Perl Training Australia - Parsing Techniques for Bioinformatics

Trainer:	Damian Conway
Length:	1 day
Target Audience:	Perl programmers in bioinformatics-related fields who are familiar with simple regular expressions and the use of modules. The techniques presented are not restricted to the particular applications mentioned, and will be useful to anyone who needs to process structured bioinformatics data of any kind.

Parsing is the process of detecting and verifying the structure of incoming data and then processing that data so as to make it available to a program in convenient ways.

This full-day tutorial will introduce beginner and intermediate Perl programmers to the wide range of parsing mechanisms available in Perl and explain specific techniques for parsing data in a variety of commonly used formats. Most examples will be based on typical parsing problems encountered in Bioinformatics.

Topics covered include:

simple parsing with regexes
linear parsing with state machines
piece-wise parsing with extractors
structured parsing with grammars
processing comma-separated text
dealing with XML and other tagged formats
dealing with BLAST output and other heterogeneous structured formats
handling queries in synthetic and natural languages
extracting data structures from structured data
processing file inclusions
coping with incomplete, malformed, and ambiguous data
selecting and using appropriate parsing tools from the CPAN
integrating parsing and object oriented programming
data mining (parsing as a data recognition tool)
error detection and consistency checking (parsing as a data validation tool) structured I/O (parsing as a data acquisition tool)
recognition and extraction (parsing as a data search tool)
hierarchical data processing (parsing as a data transformation tool)
task specific languages (parsing as a command specification tool)