Transcript Document

Introduction to Perl
Yupu Liang
cbio at MSKCC
[email protected]
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
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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
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Define the problem
Search for existing code
Plan your solution
Write the code
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Modify ->Debug ->Modify
Run the code
Unix Basic
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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
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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”
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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 $name.\n”;
Perl Data Types
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Scalar: a single piece of information. Scalars
can hold numbers or text
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List: an ordered collection of scalars
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$ is the identifier of scalar in perl
There are special variables for the system:
$ARGV,$!
@array = ( 1, 2 )
@words = ( "first", "second", "third" )
Hash: special arrays with words as index.
Scalars
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$num = 42
$num2 = “42”
$name = ‘joe’
$color = “blue”
$string_w_num = “I have 10 apples”
$foo = undef
$foo = “”
$foo =‘’
Scalar Functions:
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length
reverse
index
http://perldoc.perl.org/perlfunc.html#Perl-Functions-by-Category
Quoting:
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double quotes(“), single quotes(‘) and multiline quoting(qq) :
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$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
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if/else
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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
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Undefined values are treated as false
Scalars are evaluated as:
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numbers are evaluated as true if non-zero
strings are evaluated as true if non-empty
$var = “false”;
if($var)
{
print “$var is true!\n”;
}
Handling user inputs
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Scripts can take inputs in two ways:
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Arguments
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./print_args.pl ARG1 ARG2
Prompted inputs from users
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$user_text = <STDIN>
Error/Exception Handling
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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
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Die
Warn
Write some scripts!