Bioinformatica 06-10-2011-p2 introduction

FBW 06-10-2011 Wim Van Criekinge

Practicum Bioinformatica ,[object Object],[object Object],[object Object],[object Object],[object Object]

Programming ,[object Object],[object Object],[object Object],[object Object],[object Object]

Three Basic Data Types ,[object Object],[object Object],[object Object]

Customize textpad part 1: Create Document Class

Customize textpad part 2: Add Perl to “Tools Menu”

[object Object],[object Object],[object Object],[object Object],[object Object]

Unzip to textpad samples directory

Bereken Pi aan de hand van twee random getallen 1 x y

[object Object],[object Object],[object Object],[object Object]

Two brief diversions (warnings & strict) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Practicum Bioinformatica ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

What is a regular expression? ,[object Object],[object Object],[object Object]

Why would you use a regex? ,[object Object],[object Object],[object Object],[object Object],[object Object]

Regular Expressions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

[object Object],[object Object],[object Object]

Regular Expressions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Constructing a Regex ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Looking for a pattern ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Regular Expression Atoms ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

More atoms ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

An example ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Quantifiers ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Anchors ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Grouping ,[object Object],[object Object],[object Object],[object Object]

Alternation ,[object Object],[object Object],[object Object]

Variable interpolation ,[object Object],[object Object],[object Object],[object Object],[object Object]

Regular Expression Review ,[object Object],[object Object],[object Object],[object Object]

Remembering Stuff ,[object Object],[object Object],[object Object],[object Object],[object Object]

Memory Parentheses (pattern memory) ,[object Object],[object Object],[object Object],[object Object]

Getting at pattern memory ,[object Object],[object Object],[object Object],[object Object],[object Object]

An example of pattern memory ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Finding all instances of a match ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Perl is Greedy ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Substitute function ,[object Object],[object Object],[object Object],[object Object],[object Object]

Using s ,[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]

tr function ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Using tr ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Regex ,[object Object],[object Object],[object Object]

Oefeningen practicum 2 ,[object Object],[object Object],[object Object],[object Object],http://us.expasy.org/prosite/

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Arrays ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

The foreach construct ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Examples for using the foreach construct - cont. ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Accessing individual array elements ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

The sort function ,[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]

The push and shift functions ,[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]

How can I know the length of a given array? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Special array for command line arguments @ARGV ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Perl Array review ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Generate random string ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Text Processing Functions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Text Processing Functions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

When is an array not good enough? ,[object Object],[object Object],[object Object],[object Object]

Problem solved: The associative array ,[object Object],[object Object],[object Object],[object Object],[object Object]

The ‘structure’ of a Hash ,[object Object],[object Object],Index Value

The ‘structure’ of a Hash ,[object Object],[object Object],[object Object],Index Value Key (name) Value ,[object Object]

Hash Rules: ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Creating a hash ,[object Object],[object Object],[object Object],[object Object],[object Object]

Getting at values ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Getting at values, continued ,[object Object],[object Object],[object Object]

A phone book 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],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Count unique things with a hash

Printing a Hash ,[object Object],[object Object],[object Object],[object Object]

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Printing a hash (continued)

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Programming in general and Perl in particular

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Programming in general and Perl in particular

[object Object],[object Object],Oefeningen practicum 2

[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],[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],'AUU','I', 'AUC','I', 'AUA','I', 'AUG','M', 'ACU','T', 'ACC','T', 'ACA','T', 'ACG','T', 'AAU','N', 'AAC','N', 'AAA','K', 'AAG','K', 'AGU','S', 'AGC','S', 'AGA','R', 'AGG','R', 'GUU','V', 'GUC','V', 'GUA','V', 'GUG','V', 'GCU','A', 'GCC','A', 'GCA','A', 'GCG','A', 'GAU','D', 'GAC','D', 'GAA','E', 'GAG','E', 'GGU','G', 'GGC','G', 'GGA','G', 'GGG','G' );

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Palin.fasta ,[object Object],[object Object]

Palingram.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],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],print "Set van palingram"; while(($key, $value) = each (%palhash)) { print "$key => $value"; }

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Bioinformatica 06-10-2011-p2 introduction