mgkit.mappings.eggnog module

Module containing classes and functions to deal with eggNOG data

Todo

• unify download of data from web

class mgkit.mappings.eggnog.NOGInfo(members=None, funccat=None, description=None)

Bases: object

New in version 0.1.14.

Changed in version 0.4.0: made file reading compatible with Python 3

Mappings from Uniprot to eggNOG

..note:

load_description is optional

get_gene_funccat(gene_id)

Returns the functional category (one letter, EGGNOG_CAT keys) for the requested eggNOG gene ID

get_gene_nog(gene_id)

Returns the COG/NOG ID of the requested eggNOG gene ID

get_nog_funccat(nog_id)

Returns the functional category (one letter, EGGNOG_CAT keys) for the requested eggNOG COG/NOG ID

get_nog_gencat(nog_id)

Returns the functional category (EGGNOG_CAT_NAMES keys) for the requested eggNOG COG/NOG IDs

get_nogs_funccat(nog_ids)

Returns the functional categories for a list of COG/NOG IDs. Uses NOGInfo.get_nog_funccat()

load_description(file_handle)

Loads data from NOG.description.txt.gz

file_handle can either an open file or a path

load_funccat(file_handle)

Loads data from NOG.funccat.txt.gz

file_handle can either an open file or a path

load_members(file_handle)

Loads data from NOG.members.txt.gz

file_handle can either an open file or a path

mgkit.mappings.eggnog.get_general_eggnog_cat(category)

New in version 0.1.14.

Returns the functional category (EGGNOG_CAT_NAMES keys) for the requested single letter functional category (EGGNOG_CAT keys)