1. Perl for Bioinformatics
Stuart Brown
NYU School of Medicine

2. Sources Beginning Perl for Bioinformatics
James Tisdall, O’Reilly Press, 2000
Using Perl to Facilitate Biological Analysis in Bioinformatics: A Practical Guide (2nd Ed.)
Lincoln Stein, Wiley-Interscience, 2001
Introduction to Programming and Perl
Alan M. Durham, Computer Science Dept., Univ. of São Paulo, Brazil

3. Why Write Programs?
Automate computer work that you do by hand - save time & reduce errors
Run the same analysis on lots of similar data files = scale-up
Analyze data, make decisions
sort Blast results by e-value &/or species of best mach
Build a pipeline
Create new analysis methods

4. Why Perl? Fairly easy to learn the basics
Many powerful functions for working with text: search & extract, modify, combine
Can control other programs
Free and available for all operating systems
Most popular language in bioinformatics
Many pre-built “modules” are available that do useful things

5. Get Perl www.perl.org You can install Perl on any type of computer
Your account on mcrcr0 already has Perl
Just log in - you don’t even need to type any command to make Perl active.
Download and install Perl on your own computer:

6. Programming Concepts
Program = a text file that contains instructions for the computer to follow
Programming Language = a set of commands that the computer understands (via a “command interpreter”)
Input = data that is given to the program
Output = something that is produced by the program

7. Programming Write the program (with a text editor) Run the program
Look at the output
Correct the errors (debugging)
Repeat
(computers are VERY dumb -they do exactly what you tell them to do, so be careful what you ask for…)

8. Strings Text is handled in Perl as a string
This basically means that you have to put quotes around any piece of text that is not an actual Perl instruction.
Perl has two kinds of quotes - single ‘ ‘ and double “ “
(they are different- more about this later)

9. Print Perl uses the term “print” to create output
Without a print statement, you won’t know what your program has done
You need to tell Perl to put a carriage return at the end of a printed line
Use the “\n” (newline) command
Include the quotes
The “\” character is called an escape - Perl uses it a lot

10. Your First Perl Program
Log in to mcrcr0
Open a new text file
>emacs my_perl1.pl
Type:
#!/usr/bin/perl
# my first Perl program
print “Hello world \n”;
Awesome, isn’t it!

11. Program details #!/usr/bin/perl
Perl programs always start with the line:
#!/usr/bin/perl
this tells the computer that this is a Perl program and where to get the Perl interpreter
All other lines that start with # are considered comments, and are ignored by Perl
Lines that are Perl commands end with a ;

12. Run your Perl program >chmod u+x *.pl [#make the file executable]
>perl my_perl1.pl
[#use the perl interpreter to run your script]

13. Numbers and Functions Perl handles numbers in most common formats:
456
5.6743
6.3E-26
Mathematical functions work pretty much as you would expect:
4+7
6*4
43-27
256/12
2/(3-5)

14. Do the Math (your 2nd Perl program)
#!/usr/bin/perl
print “4+5\n”;
print 4+5 , “\n”;
print “4+5=” , 4+5 , “\n”;
[Note: use commas to separate multiple items in a print statement, whitespace is ignored]

15. Variables
To be useful at all, a program needs to be able to store information from one line to the next
Perl stores information in variables
A variable name starts with the “$” symbol, and it can store strings or numbers
Variables are case sensitive
Give them sensible names
Use the “=”sign to assign values to variables
$one_hundred = 100
$my_sequence = “ttattagcc”

16. You can do Math with Variables
#!/usr/bin/perl
#put some values in variables
$sequences_analyzed = 200 ;
$new_sequences = 21 ;
#now we will do the work
$percent_new_sequences =( $new_sequences /
$sequences_analyzed) *100 ;
print “% of new sequences = ” , $percent_new_sequences;
% of new sequences =

17. String Operations
Strings (text) in variables can be used for some math-like operations
Concatenate (join) use the dot . operator
$seq1= “ACTG”;
$seq2= “GGCTA”;
$seq3= $seq1 . $seq2;
print $seq3
ACTGGGCTA
String comparison (are they the same, > or <)
eq (equal )
ne (not equal )
ge (greater or equal )
gt (greater than )
lt (less than )
le (less or equal )
Uses some non-intuitive ways of comparing letters (ASCII values)