[BioPython] Useful modules for biological programming

[Michael Hoffman]

Hey folks. I've written some modules that may be of use to biologists
and bioinformaticians. There is a module for fast access to General
Feature Format files through a MySQL database, which seems to be
interoperable with Lincoln Stein's Bio::DB::GFF. There's also a
feature table location parser, and tools to make dealing with SQL,
flat file databases easier and some other fun stuff. A fuller
description is below.

It is available under the Biopython license. If anyone is interested
in incorporating some of this code into Biopython, let me know.

MODULE DESCRIPTIONS

Database    Easy to use SQL database access module. Just put your SQL
            query in the docstring of a Database.Query subclass
            and Database.py does the rest! Extremely easy and
            Pythonic.

GFF         Fast access to General Feature Format files via MySQL.

FlatFile    Use the Database.py row interface to flat text file databases,
            such as CSV files and tab-delimited files.

easybio	    Location parser and convenience interface to Biopython.

tools       Python 2.3 enumerate, temporary file creation, surrogate class,
	    argument and option parser, list and dictionary
	    convenience classes and functions.

template    A template for auto-testing, argument-parsing Python modules

Parser	    Convenience interface to csv module:
	    >>> Parser.comma.parse("a,b,c")
            ['a', 'b', 'c']

Please e-mail me if you have any questions or comments.
-- 
Michael Hoffman <grouse@mail.utexas.edu>
The University of Texas at Austin