mgkit.mappings.enzyme module

New in version 0.1.14.

EC mappings

mgkit.mappings.enzyme.change_mapping_level(ec_map, level=3)

New in version 0.1.14.

Given a dictionary, whose values are dictionaries, in which a key is named ec and its value is an iterable of EC numbers, returns an iterator that can be used to build a dictionary with the same top level keys and the values are sets of the transformed EC numbers.

Parameters:
Yields:

tuple – a tuple (gene_id, set(ECs)), which can be passed to dict to make a dictionary

Example

>>> from mgkit.net.uniprot import get_gene_info
>>> from mgkit.mappings.enzyme import change_mapping_level
>>> ec_map = get_gene_info('Q9HFQ1', columns='ec')
{'Q9HFQ1': {'ec': '1.1.3.4'}}
>>> dict(change_mapping_level(ec_map, level=2))
{'Q9HFQ1': {'1.1'}}
mgkit.mappings.enzyme.get_enzyme_full_name(ec_id, ec_names, sep=', ')

New in version 0.2.1.

From a EC identifiers and a dictionary of names builds a comma separated name (by default) that identifies the function of the enzyme.

Parameters:
  • ec_id (str) – EC identifier
  • ec_names (dict) – a dictionary of names that can be produced using parse_expasy_file()
  • sep (str) – string used to join the names
Returns:

the enzyme classification name

Return type:

str

mgkit.mappings.enzyme.get_enzyme_level(ec, level=4)

New in version 0.1.14.

Returns an enzyme class at a specific level , between 1 and 4 (by default the most specific, 4)

Parameters:
  • ec (str) – a string representing an EC number (e.g. 1.2.4.10)
  • level (int) – from 1 to 4, to get a different level specificity of in the enzyme classification
Returns:

the EC number at the requested specificity

Return type:

str

Example

>>> from mgkit.mappings.enzyme import get_enzyme_level
>>> get_enzyme_level('1.1.3.4', 1)
'1'
>>> get_enzyme_level('1.1.3.4', 2)
'1.1'
>>> get_enzyme_level('1.1.3.4', 3)
'1.1.3'
>>> get_enzyme_level('1.1.3.4', 4)
'1.1.3.4'
mgkit.mappings.enzyme.get_mapping_level(ec_map, level=3)

New in version 0.3.0.

Given a dictionary, whose values are iterable of EC numbers, returns an iterator that can be used to build a dictionary with the same top level keys and the values are sets of the transformed EC numbers.

Parameters:
  • ec_map (dict) – dictionary genes to EC
  • level (int) – number from 1 to 4, to specify the level of the mapping, passed to get_enzyme_level()
Yields:

tuple – a tuple (gene_id, set(ECs)), which can be passed to dict to make a dictionary

mgkit.mappings.enzyme.parse_expasy_file(file_name)

Used to load enzyme descriptions from the file enzclass.txt on expasy.

The FTP url for enzclass.txt is: ftp://ftp.expasy.org/databases/enzyme/enzclass.txt