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ENCODE experiment and file queries

Find ENCODE experiments, samples and downloadable files.

  • Purpose: Find ENCODE records by object type, keyword and field filters, such as released bigWig files.
  • Method: Submit ENCODE search filters and normalize matching objects and file metadata into QueryResult.
  • API: dnakit.search.encode_search(object_type[optional], search_term[optional], filters[optional], limit[optional], config[optional], verbose[optional])
  • Input: Optional object type, search term, filter dictionary, record limit and SearchConfig. Requires network access.
  • Output: Returns QueryResult with query records, source provider, and pagination information.
  • Example code:
from dnakit.search import encode_search

result = encode_search(
    object_type="File",
    filters={"file_format": "bigWig", "status": "released"},
    limit=20,
    verbose=False,
)
print(result.query_type, result.provider, len(result.records))
  • Example output: Return format only; the network query was not run. The live database determines the record count.
regulation ENCODE <record count returned>

2) Retrieve ENCODE experiment details by accession

  • Purpose: Retrieve ENCODE experiment details by accession.
  • Method: Query ENCODE with the supplied filters and parse experiment, file or download results.
  • API： dnakit.encode.get_experiment(accession, *, verbose=True)
  • Input: Provide accession.
  • Output: Python return type: str. JSON with full experiment details and file listing.
  • Example code:
import dnakit

result = dnakit.encode.get_experiment(
    accession='ENCSR133RZO',
    verbose=False,
)
print(result)
  • Example output: Python return type: str. JSON with full experiment details and file listing.

Full parameters and usage notes

3) Retrieve live ENCODE filter counts

  • Purpose: Retrieve live ENCODE filter counts.
  • Method: Query ENCODE with the supplied filters and parse experiment, file or download results.
  • API： dnakit.encode.get_facets(search_type='Experiment', assay_title=None, organism=None, organ=None, biosample_type=None, *, verbose=True)
  • Input: Choose filters as shown in the example; omitted options use the operation defaults.
  • Output: Python return type: str. JSON with facet names and their term counts.
  • Example code:
import dnakit

result = dnakit.encode.get_facets(
    assay_title='ATAC-seq',
    organism='Homo sapiens',
    verbose=False,
)
print(result)
  • Example output: Python return type: str. JSON with facet names and their term counts.

Full parameters and usage notes

4) Retrieve ENCODE file details

  • Purpose: Retrieve ENCODE file details.
  • Method: Query ENCODE with the supplied filters and parse experiment, file or download results.
  • API： dnakit.encode.get_file_info(accession, *, verbose=True)
  • Input: Provide accession. Retrieve a real file accession with the file query API and replace ENCFF_REPLACE_ME.
  • Output: Python return type: str. JSON with file metadata including format, size, download URL, MD5, assembly, etc.
  • Example code:
import dnakit

result = dnakit.encode.get_file_info(
    accession='ENCFF_REPLACE_ME',
    verbose=False,
)
print(result)
  • Example output: Python return type: str. JSON with file metadata including format, size, download URL, MD5, assembly, etc.

Full parameters and usage notes

5) Retrieve available ENCODE search filters

  • Purpose: Retrieve available ENCODE search filters.
  • Method: Query ENCODE with the supplied filters and parse experiment, file or download results.
  • API： dnakit.encode.get_metadata(metadata_type, *, verbose=True)
  • Input: Provide metadata_type.
  • Output: Python return type: str. JSON list of valid values for the specified metadata type.
  • Example code:
import dnakit

result = dnakit.encode.get_metadata(
    metadata_type='assays',
    verbose=False,
)
print(result)
  • Example output: Python return type: str. JSON list of valid values for the specified metadata type.

Full parameters and usage notes

6) List files belonging to an ENCODE experiment

  • Purpose: List files belonging to an ENCODE experiment.
  • Method: Query ENCODE with the supplied filters and parse experiment, file or download results.
  • API： dnakit.encode.list_files(experiment_accession, file_format=None, file_type=None, output_type=None, output_category=None, assembly=None, status=None, preferred_default=None, limit=200, *, verbose=True)
  • Input: Provide experiment_accession.
  • Output: Python return type: str. JSON list of files with accession, format, size, download URL, and metadata.
  • Example code:
import dnakit

result = dnakit.encode.list_files(
    experiment_accession='ENCSR133RZO',
    file_format='bed',
    limit=3,
    verbose=False,
)
print(result)
  • Example output: Python return type: str. JSON list of files with accession, format, size, download URL, and metadata.

Full parameters and usage notes

7) Search ENCODE experiments by experimental conditions

  • Purpose: Search ENCODE experiments by experimental conditions.
  • Method: Query ENCODE with the supplied filters and parse experiment, file or download results.
  • API： dnakit.encode.search_experiments(assay_title=None, organism='Homo sapiens', organ=None, biosample_type=None, biosample_term_name=None, target=None, status='released', lab=None, award=None, assembly=None, replication_type=None, life_stage=None, sex=None, treatment=None, genetic_modification=None, perturbed=None, search_term=None, date_released_from=None, date_released_to=None, limit=25, offset=0, *, verbose=True)
  • Input: Choose filters as shown in the example; omitted options use the operation defaults.
  • Output: Python return type: str. JSON with experiment results, total count, and pagination info.
  • Example code:
import dnakit

result = dnakit.encode.search_experiments(
    assay_title='ATAC-seq',
    organism='Homo sapiens',
    limit=3,
    verbose=False,
)
print(result)
  • Example output: Python return type: str. JSON with experiment results, total count, and pagination info.

Full parameters and usage notes

8) Search ENCODE files using experiment and file filters

  • Purpose: Search ENCODE files using experiment and file filters.
  • Method: Query ENCODE with the supplied filters and parse experiment, file or download results.
  • API： dnakit.encode.search_files(file_format=None, file_type=None, output_type=None, output_category=None, assembly=None, assay_title=None, organism=None, organ=None, biosample_type=None, target=None, status='released', preferred_default=None, search_term=None, limit=25, offset=0, *, verbose=True)
  • Input: Choose filters as shown in the example; omitted options use the operation defaults.
  • Output: Python return type: str. JSON with file results, total count, and pagination info.
  • Example code:
import dnakit

result = dnakit.encode.search_files(
    file_format='bed',
    assembly='GRCh38',
    assay_title='ATAC-seq',
    limit=3,
    verbose=False,
)
print(result)
  • Example output: Python return type: str. JSON with file results, total count, and pagination info.

Full parameters and usage notes