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.
Kegg2NogMapper
(fname=None, gen_ko_to_cat=True)¶ Bases:
mgkit.kegg.KeggMapperBase
Usage
to add a ko_id to the mapper use: * map_ko_to_eggnog(ko_id) which calls:
- get_uniprot_from_ko
- get_eggnog_from_uniprot
return None if there was no problem or a dictionary with the exception thrown
to make mappings ko_id -> eggnog-categories: * get_cat_mapping_from_file (file are in the current directory) * gen_ko_to_cat
Todo
- add method to load kos from file
- optimise querying (like Kegg2CazyMapper)
-
columns_string
= 'database(eggnog)'¶
-
gen_ko_to_cat
()¶
-
get_cat_ko_dict
()¶
-
get_cat_mapping
(f_handle)¶
-
get_cat_mapping_from_file
(files=('COG.funccat.txt', 'NOG.funccat.txt', 'KOG.funccat.txt'))¶ Duplicate functionality of load_func_cat
Categories are single letter and their descriptioons are in
EGGNOG_CAT
, while the broader categoriesEGGNOG_CAT_MAP
-
get_ko_cat
(ko_id)¶
-
get_ko_cat_dict
()¶
-
get_ko_map
()¶
-
load_data
(fname)¶
-
map_ko_to_eggnog
(ko_id, contact)¶
-
map_kos_eggnog
(kos, contact)¶
-
query_string
= 'database:(type:ko {0}) AND database:(type:eggnog)'¶
-
save_data
(fname)¶
-
class
mgkit.mappings.eggnog.
NOGInfo
¶ Bases:
object
New in version 0.1.14.
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 ID
-
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.
download_data
(contact, kegg_data='kegg.pickle', eggnog_data='eggnog.pickle', base_url='http://eggnog.embl.de/version_3.0/data/downloads/')¶
-
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)
-
mgkit.mappings.eggnog.
print_ko_to_cat
(data_file='eggnog.pickle', descr=False)¶