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.

The techniques 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

During the tutorial we will also consider the following uses for the techniques described:

• 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)