gene.query

Provides methods for handling queries.

exception gene.query.InvalidParameterException

Exception for invalid parameter args provided by the user.

class gene.query.QueryHandler(database)

Class for normalizer management. Stores reference to database instance and normalizes query input.

__init__(database)

Initialize QueryHandler instance. Requires a created database object to initialize. The most straightforward way to do this is via the create_db method in the gene.database module:

>>> from gene.query import QueryHandler
>>> from gene.database import create_db
>>> q = QueryHandler(create_db())

We’ll generally call create_db without any arguments in code examples, for the sake of brevity. See the usage page in the docs and the create_db API description for more details.

Parameters:

database (AbstractDatabase) – storage backend to search against

normalize(query)

Return normalized concept for query.

Use to retrieve normalized gene concept records:

>>> from gene.query import QueryHandler
>>> from gene.database import create_db
>>> q = QueryHandler(create_db())
>>> result = q.normalize("BRAF")
>>> result.normalized_id
'hgnc:1097'
>>> result.aliases
['BRAF1', 'RAFB1', 'B-raf', 'NS7', 'B-RAF1']

Parameters:

query (str) – String to find normalized concept for

Return type:

NormalizeService

Returns:

Normalized gene concept

normalize_unmerged(query)

Return all source records under the normalized concept for the provided query string.

>>> from gene.query import QueryHandler
>>> from gene.database import create_db
>>> from gene.schemas import SourceName
>>> q = QueryHandler(create_db())
>>> response = q.normalize_unmerged("BRAF")
>>> response.match_type
<MatchType.CONCEPT_ID: 100>
>>> response.source_matches[SourceName.ENSEMBL].concept_id
'ensembl:ENSG00000157764'

Parameters:

query (str) – string to search against

Return type:

UnmergedNormalizationService

Returns:

Normalized response object

search(query_str, incl='', excl='', **params)

Return highest match for each source.

>>> from gene.query import QueryHandler
>>> from gene.database import create_db
>>> q = QueryHandler(create_db())
>>> result = q.search("BRAF")
>>> result.source_matches[0].records[0].concept_id
'ncbigene:673'

Parameters:

• query_str (str) – query, a string, to search for

• incl (str) – str containing comma-separated names of sources to use. Will exclude all other sources. Case-insensitive.

• excl (str) – str containing comma-separated names of source to exclude. Will include all other source. Case-insensitive.

Return type:

SearchService

Returns:

SearchService class containing all matches found in sources.

Raises:

InvalidParameterException – if both incl and excl args are provided, or if invalid source names are given