https://github.com/midnighter/brenda-parser

Classes to parse the BRENDA database.
https://github.com/midnighter/brenda-parser

Last synced: 8 months ago
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Classes to parse the BRENDA database.

• Host: GitHub
• URL: https://github.com/midnighter/brenda-parser
• Owner: Midnighter
• License: other
• Created: 2011-09-19T15:35:40.000Z (over 14 years ago)
• Default Branch: master
• Last Pushed: 2021-04-16T20:10:03.000Z (about 5 years ago)
• Last Synced: 2025-05-13T01:17:42.054Z (about 1 year ago)
• Language: Python
• Homepage:
• Size: 203 KB
• Stars: 12
• Watchers: 5
• Forks: 8
• Open Issues: 3
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE.rst

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README

          
=============

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.

.. __: http://www.brenda-enzymes.org/

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).

.. code:: python

    >>> 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:

.. code:: python

    >>> 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.