program that asks the user for a DNA restriction site, and then tells them whether that particular sequence matches the site for the restriction enzyme EcoRI, or Bam HI, or Hind III.

• Site for EcoR1: GAATTC

• Bam H1: GGATCC

• Hind III: AAGCTT