PowerPoint Presentation - Introduction to Perl by ojp13483

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									Introduction to Perl

              Yupu Liang
            cbio at MSKCC
        liang@cbio.mkscc.org
what is perl
  „A general-purpose programming language originally developed for text manipulation
  and now used for a wide range of tasks including system administration,
  web development, network programming, GUI development, and more.‟


  Practical Extraction and Report Language
  And:

  „The language is intended to be PRACTICALl (easy to use, efficient, complete) rather than
   BEAUTIFUL (tiny, elegant, minimal).‟

    And Some More:

  „Many earlier computer languages, such as Fortran and C, were designed to make efficient use of expensive
  computer hardware. In contrast, Perl is designed to make efficient use of expensive computer programmers.

  Perl has many features that ease the programmer's task at the expense of greater CPU and memory requirements.
  These include automatic memory management; dynamic typing; strings, lists, and hashes; regular expressions;
  introspection and an eval() function.

  Larry Wall was trained as a linguist, and the design of Perl is very much informed by linguistic principles. Examples
  include Huffman coding (common constructions should be short), good end-weighting (the important information should
  come first), and a large collection of language primitives. Perl favors language constructs that are natural for humans to
   read and write, even where they complicate the Perl interpreter.‟
Why do Biologists Use Perl?
 Largely for the same reasons other people
  use perl
      Relatively easy to learn (and easier to make a
       mess too).
      Tones of reusable code exists (bioperl).
      incredibly flexible coding style (some argues it
       is too flexible).
How to Use Perl
   Define the problem
   Search for existing code
   Plan your solution
   Write the code
       Modify ->Debug ->Modify
   Run the code
Unix Basic
   Terminal
   Directories structure
   Files
Unix Basics: Commands
  „ls‟ - list contents of directory
  „cd‟ - change directory
  „pwd‟ - path of current directory
  „cp‟ - copy
  „mv‟ - move
  „more‟ - list contents of file
  „touch‟ - create empy file
  „chmod‟ - change file permission

  *note, to get detailed help on any command you can usually type
  „man COMMAND‟, „COMMAND -h‟, or „COMMAND --help‟.

  *google is very good on finding the right command
Unix Basic: Text Editors
   Text editors are used to view/create/edit
    text files
   You may use any text editor during the
    course
   Emacs is a popular choice among perl
    programmers
First program: “Hello World”
   Open a terminal
   Make a perl dir(directory) in your home dir
   Move into the perl directory
   Create a file named „hello_world.pl‟
   Open the file in your text editor
   Code the program
   Save the file
   Make the program executable
   Test the program.
Perl script

    #!/usr/bin/perl -w
    use strict;

    my $name = „yupu‟;
    print “\n hello world from $name.\n”;
Perl Data Types
   Scalar: a single piece of information. Scalars
    can hold numbers or text
       $ is the identifier of scalar in perl
       There are special variables for the system:
        $ARGV,$!

   List: an ordered collection of scalars
       @array = ( 1, 2 )
       @words = ( "first", "second", "third" )
   Hash: special arrays with words as index.
Scalars
   $num = 42
   $num2 = “42”
   $name = „joe‟
   $color = “blue”
   $string_w_num = “I have 10 apples”
   $foo = undef
   $foo = “”
   $foo =„‟
Scalar Functions:
   length
   reverse
   index

http://perldoc.perl.org/perlfunc.html#Perl-Functions-by-Category
Quoting:
   double quotes(“), single quotes(„) and multi-
    line quoting(qq) :
       $var =10;
       $text = “There are $var apples”
       $text2 = „There are $var apples‟
       $text3 = qq{
          There
          are
          $var
          apples};
 Functions/Subtroutines
Functions are blocks of code which perform specific task
#takes no input and returns no output… common practice to use
            #„main‟ as the starting point in a script.
            sub main {
                        …
            }

           #Takes 2 *scalars* as input sums them and returns one scalar.
           sub sum_2_numbers {
                      my ($numA,$numB) = @_; #get passed in values

                      my $sum = $numA+$numB; #sum numbers
                      return($sum); #return sum
           }
Control Structures: conditional
statements
   if/else
       If statements are conditional statements used to test whether or not
        some condition is met and then continue executing the script. The
        syntax for an if statement has a specific flow to it -
        if(conditional_statment) { code to execute; }
       Logical operators: ==, !=, &&, ||, eq and ne



   unless
Boolean
   Undefined values are treated as false
   Scalars are evaluated as:
        numbers are evaluated as true if non-zero
        strings are evaluated as true if non-empty

$var = “false”;
if($var)
{
    print “$var is true!\n”;
}
Handling user inputs
   Scripts can take inputs in two ways:
       Arguments
            ./print_args.pl ARG1 ARG2
       Prompted inputs from users
            $user_text = <STDIN>
Error/Exception Handling
   Things don‟t always come out as
    expected. It is good to check the output
    of important functions for errors, it is
    highly recommended to validate any
    input from users or external sources
       Die
       Warn
Write some scripts!

								
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