diegovalenzuelaiturra / BRENDA-Parser

Classes to parse the BRENDA database.

BRENDA Parser

This Python module provides classes that encapsulate information provided by the BRENDA database and a parser that generates relevant content from the text file that can be downloaded for free.

Copyright

Author

Moritz Emanuel Beber

License

Please see the LICENSE.rst file distributed with this module.

Recent Changes

• Parser no longer hick-ups on empty lines, continued lines not starting with a tab, and other format breaking content.
• Parser now prints progress to stdout.
• Soon, support for the SOAP interface will be added.
• If desired, a setup script could be added.

Usage

If you want to use this module outside its directory, you will have to add it to your PYTHONPATH environment variable (unix).

>>> from brenda import BRENDAParser
>>> with BRENDAParser("brenda_download.txt") as bp:
...     content = bp.parse()

The method parse returns a dictionary with all enzymes that were parsed. Every key in the dictionary is a string representing an EC number starting form the 6 general classes down to the individual enzymes. The values in the dictionary are always lists, as an example:

>>> len(content["1"])
1348
>>> len(content["1.1.1.1"])
1

Warning

The API changed slightly.

Notes

There is one additional key "file_encoding" which contains the argument used for the parser when reading the file.