KEGG - Kyoto Encyclopedia of Genes and Genomes

kegg is a python module for accessing KEGG (Kyoto Encyclopedia of Genes and Genomes) using its web services.

Note

This module requires slumber and requests packages.

>>> # Create a KEGG Genes database interface
>>> genome = KEGGGenome()
>>> # List all available entry ids
>>> keys = list(genome.keys())
>>> print(keys[0])
T01001
>>> # Retrieve the entry for the key.
>>> entry = genome[keys[0]]
>>> print(entry.entry_key)
T01001
>>> print(entry.definition)
Homo sapiens (human)
>>> print(entry)  
ENTRY       T01001            Complete  Genome
NAME        hsa, HUMAN, 9606
DEFINITION  Homo sapiens (human)
...

The Organism class can be a convenient starting point for organism specific databases.

>>> organism = Organism("Homo sapiens")  # searches for the organism by name
>>> print(organism.org_code)  # prints the KEGG organism code
hsa
>>> genes = organism.genes  # get the genes database for the organism
>>> gene_ids = list(genes.keys()) # KEGG gene identifiers
>>> entry = genes["hsa:672"]
>>> print(entry.definition) 
(RefSeq) BRCA1, DNA repair associated
>>> # print the entry in DBGET database format.
>>> print(entry) 
ENTRY       672               CDS       T01001
NAME        BRCA1, BRCAI, BRCC1, BROVCA1, FANCS, IRIS, PNCA4, PPP1R53, PSCP, RNF53
DEFINITION  ...

class Organism(org)[source]

A convenience class for retrieving information regarding an organism in the KEGG Genes database.

Parameters: org (str) – KEGG organism code (e.g. “hsa”, “sce”). Can also be a descriptive name (e.g. ‘yeast’, “homo sapiens”) in which case the organism code will be searched for by using KEGG find api.

DBEntry (`entry`)

The entry.DBEntry represents a DBGET databas entry. The individual KEGG Database interfaces below provide their own specialization for this base class.

class DBEntry(text=None)[source]

Bases: object

A DBGET entry object.

property entry_key: Primary entry key used for identifying the entry.

parse(text)[source]: Parse text string containing a formated DBGET entry.

format(section_indent=12)[source]: Return a DBGET formated string representation.

KEGG Databases interface (`databases`)

class DBDataBase(**kwargs)[source]

Bases: object

Base class for a DBGET database interface.

ENTRY_TYPE

ENTRY_TYPE constructor (a DBEntry subclass). This should be redefined in subclasses.

alias of DBEntry

DB = None: A database name/abbreviation (e.g. ‘pathway’). Needs to be set in a subclass or object instance’s constructor before calling the base. __init__

iterkeys()[source]: Return an iterator over the keys.

iteritems()[source]: Return an iterator over the items.

itervalues()[source]: Return an iterator over all DBDataBase.ENTRY_TYPE instances.

keys()[source]: Return an iterator over all database keys. These are unique KEGG identifiers that can be used to query the database.

values()[source]: Return an iterator over all DBDataBase.ENTRY_TYPE instances.

items()[source]: Return an iterator over all (key, DBDataBase.ENTRY_TYPE) tuples.

get(key, default=None)[source]: Return an DBDataBase.ENTRY_TYPE instance for the key. Raises KeyError if not found.

get_text(key)[source]: Return the database entry for key as plain text.

get_entry(key)[source]: Return the database entry for key as an instance of ENTRY_TYPE.

find(name)[source]: Find name using kegg find api.

pre_cache(keys=None, batch_size=10, progress_callback=None)[source]: Retrieve all the entries for keys and cache them locally for faster subsequent retrieval. If keys is None then all entries will be retrieved.

batch_get(keys)[source]: Batch retrieve all entries for keys. This can be significantly faster then getting each entry separately especially if entries are not yet cached.

class GenomeEntry(text)[source]

Bases: DBEntry

Entry for a KEGG Genome database.

property organism_code: A three or four letter KEGG organism code (e.g. ‘hsa’, ‘sce’, …)

property taxid: Organism NCBI taxonomy id.

property annotation: ANNOTATION

property chromosome: CHROMOSOME

property comment: COMMENT

property data_source: DATA_SOURCE

property definition: DEFINITION

property disease: DISEASE

property entry: ENTRY

property keywords: KEYWORDS

property name: NAME

property org_code: ORG_CODE

property original_db: ORIGINAL_DB

property plasmid: PLASMID

property reference: REFERENCE

property statistics: STATISTICS

property taxonomy: TAXONOMY

class Genome[source]

Bases: DBDataBase

An interface to the A KEGG GENOME database.

DB = 'genome': A database name/abbreviation (e.g. ‘pathway’). Needs to be set in a subclass or object instance’s constructor before calling the base. __init__

ENTRY_TYPE: alias of GenomeEntry

org_code_to_entry_key(code)[source]: Map an organism code (‘hsa’, ‘sce’, …) to the corresponding kegg identifier (T + 5 digit number).

search(string, relevance=False)[source]: Search the genome database for string using bfind.

class GeneEntry(text=None)[source]

Bases: DBEntry

property aaseq: AASEQ

property brite: BRITE

property class_: CLASS

property dblinks: DBLINKS

property definition: DEFINITION

property disease: DISEASE

property drug_target: DRUG_TARGET

property entry: ENTRY

property module: MODULE

property motif: MOTIF

property name: NAME

property ntseq: NTSEQ

property organism: ORGANISM

property orthology: ORTHOLOGY

property pathway: PATHWAY

property position: POSITION

property structure: STRUCTURE

class Genes(org_code)[source]

Bases: DBDataBase

Interface to the KEGG Genes database.

Parameters: org_code (str) – KEGG organism code (e.g. ‘hsa’).

ENTRY_TYPE: alias of GeneEntry

DB = None: A database name/abbreviation (e.g. ‘pathway’). Needs to be set in a subclass or object instance’s constructor before calling the base. __init__

class CompoundEntry(text=None)[source]

Bases: DBEntry

property atom: ATOM

property bond: BOND

property brite: BRITE

property comment: COMMENT

property dblinks: DBLINKS

property entry: ENTRY

property enzyme: ENZYME

property exact_mass: EXACT_MASS

property formula: FORMULA

property mol_weight: MOL_WEIGHT

property name: NAME

property pathway: PATHWAY

property reaction: REACTION

property reference: REFERENCE

property remark: REMARK

class Compound[source]

Bases: DBDataBase

DB = 'cpd': A database name/abbreviation (e.g. ‘pathway’). Needs to be set in a subclass or object instance’s constructor before calling the base. __init__

ENTRY_TYPE: alias of CompoundEntry

class ReactionEntry(text=None)[source]

Bases: DBEntry

property definition: DEFINITION

property entry: ENTRY

property enzyme: ENZYME

property equation: EQUATION

property name: NAME

class Reaction[source]

Bases: DBDataBase

DB = 'rn': A database name/abbreviation (e.g. ‘pathway’). Needs to be set in a subclass or object instance’s constructor before calling the base. __init__

ENTRY_TYPE: alias of ReactionEntry

class EnzymeEntry(text=None)[source]

Bases: DBEntry

property all_reac: ALL_REAC

property class_: CLASS

property comment: COMMENT

property dblinks: DBLINKS

property entry: ENTRY

property genes: GENES

property name: NAME

property orthology: ORTHOLOGY

property pathway: PATHWAY

property product: PRODUCT

property reaction: REACTION

property reference: REFERENCE

property substrate: SUBSTRATE

property sysname: SYSNAME

class Enzyme[source]

Bases: DBDataBase

DB = 'ec': A database name/abbreviation (e.g. ‘pathway’). Needs to be set in a subclass or object instance’s constructor before calling the base. __init__

ENTRY_TYPE: alias of EnzymeEntry

class PathwayEntry(text=None)[source]

Bases: DBEntry

property class_: CLASS

property compound: COMPOUND

property dblinks: DBLINKS

property description: DESCRIPTION

property disease: DISEASE

property drug: DRUG

property entry: ENTRY

property enzyme: ENZYME

property ko_pathway: KO_PATHWAY

property module: MODULE

property name: NAME

property organism: ORGANISM

property pathway_map: PATHWAY_MAP

property reference: REFERENCE

property rel_pathway: REL_PATHWAY

class Pathway(prefix='map')[source]

Bases: DBDataBase

KEGG Pathway database

Parameters: prefix (str) – KEGG Organism code (‘hsa’, …) or ‘map’, ‘ko’, ‘ec’ or ‘rn’

DB = 'path': A database name/abbreviation (e.g. ‘pathway’). Needs to be set in a subclass or object instance’s constructor before calling the base. __init__

ENTRY_TYPE: alias of PathwayEntry

KEGG Pathway (`pathway`)

class Pathway(pathway_id, local_cache=None, connection=None)[source]

Bases: object

Class representing a KEGG Pathway (parsed from a “kgml” file)

Parameters: pathway_id (str) – A KEGG pathway id (e.g. ‘path:hsa05130’)

property name

hsa05130”)

Type: Pathway name/id (e.g. “path

property org: Pathway organism code (e.g. ‘hsa’)

property number: Pathway number as a string (e.g. ‘05130’)

property title: Pathway title string.

property image: URL of the pathway image.

property link: URL to a pathway on the KEGG web site.

get_image()[source]: Return an local filesystem path to an image of the pathway. The image will be downloaded if not already cached.

classmethod list(organism)[source]: List all pathways for KEGG organism code organism.

Utilities

class DBGETEntryParser[source]

A DBGET entry parser (inspired by xml.dom.pulldom).

Example

>>> stream = StringIO(
...     "ENTRY foo\n"
...     "NAME  foo's name\n"
...     "  BAR A subsection of 'NAME'\n"
... )
>>> parser = DBGETEntryParser()
>>> for event, title, contents_part in parser.parse(stream):
...    print(parser.EVENTS[event], title, repr(contents_part))
...
ENTRY_START None None
SECTION_START ENTRY 'foo\n'
SECTION_END ENTRY None
SECTION_START NAME "foo's name\n"
SUBSECTION_START BAR "A subsection of 'NAME'\n"
SUBSECTION_END BAR None
SECTION_END NAME None
ENTRY_END None None

ENTRY_END = 1: Entry end event

ENTRY_START = 0: Entry start events

SECTION_END = 3: Section end event

SECTION_START = 2: Section start event

SUBSECTION_END = 5: Subsection end event

SUBSECTION_START = 4: Subsection start event

TEXT = 6: Text element event

KEGG - Kyoto Encyclopedia of Genes and Genomes