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FBW 30-09-2010 Wim Van Criekinge
 
Practicum Bioinformatica ,[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],What is Perl ?
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],What is Perl ?
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Why use Perl for bioinformatics ?
[object Object],[object Object],[object Object],[object Object],[object Object],Why NOT use Perl for bioinformatics ?
[object Object],[object Object],[object Object],[object Object],[object Object],What bioinformatics tasks are suited to Perl ?
Example of problems we will be solving ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Perl installation
Check installation ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
How to enter your first program ? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],The Command Prompt Text Editor
[object Object],[object Object],[object Object],[object Object],Some MSDOS commands
[object Object],[object Object],[object Object],[object Object],Review of File-Naming Rules
[object Object],[object Object],[object Object],[object Object],[object Object],The COPY Command
[object Object],[object Object],[object Object],[object Object],DOSKEY
[object Object],[object Object],Brief Introduction to Subdirectories—The Path
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Het absolute pad probleem …
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Het absolute pad probleem …
[object Object],[object Object],[object Object],[object Object],Redirection ,[object Object],[object Object]
[object Object],[object Object],Redirection
Perl
[object Object],[object Object],[object Object],[object Object],General Remarks
How does the  real  perl program look like:  #!/usr/local/bin/perl print “Hello everyone”; Mandatory first line (on UNIX) How to run it:  1. Save the text of your code as a file --  program.pl 2. Execute it: perl program.pl Hello everyone
Three Basic Data Types ,[object Object],[object Object],[object Object]
2+2 = ?   $a = 2; $b = 2; $c = $a + $b; $ - indicates a variable ; - ends every command = - assigns a value to a variable $c = 2 + 2; or $c = 2 * 2; or $c = 2 / 2; or $c = 2 ^ 4; or 2^4 <-> 2 4  =16 $c = 1.35 * 2 - 3 / (0.12 + 1); or
Ok, $c is 4. How do we know it?  print “Hello ”; print  command:  $c = 4; print “$c”; “ ” - bracket output expression  - print a end-of-the-line character (equivalent to pressing ‘Enter’) print “Hello everyone”; print “Hello” . ” everyone” . “”; Strings concatenation:  Expressions and strings together:  print “2 + 2 = “ . (2+2) . ””; expression 2 + 2 = 4
Loops and cycles ( for  statement):  # Output all the numbers from 1 to 100 for ($n=1; $n<=100; $n+=1) { print “$n ”; } 1. Initialization : for (  $n=1  ;  ;  ) { … } 2. Increment : for (  ;  ;  $n+=1  ) { … } 3. Termination (do until the criteria is satisfied) : for (  ;  $n<=100  ;  ) { … } 4. Body of the loop - command inside curly brackets : for (  ;  ;  )  { … }
FOR & IF -- all the even numbers from 1 to 100:  for ($n=1; $n<=100; $n+=1) { if (($n % 2) == 0) { print “$n”; } } Note: $a % $b -- Modulus    -- Remainder when $a is divided by $b
Two brief diversions (warnings & strict) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Grabbing user input ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Voorbeeldprogramma: DNA-invoer.pl ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Unary Arithmetic Operators eg. Autoincrement ++ ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Logical and Comparison operators ,[object Object],[object Object],[object Object],[object Object],[object Object]
Schuifoperatoren ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],>>2 <<3
Text Processing Functions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Random ,[object Object],[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object]
Bereken Pi aan de hand van twee random getallen 1 x y
Textpad ,[object Object],[object Object],[object Object],[object Object]

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Bioinformatica 29-09-2011-p1-introduction

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  • 2. FBW 30-09-2010 Wim Van Criekinge
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  • 24. Perl
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  • 26. How does the real perl program look like: #!/usr/local/bin/perl print “Hello everyone”; Mandatory first line (on UNIX) How to run it: 1. Save the text of your code as a file -- program.pl 2. Execute it: perl program.pl Hello everyone
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  • 28. 2+2 = ? $a = 2; $b = 2; $c = $a + $b; $ - indicates a variable ; - ends every command = - assigns a value to a variable $c = 2 + 2; or $c = 2 * 2; or $c = 2 / 2; or $c = 2 ^ 4; or 2^4 <-> 2 4 =16 $c = 1.35 * 2 - 3 / (0.12 + 1); or
  • 29. Ok, $c is 4. How do we know it? print “Hello ”; print command: $c = 4; print “$c”; “ ” - bracket output expression - print a end-of-the-line character (equivalent to pressing ‘Enter’) print “Hello everyone”; print “Hello” . ” everyone” . “”; Strings concatenation: Expressions and strings together: print “2 + 2 = “ . (2+2) . ””; expression 2 + 2 = 4
  • 30. Loops and cycles ( for statement): # Output all the numbers from 1 to 100 for ($n=1; $n<=100; $n+=1) { print “$n ”; } 1. Initialization : for ( $n=1 ; ; ) { … } 2. Increment : for ( ; ; $n+=1 ) { … } 3. Termination (do until the criteria is satisfied) : for ( ; $n<=100 ; ) { … } 4. Body of the loop - command inside curly brackets : for ( ; ; ) { … }
  • 31. FOR & IF -- all the even numbers from 1 to 100: for ($n=1; $n<=100; $n+=1) { if (($n % 2) == 0) { print “$n”; } } Note: $a % $b -- Modulus -- Remainder when $a is divided by $b
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  • 41. Bereken Pi aan de hand van twee random getallen 1 x y
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