3.1.1.1. datanator_api.query package

3.1.1.1.1. Submodules

3.1.1.1.2. datanator_api.query.front_end_query module

class datanator_api.query.front_end_query.QueryFrontEnd

Bases: object

get_conc_ids(list_names)

get_ecmdb_entries(m2m_ids)

get_generic_concs(molecule_name)

get_ymdb_entries(ymdb_ids)

molecule_name_query(molecule_name, organism, abstract_default=False)

3.1.1.1.3. datanator_api.query.query_metabolites_meta module

class datanator_api.query.query_metabolites_meta.QueryMetabolitesMeta(cache_dirname=None, MongoDB=None, replicaSet=None, db=None, collection_str='metabolites_meta', verbose=False, max_entries=inf, username=None, password=None, authSource='admin')

Bases: datanator_api.query.query_nosql.DataQuery

Queries specific to metabolites_meta collection

get_ids_from_hash(hashed_inchi)

Given a hashed inchi string, find its corresponding m2m_id and/or ymdb_id :param hashed_inchi: string of hashed inchi

Returns:

dictionary of ids and their keys

{‘m2m_id’: …, ‘ymdb_id’: …}

Return type:result

get_metabolite_hashed_inchi(compounds)

Given a list of compound name(s) Return the corresponding hashed inchi string :param compounds: [‘ATP’, ‘2-Ketobutanoate’]

Returns:[‘3e23df….’, ‘7666ffa….’] Return type:hashed_inchi

get_metabolite_inchi(compounds)

Given a list of compound name(s) Return the corrensponding inchi string :param compounds: list of compounds :param [‘ATP’, ‘2-Ketobutanoate’]:

Returns:[‘….’, ‘InChI=1S/C4H6O3/c1-2-3(5)4(6)7/…’]

get_metabolite_name_by_hash(compounds)

Given a list of hashed inchi, return a list of name (one of the synonyms) for each compound :param compounds: list of compounds in hashed_inchi format

Returns:

list of names

[name, name, name]

Return type:result

get_metabolite_similar_compounds(compounds, num=0, threshold=0)

Given a list of compound names Return the top num number of similar compounds with tanimoto score above threshold values :param compounds: list of compound names :param num: number of similar compounds to return :param threshold: threshold tanimoto coefficient value :param return_format: return dictionary key format, either

hashed inchi or name

Returns:list of similar compounds and their tanimoto score [ {‘compound1’: score, ‘compound2’: score, … ‘compound_num’: score},

{‘compound1’: score, ‘compound2’: score, … ‘compound_num’: score}, …]

compound(1-n) will be in name format

raw: list of similar compounds and their tanimoto score [ {‘compound1’: score, ‘compound2’: score, … ‘compound_num’: score},

{‘compound1’: score, ‘compound2’: score, … ‘compound_num’: score}, …]

compound(1-n) will be in hashed_inchi format

Return type:result

get_metabolite_synonyms(compounds)

Find synonyms of a compound :param compound: name(s) of the compound e.g. “ATP”, [“ATP”, “Oxygen”, …]

Returns:

dictionary of synonyms of the compounds

{‘ATP’: [], ‘Oxygen’: [], …}

rxns: dictionary of rxns in which each compound is found

{‘ATP’: [12345,45678,…], ‘Oxygen’: […], …}

Return type:synonyms

3.1.1.1.4. datanator_api.query.query_nosql module

class datanator_api.query.query_nosql.DataQuery(cache_dirname=None, MongoDB=None, replicaSet=None, db=None, verbose=False, max_entries=inf, username=None, password=None, authSource='admin')

Bases: datanator_api.util.mongo_util.MongoUtil

Collection agnostic queries

ask(prompt, options='YN')

Prompt Yes or No,return the upper case ‘Y’ or ‘N’.

doc_feeder(collection_str=None, sym_link=False, step=1000, s=None, e=None, inbatch=False, query=None, batch_callback=None, projection=None, verbose=False)

An iterator for returning docs in a collection, with batch query. additional filter query can be passed via “query”, e.g., doc_feeder(collection_str, query={‘taxid’: {‘$in’: [9606, 10090, 10116]}}) batch_callback is a callback function as fn(cnt, t), called after every batch fields is optional parameter passed to find to restrict fields to return.

find_text(v, collection=None)

Find documents containing string v v cannot be part of a word (e.g. ‘wor’ of ‘word’) v needs to be in a previously indexed field :param v: value to be matched

timesofar(t0, clock=0, t1=None)

return the string(eg.‘4m5.32s’) for the passed real time/CPU time so far from given t0 (clock 0 for cpu time 1 for realtime).

3.1.1.1.5. datanator_api.query.query_sabiork module

class datanator_api.query.query_sabiork.QuerySabio(cache_dirname=None, MongoDB=None, replicaSet=None, db=None, collection_str='sabio_rk', verbose=False, max_entries=inf, username=None, password=None, authSource='admin')

Bases: datanator_api.query.query_nosql.DataQuery

Queries specific to sabio_rk collection

find_reaction_participants(kinlaw_id)

Find the reaction participants defined in sabio_rk using kinetic law id :param kinlaw_id: list of kinlaw_id to search for

Returns:list of dictionaries containing names of reaction participants [{‘substrates’: [], ‘products’: [] }, … {} ] Return type:rxns

get_kinlawid_by_inchi(inchi)

Find the kinlaw_id defined in sabio_rk using rxn participants’ inchi string :param inchi: list of inchi, all in one rxn

Returns:list of kinlaw_ids that satisfy the condition [id0, id1, id2,…, ] Return type:rxns

get_kinlawid_by_inchi_slow(inchi)

Find the kinlaw_id defined in sabio_rk using rxn participants’ inchi string :param inchi: list of inchi, all in one rxn

Returns:list of kinlaw_ids that satisfy the condition [id0, id1, id2,…, ] Return type:rxns

get_kinlawid_by_rxn(substrates, products)

Find the kinlaw_id defined in sabio_rk using rxn participants’ inchi string :param substrates: list of substrates’ inchi :param products: list of products’ inchi

Returns:list of kinlaw_ids that satisfy the condition [id0, id1, id2,…, ] Return type:rxns

3.1.1.1.6. datanator_api.query.query_taxon_tree module

class datanator_api.query.query_taxon_tree.QueryTaxonTree(cache_dirname=None, MongoDB=None, replicaSet=None, db=None, collection_str='taxon_tree', verbose=False, max_entries=inf, username=None, password=None, authSource='admin')

Bases: datanator_api.query.query_nosql.DataQuery

Queries specific to taxon_tree collection

get_all_species()

get_anc_by_id(ids)

Get organism’s ancestor ids by using organism’s ids :param ids: list of organism’s ids e.g. Candidatus Diapherotrites

Returns:list of ancestors in order of the farthest to the closest Return type:result

get_anc_by_name(names)

Get organism’s ancestor ids by using organism’s names :param names: list of organism’s names e.g. Candidatus Diapherotrites

Returns:list of ancestors ids in order of the farthest to the closest result_name: list of ancestors’ names in order of the farthest to the closest Return type:result_id

get_common_ancestor(org1, org2, org_format='name')

Get the closest common ancestor between two organisms and their distances to the said ancestor :param org1: organism 1 :param org2: organism 2 :param org_format: the format of organism eg tax_id or tax_name

Returns:closest common ancestor’s name distance: each organism’s distance to the ancestor Return type:ancestor

get_name_by_id(ids)

Get organisms’ names given their tax_ids :param ids: organisms’ tax_ids

Returns:organisms’ names Return type:names

get_rank(ids)

Given a list of taxon ids, return the list of ranks. no rank = ‘+’ :param ids: list of taxon ids [1234,2453,431]

Returns:list of ranks [‘kingdom’, ‘+’, ‘phylum’] Return type:ranks

3.1.1.1.7. Module contents