Skip to content

Latest commit

 

History

History
198 lines (156 loc) · 10.7 KB

README.md

File metadata and controls

198 lines (156 loc) · 10.7 KB
Raw

BRENDA Parser

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

The starting point of this BRENDA parser is a project by Moritz Emanuel Beber that I have improved by handling various parsing issues and edge cases in current BRENDA flat files (e.g., v2018.2). The project by Moritz has a new branch in the making, so you might want to check it out when it's finished. For the time being, I needed to have the BRENDA flat file v2018.2 correctly parsed, and this project achieves just that.

Usage

In order to use this module outside of its directory, you will have to add it to your system path:

import sys
sys.path.insert(0, '/path/to/BRENDA-Parser')

Provided you saved the BRENDA flat file under the name brenda_download.txt, parse it using BRENDA-Parser as follows:

>>> from brenda.parser import BRENDAParser
>>> with BRENDAParser('brenda_download.txt') as parser:
...     brenda = parser.parse()

The method parse returns a dictionary with all EC numbers (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, e.g.:

>>> len(brenda['1'])
2049
>>> len(brenda['1.1.1.1'])
1
>>> brenda['1.1.1.1'][0]
1.1.1.1

In the following, we will briefly survey how information in the BRENDA flat file is parsed and stored; to these means, BRENDA-Parser provides the classes Enzyme, Protein, Entry, and EntryComment.

API

EC number information (Enzyme class)

For every EC number, the following fields may be accessed:

  • ec_number -- a string designating the EC number.
  • comment -- either None or a string representing a comment associated to an EC number.
  • proteins -- a dict storing protein information for an EC number. Dict keys are numerical protein identifiers as they appearin the BRENDA flat file between #...# tags. Dict values are Protein objects.
  • references -- a dict storing literature references for an EC number (see TODO).
  • entries -- a dict storing every entry in the BRENDA flat file for a given EC number, with the exception of protein (see proteins above) and literature (see references above) references. Dict keys are section names in the BRENDA flat file, such as REACTION, SUBSTRATE_PRODUCT, etc. Dict values are lists of Entry objects.

For example, suppose you wish to list all EC numbers having an associated comment in the BRENDA flat file, such as:

...
ID      1.1.1.109 (transferred to EC 1.3.1.28)
...
ID      5.4.99.10 (deleted, included in EC 5.4.99.11)
...

Here is how to retrieve EC numbers with associated comments:

>>> ec_comment = [ec for ec in brenda if brenda[ec][0].comment is not None]
>>> len(ec_comment)
910
>>> print(brenda[ec_comment[0]][0].ec_number, brenda[ec_comment[0]][0].comment)
1.1.1.109 transferred to EC 1.3.1.28

Protein information (Protein class)

For a given protein (recall that proteins are stored in a dict where keys are protein numerical identifiers between #...# tags in the BRENDA flat file), the following fields may be accessed:

  • information -- either None or a string representing information associated to the current protein ({...} tags in the BRENDA flat file).
  • comment -- EntryComment object representing a comment associated to the current protein.
  • organism -- string representing the species for which the current protein is reported present.
  • identifiers -- list of strings representing UniProt accessions for the current protein.
  • references -- list of numerical identifiers representing literature references for the current protein (<...> tags in the BRENDA flat file).

For example, suppose you wish to display all protein information associated to EC number 6.6.1.2:

>>> for prot_id in brenda['6.6.1.2'][0].proteins: 
...     print(prot_id) 
...     protein = brenda['6.6.1.2'][0].proteins[prot_id] 
...     print('\tInformation:', protein.information) 
...     print('\tComment:', protein.comment) 
...     print('\tOrganism:', protein.organism) 
...     print('\tIdentifiers:', protein.identifiers) 
...     print('\tReferences:', protein.references) 
1
        Information: None
        Comment: nomen rejiciendum
        Organism: Pseudomonas denitrificans
        Identifiers: []
        References: [1]
2
        Information: None
        Comment: None
        Organism: Salmonella enterica
        Identifiers: []
        References: [4]
3
        Information: None
        Comment: None
        Organism: Desulfovibrio vulgaris
        Identifiers: []
        References: [4]
4
        Information: None
        Comment: None
        Organism: Brucella melitensis
        Identifiers: []
        References: [3]
5
        Information: None
        Comment: nomen rejiciendum
        Organism: Pseudomonas denitrificans
        Identifiers: ['P29929', 'P29933', 'P29934', 'Q9HZQ3']
        References: [2]

BRENDA entries (Entry class)

The BRENDA flat file contains several sections for every EC number, such as REACTION, SUBSTRATE_PRODUCT, COFACTOR, etc. This information is encapsulated as a list of Entry objects. Each Entry has the following fields:

  • msg -- the Entry content.
  • information -- additional information on the Entry ({...} tags in the BRENDA flat file).
  • comment -- EntryComment object representing a comment associated to the current Entry.
  • proteins -- list of list of numerical identifiers representing protein references for the current Entry (#...# tags in the BRENDA flat file).
  • references -- list of list of numerical identifiers representing literature references for the current Entry (<...> tags in the BRENDA flat file).

For example, suppose you wish to display information for the first SP (SUBSTRATE_PRODUCT) entry for EC number 1.1.1.261:

>>> entry = brenda['1.1.1.261'][0].entries['SUBSTRATE_PRODUCT'][0]
>>> print(entry.msg)
dihydroxyacetone phosphate + NAD(P)H = sn-glycerol-1-phosphate + NAD(P)+
>>> print(entry.information)                                                                                              
ir
>>> print(entry.comment)                                                                                                  
#1,2,3,4,5,7# method specific to glycerol-1-phosphate <2>; #2# significant lower reverse reaction <2>; #3# reverse reaction 1/16 of the forward reaction <2>; #3# formation of glycerol-1-phosphate is the natural direction of the reaction <3,5>; #3# key enzyme in the biosynthesis of the enantiomeric glycerophosphate backbone of ether phospholipids of archaebacteria <6>; #3# involved in the biosynthesis of archeal lipids <7>; #8# key enzyme in the formation of archeal enantiomeric polar lipid structures <8>; #8# reverse reaction only with NAD+ as cofactor <8>
>>>  print(entry.proteins)                                                                                                 
[1, 2, 3, 4, 5, 7, 8, 9]
>>> print(entry.references)                                                                                               
[2, 3, 4, 5, 6, 7, 8, 9, 10, 11]

BRENDA comments (EntryComment class)

Comments in the BRENDA flat file may provide protein and literature references. It is possible to access these references through the proteins and references fields of an EntryComment object. Here is how to access them for the comment in the above example:

>>> entry = brenda['1.1.1.261'][0].entries['SUBSTRATE_PRODUCT'][0]
>>> print(entry.comment.proteins)
[1, 2, 3, 4, 5, 7, 8]
>>> print(entry.comment.references)
[2, 3, 5, 6, 7, 8]

Note that protein and literature references in comments are stored in the order in which they are encountered.

Dependencies

BRENDA-Parser needs Python 3, as well as recordclass. Optionally, nose is needed to run the tests. You may install them with pip:

pip install recordclass nose

Tests

Run the tests in the tests/ directory as follows:

cd BRENDA-Parser
nosetests tests/

What is different with respect to the forked project

  • UniProt accessions:
    • They are now correctly parsed (both 6- and 10-character accession types).
    • They are sometimes present in the BRENDA flat file with different data bank identifiers ('UniProt', even 'Unipro' (!), 'SwissProt', 'GenBank', 'TrEMBL', 'EMBL'), with different combinations of upper- and lowercase letters. This is now taken care of.
    • Sometimes the data bank identifier is not present, e.g. BRENDA contains entries such as PR #50# Plasmodium falciparum Q965D6 <17>. This case is now handled.
  • EC numbers with associated comments are now handled (see example above).
  • The BRENDA flat file is notoriously badly formatted.
    • Empty information ({}) and comment (() or ||, see below) fields are now ignored (whitespace included).
    • # artifacts appearing in entries where they should not appear. Extra # characters are removed.
    • Unmatched opening and closing parentheses in compound names led the initial parser to incorrectly delimit comments (typically between (...) tags). Unmatched parentheses in compound names are now ignored.
    • Unmatched opening and closing parentheses in comments are now ignored and the comments are correctly retrieved.
    • Some entries in the BRENDA flat file use the undocumented comment tags |...|. Sometimes only comments delimited by either (...) or |...| are present, and sometimes both are present. Such comments are now fused together.
    • To make matters more interesting, there may also be extra | characters, seemingly inserted at random by BRENDA maintainers. This parser cleans up such spurious characters, then retrieves the (hopefully) correct comment.
  • The SOAP-parsing part has been removed.
  • The refactor/lexer branch has been removed (check out the forked repository for progress on that branch).

TODO

  • Parse and store references (RF entries).