@@ -64,6 +64,35 @@ def get_meta_by_id(self, _id):
6464 result .append (doc )
6565 return result
6666
67+ def get_ortho_by_id (self , _id ):
68+ '''
69+ Get protein's metadata given uniprot id
70+
71+ Args:
72+ _id (:obj:`str`): uniprot id.
73+
74+ Returns:
75+ (:obj:`list` of :obj:`dict`): list of information.
76+ '''
77+ result = []
78+ query = {'uniprot_id' : _id }
79+ doc = self .collection .find_one (filter = query , projection = {"_id" : 0 })
80+ if doc is None :
81+ return {'uniprot_id' : 'None' ,
82+ 'entry_name' : 'None' ,
83+ 'gene_name' : 'None' ,
84+ 'protein_name' : 'None' ,
85+ 'canonical_sequence' : 'None' ,
86+ 'length' : 99999999 ,
87+ 'mass' : '99999999' ,
88+ 'abundances' : [],
89+ 'ncbi_taxonomy_id' : 99999999 ,
90+ 'species_name' : '99999999' }
91+ else :
92+ doc = json .loads (json .dumps (doc , ignore_nan = True ))
93+ result .append (doc )
94+ return result
95+
6796 def get_meta_by_name_taxon (self , name , taxon_id ):
6897 '''
6998 Get protein's metadata given protein name
@@ -869,4 +898,90 @@ def get_all_kegg(self, ko, anchor, max_distance):
869898 species_canon_ancestor = obj [species + '_canon_ancestors' ]
870899 doc ['canon_ancestors' ] = species_canon_ancestor
871900 result [distance - 1 ]['documents' ].append (doc )
901+ return result
902+
903+ def get_all_ortho (self , ko , anchor , max_distance ):
904+ '''Get replacement abundance value by taxonomic distance
905+ with the same OrthoDB group number.
906+
907+ Args:
908+ ko (:obj:`str`): OrthoDB group id to query for.
909+ anchor (:obj:`str`): anchor species' name.
910+ max_distance (:obj:`int`): max taxonomic distance from origin protein allowed for
911+ proteins in results.
912+ max_depth (:obj:`int`) max depth allowed from the common node.
913+
914+ Returns:
915+ (:obj:`list` of :obj:`dict`): list of result proteins and their info
916+ [
917+ {'distance': 1, 'documents': [{}, {}, {} ...]},
918+ {'distance': 2, 'documents': [{}, {}, {} ...]}, ...].
919+ '''
920+ if max_distance <= 0 :
921+ return 'Please use get_abundance_by_id to check self abundance values'
922+
923+ result = []
924+ for i in range (max_distance ):
925+ result .append ({'distance' : i + 1 , 'documents' : []})
926+
927+ projection = {
928+ 'orthodb_id' : 1 ,
929+ 'orthodb_name' : 1 ,
930+ 'ancestor_name' : 1 ,
931+ 'ncbi_taxonomy_id' : 1 ,
932+ 'abundances' : 1 ,
933+ 'species_name' : 1 ,
934+ 'uniprot_id' : 1 ,
935+ '_id' : 0 ,
936+ 'ancestor_taxon_id' : 1 ,
937+ 'protein_name' : 1 ,
938+ 'gene_name' : 1 ,
939+ 'modifications' : 1
940+ }
941+ con_0 = {'orthodb_id' : ko }
942+ con_1 = {'abundances' : {'$exists' : True }}
943+ query = {'$and' : [con_0 , con_1 ]}
944+ docs = self .collection .find (filter = query , projection = projection )
945+ queried = deque ()
946+ names = {}
947+ for doc in docs :
948+ doc = json .loads (json .dumps (doc , ignore_nan = True ))
949+ species = doc .get ('species_name' )
950+ if species is None and species not in queried :
951+ taxon_id = doc ['ncbi_taxonomy_id' ]
952+ species = self .db_obj ['taxon_tree' ].find_one ({"tax_id" : taxon_id })['tax_name' ]
953+ queried .append (taxon_id )
954+ names [taxon_id ] = species
955+ elif species is None and species in queried :
956+ species = names [doc ['ncbi_taxonomy_id' ]]
957+ obj = self .taxon_manager .get_canon_common_ancestor_fast (anchor , species , org_format = 'tax_name' )
958+ distance = obj [anchor ]
959+ if distance != - 1 and distance <= max_distance :
960+ species_canon_ancestor = obj [species + '_canon_ancestors' ]
961+ doc ['canon_ancestors' ] = species_canon_ancestor
962+ result [distance - 1 ]['documents' ].append (doc )
963+ return result
964+
965+ def get_info_by_orthodb (self , orthodb ):
966+ '''
967+ Find all proteins with the same kegg orthology id.
968+
969+ Args:
970+ orthodb(:obj:`str`): kegg orthology ID.
971+
972+ Returns:
973+ (:obj:`list` of :obj:`dict`): list of dictionary containing
974+ protein's uniprot_id and kegg information
975+ [{'orthodb_id': ... 'orthodb_name': ... 'uniprot_ids': []},
976+ {'orthodb_id': ... 'orthodb_name': ... 'uniprot_ids': []}].
977+ '''
978+ ko = orthodb .lower ()
979+ result = [{'orthodb_id' : ko , 'uniprot_ids' : []}]
980+ query = {'orthodb_id' : ko }
981+ projection = {'uniprot_id' : 1 , '_id' : 0 , 'orthodb_name' : 1 , 'orthodb_id' : 1 }
982+ docs = self .collection .find (filter = query , projection = projection )
983+
984+ for doc in docs :
985+ result [0 ]['orthodb_name' ] = doc .get ('orthodb_name' , ['no name' ])
986+ result [0 ]['uniprot_ids' ].append (doc .get ('uniprot_id' ))
872987 return result
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