Introduction to Perl

1
Introduction to Perl

• Bioinformatics

2
What is Perl?

• Practical Extraction and Report Language
• A scripting language
• Components
• an interpreter
• scripts text files created by user describing a
  sequence of steps to be performed by the
  interpreter

3
Installation

• Create a Perl directory under C\
• Either
• Download AP.msi from the course website
  (http//curry.ateneo.net/jpv/BioInf07/) and
  execute (installs into C\Perl directory)
• Or download and unzip AP.zip into C\Perl
• Reset path variable first (or edit
  C\autoexec.bat) so that you can execute scripts
  from MSDOS
• Cgt pathpathc\Perl\bin

4
Writing and RunningPerl Scripts

• Create/edit script (extension .pl)
• Cgt edit first.pl
• Execute script
• Cgt perl first.pl
• Tip place your scripts in a separate work
  directory

my first script print Hello World print
this is my first script
5
Perl Features

• Statements
• Strings
• Numbers and Computation
• Variables and Interpolation
• Input and Output
• Files
• Conditions and Loops
• Pattern Matching
• Arrays and Lists

6
Statements

• A Perl script is a sequence of statements
• Examples of statements
• print Type in a value
• value ltgt
• square value value
• print The square is , square, \n

7
Comments

• Lines that start with are ignored by the Perl
  interpreter
• this is a comment line
• In a line, characters that follow are also
  ignored
• count count 1 increment count

8
Strings

• String
• Sequence of characters
• Text
• In Perl, characters should be surrounded by
  quotes
• I am a string
• I am a string
• Special characters specified through escape
  sequences (preceded by a \ )
• a newline\n and a tab\t

9
Numbers

• Integers specified as a sequence of digits
• 6
• 453
• Decimal numbers
• 33.2
• 6.04E24 (scientific notation)

10
Variables

• Variable named storage for values (such as
  strings and numbers)
• Names preceded by a
• Sample use
• count 5 assignment statement
• message Hello another assignment
• print count print the value of a variable

11
Computation

• Fundamental arithmetic operations
• - /
• Others
• exponentiation
• () grouping
• Example (try this out as a Perl script)
• x 4
• y 2
• z (3 x) y
• print z, \n

12
Interpolation

• Given the following script
• x Smith
• print Good morning, Mr. x
• print Good morning, Mr. x
• Strings quoted with perform expansions on
  variables
• escape characters like \n are also interpreted
  when strings are quoted with but not when they
  are quoted with

13
Input and Output

• Output
• print function
• Escape characters
• Interpolation
• Input
• Bracket operator (e.g., line ltgt )
• Not typed (takes in strings or numbers)

14
Input Files

• Opening a file
• open INFILE, data.txt
• Input
• line ltINFILEgt
• Closing a file
• close INFILE

15
Output Files

• Opening
• open OUTFILE, gtresult.txt
• Or, open OUTFILE, gtgtresult.txt append
• Input
• print OUTFILE Hello
• Closing files
• close OUTFILE

16
Conditions

• Can execute statements conditionally
• Syntax Example if ( condition ) if ( num gt
  1000 ) statement print Large
  statement

17
If - Else

• num ltgt
• if ( num gt 1000 )
• print Large number\n
• else
• print Small number\n
• print Thanks\n

18
Loops

• Repetitive execution
• Syntax Example while ( condition ) count
  0 while ( count lt 10 ) statement
  statement print counting-, count
  count count 1

19
Conditions

• ( expr symbol expr )
• Numbers equal lt less than or equal ! not
  equal gt greater than or equallt less
  thangt greater than
• Stringseq ne lt gt le ge pattern match

20
Functions

• length str returns number of characters in str
• defined str tests if str is a valid
  string (useful for testing if
  lineltgt suceeded)
• chomp str removes last character from
  str (useful because lineltgt includes the
  newline character)
• print var displays var on output device

21
Pattern Matching

• ltstringgt ltpatterngtis a condition that that
  checks if a string matches a pattern
• Simplest case ltpatterngt specifies a search
  substring
• Example if (s /bio/) holds TRUE if s is
  molecular biology, bioinformatics, the
  bionic manFALSE if s is chemistry,
  bicycle, a BiOpsy

22
Special pattern matching characters

• \w letters (word character)
• \d digit
• \s space character (space, tab \n)
• if ( s /\w\w\s\d\d\d/ ) holds TRUE for CS
  123 course,Take Ma 101 todayFALSE for Only
  1 number here

23
Special pattern matching characters

• . any character
• beginning of string/line
• end of string or line
• if ( s /\d\d\d\ss..r/ ) holds TRUE for 300
  spartansFALSE for all 100 stars

24
Groups and Quantifiers

• xyz character set
• alternatives
• zero or more
• 1 or more
• ? 0 or 1
• M exactly M
• M,N between M and N characters

25
NCBI file Example

• /VERSION\s(\S)\sGI(\S)/
• Matches a version line
• Parenthesis groups characters for future
  retrieval
• 1 stands for the first version number,2 gets
  the number after GI