[BioPython] Useful modules for biological programming
Michael Hoffman
grouse@mail.utexas.edu
Mon, 29 Jul 2002 21:36:40 -0500
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