Introduction to Perl
Matt Hudson
• blastall: Do a blast search
hmmpfam: search against HMM database
hmmsearch: search proteins with HMM
hmmbuild: make an HMM from a protein
alignment, as made by clustalw
• 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
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
go to the NCBI site
open a connection
same as UNIX
same as UNIX
get me this file
get more than one file
put a file on the server
local cd
local shell
close connection
exit the ftp program
• ftp
• 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
Perl books
For some reason, although there are hundreds of Perl books out there, none of
them are really that good. Here are some that might be useful, but none are
completely recommended.
This one I recommend EXCEPT that it uses tools that come with the book that
are non-standard:
Beginning Perl for Bioinformatics (Paperback)
by James Tisdall
This I have heard good things about but not used much myself:
Beginning Perl, Second Edition (Paperback)
by James Lee
This is a classic but slow going if you know no programming:
Learning Perl, Fourth Edition (Paperback)
by Randal L. Schwartz, Tom Phoenix, brian d foy
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, 3rd edition,
by Larry Wall, O’Reilly, 2001
Why use Perl?
• Interpreted language – quick to program
• Easy to learn compared to most
• 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.
• In Perl, the program, or script, is just a text
• You write it with ANY text editor (we are using
WordPad and/or nano).
• Run the program
• Look at the output
• Correct the errors (debugging)
• Edit the script and try again.
Remember your program?
All programming courses traditionally start with a
program that prints “Hello, world!”. So in keeping with
that tradition:
print “Hello, world\n”;
No line numbers.
Each command line ends with a semicolon
• All programming languages use “print” to mean “write this to
the console” – i.e. the command line.
• Once opon a time, the console was a typewriter. But now “print”
never means print on a printer.
• print statements are necessary to keep tabs on what your
program is doing.
• You need to tell Perl to put a carriage return at the end of a
printed line
– 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:
• 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
#cd scratch
(paste or type text into editor, save, and exit)
#chmod 755
• Programmers often find it easier to write out
the things the program is doing in “normal”
language. We call this pseudocode.
print “Hello, world\n”;
Output the text “Hello, world” to the terminal,
followed by a newline character.
• In Perl, strings are very important. They are
just a series of any text characters – letters,
numbers, ><?>:$%^&*, etc.
• In the statement
print “Hello, world\n”;
---- this is a string----
Numbers, etc
• The other common type of data is a number.
• Perl can handle numbers in most common formats,
without any complications:
• Arithmetic functions:
A program using numbers
print “2+2\n”;
print 3*4 , “\n”;
print “8/2=” , 8/2 , “\n”;
Do you get it?
Numbers in quotes are part of a string.
Numbers outside quotes are numbers, and
the computer does the math before printing.
print “2+2\n”;
Output “2+2”, followed by a newline, to the
print 3*4 , “\n”;
Evaluate 3 x 4, and print the answer, followed
by a newline, to the terminal
• Up till now, we’ve been telling the
computer exactly what to print. But in
order for the program to generate what
is printed, we need to use variables.
• A variable name starts with “$”
• 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;
my $dna_sequence_string = “acgt”;
A program with variables
#!/usr/bin/perl -w
#this program uses variables containing numbers
my $two = 2;
my $three = $two + 1;
print “\$two * \$three = $two * $three = “,($two *
print "\n";
my $two = 2;
Assign the value 2 to the variable $two
• When you print the variable, Perl gives the contents
rather than the name of the variable.
print $number;
• 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”;
The value of $number is 9
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
• 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.
– The angle bracket operator (<>) tells Perl to
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”;
my $num = <STDIN>;
Stop the program, and wait until the user
types input. Once the user hits the
“enter” key, take the input (including the
newline character) and put it into the
variable $num.
• When data is entered from the keyboard, the program
waits for you to type the carriage return key.
• But.. the string which is captured includes a newline
(carriage return) at its end
• You can use the chomp function to remove the
newline character:
“Enter your name: ”;
= <STDIN>;
“Hello $name, happy to meet you!\n”;
print “Hello $name, happy to meet you!\n”;
if and True/False
• All programming works on ones and zeros – true and
if (1 == 1) {
print “one equals one”;
Perl evaluates the expression (1 == 1 )
The if operator causes the command in curly
brackets to be executed ONLY IF the expression is true
• if evaluates some statement in
parentheses (must be true or false)
• Note: conditional block is indented,
using tabs.
– Perl doesn’t care about indents, but it
makes your code more “human readable”
Comparing variables
if ($one == $two) {print “one equals two”;}
Note there are TWO equals signs in this expression. If you
remember, = means “assign this variable this value”. So ==
actually means “equals”. You can also use
Greater than
Less than
Greater than or equal to
Less than or equal to
Not equal to
if ($one == $two) {print “one equals two”;}
If the contents of the variable $one are identical
to the contents of the variable $two, print “one
equals two”
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
• 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)
output “Enter your age: ” to the terminal
Stop the program, and wait until the user types input. Once the
user hits the “enter” key, take the input (including the newline
character) and put it into the variable $age.
Remove newline from $age if present
If the value in $age is less than 15, output “You are too young for
this kind of
work!” followed by a newline, then terminate the program with
the text “too young”
If the value in $age is more than 25,
output “You’re old enough to know better!” and then
terminate the program with the text “too old”.
If the program is still running (i.e. $age is between 15 and 25),
then output “You have much to learn!” followed by a newline.
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
die “too young”;
if ($age > 25) {
print “You’re old enough to know better!”;
die “too old”;
print “You have much to learn!\n”;
• An array can store multiple pieces of data.
• They are essential for the most useful
functions of Perl. They can store data such
– 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)
Converting an array to a variable
• join combines the elements of an array into a
single scalar variable (a string)
$dnastring = join('', @dnaarray);
(empty here)
which array
• 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 “;
Comparing strings
• String comparison (is the text the same?)
• eq (equal )
• ne (not equal )
There are others but beware of them!
Getting part of a string
• substr takes characters out of a
$letter = substr($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
$seq1= “ACTG”;
$seq2= “GGCTA”;
$seq3= $seq1 . $seq2;
print $seq3;
Making Decisions - review
• The if operator is generally used together
with numerical or string comparison
operators, inside an (expression).
==, !=, >, <, ≥, ≤
eq, ne
• 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

Perl for Bioinformatics - University of Illinois Crop Sciences