1. Bioperl modules

2. Object Oriented Programming in Perl (1)
Defining a class
A class is simply a package with subroutines that function as methods.
#!/usr/local/bin/perl
package Cat;
sub new { … }
sub meow {

3. Object Oriented Programming in Perl (2)
Perl Object
To initiates an object from a class, call the class “new” method.
$new_object = new ClassName;
Using Method
To use the methods of an object, use the “->” operator.
$cat->meow();

4. Object Oriented Programming in Perl (3)
Inheritance
Declare a class array
This array store the name and parent class(es) of the new species.
package NorthAmericanCat;
@NorthAmericanCat::ISA = (“Cat”);
sub new { … }

5. Perl Modules
A Perl module is a reusable package defined in a library file whose name is the same as the name of the package.

6. Names of perl modules Each Perl module has a unique name.
To minimize name space collision, Perl provides a hierarchical name space for modules.
Components of a module name are separated by double colons (::).
For example,
Math::Complex
Math::Approx
String::BitCount
String::Approx

7. Module files Each module is contained in a single file.
Module files are stored in a subdirectory hierarchy that parallels the module name hierarchy.
All module files have an extension of .pm.
Module
Is stored in
Config
Config.pm
Math::Complex
Math/Complex.pm
String::Approx
String/Approx.pm

8. Module libraries
The Perl interpreter has a list of directories in which it searhces for modules.
Global
>perl –V
@INC:
/usr/local/lib/perl5/ /sun4-solaris
/usr/local/lib/perl5/
/usr/local/lib/perl5/site-perl/5.005/sun4-solaris
/usr/local/lib/perl5/site-perl/5.005

9. Using Modules A module can be loaded by calling the use function.
use Foo;
bar( “a” ); # using bar method
blat( “b” ); # using blat method

10. Bioperl toolkit Core package (bioperl-live) Run package (bioperl-run)
THE basic package and it’s required by all the other packages
Run package (bioperl-run)
Providing wrappers for executing some 60 common bioinformatics applications
DB package (bioperl-db)
Subproject to store sequence and annotation data in a BioSQL relational database
Network package (bioperl-network)
Parses and analyzes protein-protein interaction data
Dev package (bioperl-dev)
New and exploratory bioperl development

12. Bioperl Object-Oriented
The Bioperl takes advantages of the OO design to create a consistent, well documented, object model for interacting with biological data in the life sciences.
Bioperl Name space
The Bioperl package installs everything in the Bio:: namespace.
(where are the packages stored???)

13. Bioperl Objects Sequence handling objects Other Objects:
Sequence objects
Alignment objects
Location objects
Other Objects:
3D structure objects, tree objects and phylogenetic trees, map objects, bibliographic objects and graphics objects

14. Sequence handling Typical sequence handling tasks: Access the sequence
Format the sequence
Sequence alignment and comparison
Search for similar sequences
Pairwise comparisons
Multiple alignment

15. Sequence Annotation
Bio::SeqFeature Sequence object can have multiple sequence feature (SeqFeature) objects (e.g. Gene, Exon, or Promoter objects) associated with it.
Bio::Annotation A Seq object can also have an Annotation object (used to store database links, literature references and comments) associated with it

16. Sequence Input/Output
The Bio::SeqIO system was designed to make getting and storing sequences to and from the myriad of formats as easy as possible.

17. Accessing sequence data
Bioperl supports accessing remote databases as well as local databases.
Bioperl currently supports sequence data retrieval from the GenBank, Genpept, RefSeq, SwissProt, and EMBL databases

18. Format the sequences
SeqIO object can read a stream of sequences in one format: Fasta, EMBL, GenBank, Swissprot, PIR, GCG, SCF, phd/phred, Ace, or raw (plain sequence), then write to another file in another format

19. Manipulating sequence data
$seqobj->display_id() # the human readable id of the sequence
$seqobj->subseq(5,10) # part of the sequence as a string $seqobj->desc() # a description of the sequence
$seqobj->trunc(5,10) # truncation from 5 to 10 as new object
$seqobj->revcom # reverse complements sequence
$seqobj->translate # translation of the sequence …

20. Search result parsing
The Bio::SearchIO system was designed for parsing sequence database searches (BLAST, sim4, waba, FASTA, HMMER, exonerate, etc.)

21. Manipulating alignment
The Bio::AlignIO system was designed for manipulating the alignment objects in different formats including aln, phylip, fasta, etc.

22. Example: Format the sequences
Example: using “seq_formating.pl” to convert “sequences.gb” to another format

23. Copy the files to the current directory
Check whether the files are executable
Now, let’s look at the genbank file.

24. The home directory in Windows system.
If you have Notepad++ installed, click “Edit with Notepad++”.
If not, try to open “sequence.gb” with Notepad program.

26. uncheck

27. The format of the input sequences.

28. The perl script file

30. If no arguments were supplied, a usage information will appear for instructions.

31. Input file Output file <enter> Program name
Format of the input sequences
Format of the output sequences
Input file
Output file

32. Program suceeded!
Now it’s time to look at the file generated.

33. Use ‘command prompt’ to run the script

34. Type:
cd<space>c:\BioDownload
To enter the BioDownload folder

35. Type:
dir
To display the files in the current folder (NOT ls)
You should have the following files in the folder
(you may have other files, but that’s fine):
seq_formating.pl
sequences.gb.txt

36. Type:
perl<space>seq_formating.pl<space>sequences.gb.txt<space>genbank<space>sequences.fasta<space>fasta

37. Output file

38. The format of the output sequences.

39. Parsing the BLAST output
What’s next:
Parsing the BLAST output