diegovalenzuelaiturra / BRENDA-Parser

Classes to parse the BRENDA database.

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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.

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Classes to parse the BRENDA database.

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