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Populations, Samples and Linkage Disequilibrium

See the FAQ for dependencies and return conventions.

1) List IGSR and 1000 Genomes data collections

  • Purpose: List IGSR and 1000 Genomes data collections.
  • Method: Use IGSR to query or submit the supplied input and parse the response.
  • API： dnakit.databases.igsr_list_data_collections(*, operation=None, limit=None, verbose=True)
  • Input: Choose filters as shown in the example; omitted options use the operation defaults.
  • Output: Returns a mapping with total, returned, collections and related fields.
  • Example code:
import dnakit

result = dnakit.databases.igsr_list_data_collections(
    operation='list_data_collections',
    limit=20,
    verbose=False,
)
print(result)
  • Example output: The response has the following shape; records depend on the input and source.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

{
  "total": "<integer>",
  "returned": "<integer>",
  "collections": [
    {
      "code": "<string>",
      "title": "<string>",
      "short_title": "<string>",
      "sample_count": "<integer>",
      "population_count": "<integer>",
      "data_types": "<array>",
      "website": "<string>"
    }
  ]
}

Full parameters and usage notes

2) Search 1000 Genomes populations

  • Purpose: Search 1000 Genomes populations.
  • Method: Use IGSR to query or submit the supplied input and parse the response.
  • API： dnakit.databases.igsr_search_populations(*, operation=None, superpopulation=None, query=None, limit=None, verbose=True)
  • Input: Choose filters as shown in the example; omitted options use the operation defaults.
  • Output: Returns a mapping with total, returned, populations and related fields.
  • Example code:
import dnakit

result = dnakit.databases.igsr_search_populations(
    operation='search_populations',
    superpopulation='EAS',
    limit=10,
    verbose=False,
)
print(result)
  • Example output: The response has the following shape; records depend on the input and source.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

{
  "total": "<integer>",
  "returned": "<integer>",
  "populations": [
    {
      "code": "<string>",
      "name": "<string>",
      "description": "<string>",
      "sample_count": "<integer>",
      "superpopulation_code": "<string>",
      "superpopulation_name": "<string>",
      "latitude": "<number>",
      "longitude": "<number>"
    }
  ]
}

Full parameters and usage notes

3) Search 1000 Genomes samples by population or collection

  • Purpose: Search 1000 Genomes samples by population or collection.
  • Method: Use IGSR to query or submit the supplied input and parse the response.
  • API： dnakit.databases.igsr_search_samples(*, operation=None, population=None, data_collection=None, sample_name=None, limit=None, verbose=True)
  • Input: Choose filters as shown in the example; omitted options use the operation defaults.
  • Output: Returns a mapping with total, returned, samples and related fields.
  • Example code:
import dnakit

result = dnakit.databases.igsr_search_samples(
    operation='search_samples',
    population='GBR',
    limit=5,
    verbose=False,
)
print(result)
  • Example output: The response has the following shape; records depend on the input and source.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

{
  "total": "<integer>",
  "returned": "<integer>",
  "samples": [
    {
      "name": "<string>",
      "sex": "<string>",
      "biosample_id": "<string>",
      "populations": "<array>",
      "data_collections": "<array>"
    }
  ]
}

Full parameters and usage notes

  • Purpose: Find population-specific LD proxy variants.
  • Method: Use LDlink to query or submit the supplied input and parse the response.
  • API： dnakit.databases.ldlink_get_proxies(*, variant, population=None, r2_threshold=None, genome_build=None, limit=None, verbose=True)
  • Input: Provide variant.
  • Output: Returns a list of records; each record includes rsid, r2, coord, alleles and related fields.
  • Example code:
import dnakit

result = dnakit.databases.ldlink_get_proxies(
    variant='rs7903146',
    population='CEU',
    verbose=False,
)
print(result)
  • Example output: The response has the following shape; records depend on the input and source.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

[
  {
    "rsid": "<string>",
    "r2": "<number>",
    "coord": "<string>",
    "alleles": "<string>",
    "maf": "<string>",
    "distance": "<string>"
  }
]

Full parameters and usage notes