UPDATED (Sun Feb 19 14:56:28 PST 2012)
High-throughput sequencing (HTS) is rapidly advancing our ability to understand how the genome responds to its environment. It also presents a challenge to those tasked with analyzing the results. Massive files can be produced that can overwhelm a modest computer’s store of available memory. The simplest way around this problem is to only work with a small part of the file at a time. I have provided an example of a very simple; easy to extend; and stand-alone python parser that returns a single fastQ record at a time to provide memory efficient access to these commonly massive files. It is also small, simple to understand, and does not depend on other packages.
