benchling_sdk.services.v2.stable.dna_sequence_service module

class DnaSequenceService

Bases: benchling_sdk.services.v2.base_service.BaseService

DNA Sequences.

DNA sequences are the bread and butter of the Benchling Molecular Biology suite. On Benchling, these are comprised of a string of nucleotides and collections of other attributes, such as annotations and primers.

See https://benchling.com/api/reference#/DNA%20Sequences

archive(dna_sequence_ids: Iterable[str], reason: EntityArchiveReason) → DnaSequencesArchivalChange

Archive DNA sequences.

See https://benchling.com/api/reference#/DNA%20Sequences/archiveDNASequences

auto_annotate(auto_annotate: AutoAnnotateDnaSequences) → TaskHelper[EmptyTaskResponse]

Auto-annotate DNA sequences with matching features from specified Feature Libraries.

See https://benchling.com/api/reference#/DNA%20Sequences/autoAnnotateDnaSequences

autofill_parts(dna_sequence_ids: Iterable[str]) → TaskHelper[EmptyTaskResponse]

Autofill DNA sequence parts.

See https://benchling.com/api/reference#/DNA%20Sequences/autofillDNASequenceParts

autofill_transcriptions(dna_sequence_ids: Iterable[str]) → TaskHelper[EmptyTaskResponse]

Autofill DNA sequence transcriptions.

See https://benchling.com/api/reference#/DNA%20Sequences/autofillDNASequenceTranscriptions

autofill_translations(dna_sequence_ids: Iterable[str]) → TaskHelper[EmptyTaskResponse]

Autofill DNA sequence translations.

See https://benchling.com/api/reference#/DNA%20Sequences/autofillDNASequenceTranslations

bulk_create(dna_sequences: Iterable[DnaSequenceBulkCreate]) → TaskHelper[BulkCreateDnaSequencesAsyncTaskResponse]

Bulk create DNA sequences.

See https://benchling.com/api/reference#/DNA%20Sequences/bulkCreateDNASequences

bulk_get(dna_sequence_ids: Iterable[str], returning: Optional[Iterable[str]] = None) → Optional[List[DnaSequence]]

Bulk get DNA sequences.

See https://benchling.com/api/reference#/DNA%20Sequences/bulkGetDNASequences

bulk_update(dna_sequences: Iterable[DnaSequenceBulkUpdate]) → TaskHelper[BulkUpdateDnaSequencesAsyncTaskResponse]

Bulk update DNA sequences.

See https://benchling.com/api/reference#/DNA%20Sequences/bulkUpdateDNASequences

bulk_upsert(body: DnaSequencesBulkUpsertRequest, returning: Optional[Iterable[str]] = None) → TaskHelper[BulkUpdateDnaSequencesAsyncTaskResponse]

Bulk create or update DNA sequences.

See https://benchling.com/api/reference#/DNA%20Sequences/bulkUpsertDnaSequences

create(dna_sequence: DnaSequenceCreate) → DnaSequence

Create a DNA sequence.

See https://benchling.com/api/reference#/DNA%20Sequences/createDNASequence

find_matching_regions(find_matching_region: DnaSequencesFindMatchingRegion) → TaskHelper[FindMatchingRegionsDnaAsyncTaskResponse]

Find matching regions for DNA sequences.

See https://benchling.com/api/v2/reference#/DNA%20Sequences/findMatchingRegionsDnaSequences

get_by_id(dna_sequence_id: str, returning: Optional[Iterable[str]] = None) → DnaSequence

Get a DNA sequence.

See https://benchling.com/api/reference#/DNA%20Sequences/getDNASequence

list(modified_at: Optional[str] = None, name: Optional[str] = None, bases: Optional[str] = None, folder_id: Optional[str] = None, mentioned_in: Optional[List[str]] = None, project_id: Optional[str] = None, registry_id: Optional[str] = None, schema_id: Optional[str] = None, archive_reason: Optional[str] = None, mentions: Optional[List[str]] = None, ids: Optional[Iterable[str]] = None, entity_registry_ids_any_of: Optional[Iterable[str]] = None, name_includes: Optional[str] = None, names_any_of: Optional[Iterable[str]] = None, names_any_of_case_sensitive: Optional[Iterable[str]] = None, creator_ids: Optional[Iterable[str]] = None, schema_fields: Optional[Dict[str, Any]] = None, sort: Optional[Union[str, ListDNASequencesSort]] = None, page_size: Optional[int] = None, author_idsany_of: Optional[Iterable[str]] = None, returning: Optional[Iterable[str]] = None) → PageIterator[DnaSequence]

List DNA sequences.

See https://benchling.com/api/reference#/DNA%20Sequences/listDNASequences

match_bases(match_bases_request: MatchBasesRequest) → DnaSequencesPaginatedList

Match bases.

Returns DNA Sequences that exactly match the provided bases.

See https://benchling.com/api/reference#/DNA%20Sequences/matchBasesDnaSequences

optimize_codons(optimize_request: OptimizeCodons) → TaskHelper[EmptyTaskResponse]

Create codon-optimized DNA sequences.

See https://benchling.com/api/reference#/DNA%20Sequences/optimizeCodons

search_bases(search_bases_request: SearchBasesRequest) → DnaSequencesPaginatedList

Search bases.

Returns DNA Sequences that contain the provided bases. Search indexing is asynchronous, so results may be not be available immediately after creation.

See https://benchling.com/api/reference#/DNA%20Sequences/searchDnaSequences

unarchive(dna_sequence_ids: Iterable[str]) → DnaSequencesArchivalChange

Unarchive DNA sequences.

See https://benchling.com/api/reference#/DNA%20Sequences/unarchiveDNASequences

update(dna_sequence_id: str, dna_sequence: DnaSequenceUpdate) → DnaSequence

Update a DNA sequence.

See https://benchling.com/api/reference#/DNA%20Sequences/updateDNASequence

upsert(entity_registry_id: str, dna_sequence: DnaSequenceUpsertRequest) → DnaSequence

Create or modify a DNA sequence.

See https://benchling.com/api/reference#/DNA%20Sequences/upsertDNASequence