An introduction to Perl programming for bioinformatics

Overview
The course starts by covering the standard syntax of the Perl programming language - variables, subroutines, operators, datatypes (scalars, arrays, and hashes) and the many Unix like functions built into Perl. Perl regular expressions and their uses in Bioinformatics are then covered. The penultimate parts of the course deal with Perl Objects, References and Modules and the basic implementation and use of Perl Modules, as well as using the Perl DBI module to access and manipulate databases.
The final part of the course provides an overview of CPAN and the various Perl Modules used in Bioinformatics.

Course Benefits
This course will benefit programmers who will be implementing Perl scripts and modifying or maintaining existing Perl scripts in their work as Bioinformatics professionals who need to familiarise themselves with Perl programming and how it can be used to tackle various problems that crop up in Bioinformatics.

Course Contents
Perl keywords, subroutines and variables Perl data types

• Scalars
• Arrays
• Hashes

Perl builtins and operators Control structures

• if - else blocks
• for loops, while loops and do - while loops

Regular expressions, string processing and pattern matching

• Record processing using split and join
• Regular expression syntax
• awk and sed style processing in Perl

Subroutines

• Defining
• Calling and parameter passing
• my local variables

File I/O in Perl

• Reading records into a Perl array
• Reading from and writing to Unix pipes

More complex data structures and their uses

• References to scalars, arrays and hashes
• Matrices
• Arrays of references to hashes
• Hashes of references to arrays
• Dynamic programming and approximate string matching

References to subroutines

• Basics
• Principles of object oriented programming in Perl
• Basics of Perl modules and their uses

Introduction to Perl and databases

• Overview of databases and SQL
• Perl DBI module
  • Connecting to a database (Data Source Name - DSN)
  • Creating, altering and deleting tables
  • Retrieving data from databases
  • Modifying data (ADD, UPDATE, DELETE)

Introduction to Bioperl

• Installing and testing Bioperl
• Overview of the Bioperl modules and their uses
  • Database modules
  • Sequence modules
  • Alignment modules
  • Modules for locating features and genes on sequences