Bioperl modules

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Bioperl modules
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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
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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 -gt
  operator.

cat-gtmeow()
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Object Oriented Programming in Perl (3)

• Inheritance
• Declare a class array called _at_ISA.
• This array store the name and parent class(es) of
  the new species.

package NorthAmericanCat _at_NorthAmericanCatISA
(Cat) sub new
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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.

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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,
• MathComplex
• MathApprox
• StringBitCount
• StringApprox

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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
MathComplex Math/Complex.pm
StringApprox String/Approx.pm
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Module libraries

• The Perl interpreter has a list of directories in
  which it searhces for modules.
• Global arry _at_INC

• gtperl V
• _at_INC
• /usr/local/lib/perl5/5.00503/sun4-solaris
• /usr/local/lib/perl5/5.00503
• /usr/local/lib/perl5/site-perl/5.005/sun4-solaris
  
• /usr/local/lib/perl5/site-perl/5.005

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Using Modules

• A module can be loaded by calling the use
  function.
• use Foo
• bar( a ) using bar method
• blat( b ) using blat method

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Bioperl toolkit

• Core package (bioperl-live)
• THE basic package and its 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

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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???)

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Bioperl Objects

• Sequence handling objects
• Sequence objects
• Alignment objects
• Location objects
• Other Objects
• 3D structure objects, tree objects and
  phylogenetic trees, map objects, bibliographic
  objects and graphics objects

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Sequence handling

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

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Sequence Annotation

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

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Sequence Input/Output

• The BioSeqIO system was designed to make
  getting and storing sequences to and from the
  myriad of formats as easy as possible.

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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

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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

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Manipulating sequence data

• seqobj-gtdisplay_id() the human readable id of
  the sequence
• seqobj-gtsubseq(5,10) part of the sequence as
  a string seqobj-gtdesc() a description of the
  sequence
• seqobj-gttrunc(5,10) truncation from 5 to 10
  as new object
• seqobj-gtrevcom reverse complements sequence
• seqobj-gttranslate translation of the
  sequence

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Search result parsing

• The BioSearchIO system was designed for
  parsing sequence database searches (BLAST, sim4,
  waba, FASTA, HMMER, exonerate, etc.)

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Manipulating alignment

• The BioAlignIO system was designed for
  manipulating the alignment objects in different
  formats including aln, phylip, fasta, etc.

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Example Format the sequences

• Example
• using seq_formating.pl to convert
  sequences.gb to another format

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Copy the files to the current directory
Check whether the files are executable
Now, lets look at the genbank file.
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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.
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uncheck
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The format of the input sequences.
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The perl script file
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If no arguments were supplied, a usage
information will appear for instructions.
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ltentergt
Program name
Format of the input sequences
Format of the output sequences
Input file
Output file
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Program suceeded! Now its time to look at the
file generated.
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Use command prompt to run the script
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Type cdltspacegtc\BioDownload To enter the
BioDownload folder
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• 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 thats fine)
• seq_formating.pl
• sequences.gb.txt

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Type perlltspacegtseq_formating.plltspacegtsequences.
gb.txtltspacegtgenbankltspacegtsequences.fastaltspacegtf
asta
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Output file
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The format of the output sequences.
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Parsing the BLAST output
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