Perl for Bioinformatics

1
Perl for Bioinformatics

• Stuart Brown
• NYU School of Medicine

2
Sources

• Beginning Perl for Bioinformatics
• James Tisdall, OReilly 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

• You can install Perl on any type of computer
• Your account on mcrcr0 already has Perl
• Just log in - you dont even need to type any
  command to make Perl active.
• Download and install Perl on your own computer
• www.perl.org

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 wont 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
• gtemacs my_perl1.pl
• Type
• !/usr/bin/perl
• my first Perl program
• print Hello world \n
• Awesome, isnt it!

11
Program details

• 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

• gtchmod ux .pl make the file executable
• gtperl 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
• 47
• 64
• 43-27
• 256/12
• 2/(3-5)

14
Do the Math (your 2nd Perl program)

• !/usr/bin/perl
• print 45\n
• print 45 , \n
• print 45 , 45 , \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 952.381

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, gt or lt)
• eq (equal )
• ne (not equal )
• ge (greater or equal )
• gt (greater than )
• lt (less than )
• le (less or equal )

Uses some non-intuitiveways of comparing
letters (ASCII values)