Structural Variant Queries¶

See the FAQ for dependencies and return conventions.

1) Retrieve Ensembl structural variants in an interval¶

Purpose: Retrieve Ensembl structural variants in an interval.
Method: Use Ensembl to query or submit the supplied input and parse the response.
API： dnakit.databases.ensembl_get_structural_variants(*, species, region=None, feature=None, chrom=None, start=None, end=None, verbose=True)
Input: Provide species.
Output: Returns a list of records; each record includes id, seq_region_name, start, end and related fields.
Example code:

import dnakit

result = dnakit.databases.ensembl_get_structural_variants(
    species='human',
    region='22:27000000-27050000',
    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.

[
  {
    "id": "<string>",
    "seq_region_name": "<string>",
    "start": "<integer>",
    "end": "<integer>",
    "strand": "<integer>",
    "feature_type": "<string>",
    "assembly_name": "<string>"
  }
]

Full parameters and usage notes

2) Retrieve Ensembl structural variant details¶

Purpose: Retrieve Ensembl structural variant details.
Method: Use Ensembl to query or submit the supplied input and parse the response.
API： dnakit.databases.ensembl_get_sv_detail(*, species, id=None, sv_id=None, verbose=True)
Input: Provide species.
Output: Returns a mapping with name, var_class, source, clinical_significance and related fields.
Example code:

import dnakit

result = dnakit.databases.ensembl_get_sv_detail(
    species='human',
    id='esv3647486',
    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.

{
  "name": "<string>",
  "var_class": "<string>",
  "source": "<string>",
  "clinical_significance": [
    "<string>"
  ],
  "alias": "<string>",
  "supporting_evidence": [
    {
      "name": "<string>",
      "var_class": "<string>",
      "source": "<string>",
      "clinical_significance": "<array>",
      "copy_number": "<integer>",
      "study": "<object>",
      "mappings": "<array>"
    }
  ]
}

Full parameters and usage notes

3) Find gnomAD structural variants by gene¶

Purpose: Find gnomAD structural variants by gene.
Method: Use gnomADGraphQLQuery to query or submit the supplied input and parse the response.
API： dnakit.databases.gnomad_get_sv_by_gene(*, gene_symbol, reference_genome=None, verbose=True)
Input: Provide gene_symbol.
Output: Returns a mapping with gene, dataset, reference_genome, dataset_note and related fields.
Example code:

import dnakit

result = dnakit.databases.gnomad_get_sv_by_gene(
    gene_symbol='BRCA1',
    reference_genome='GRCh38',
    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.

{
  "gene": {
    "symbol": "<string>",
    "gene_id": "<string>",
    "chrom": "<string>",
    "start": "<integer>",
    "stop": "<integer>",
    "structural_variants": [
      "<object>"
    ]
  },
  "dataset": "<string>",
  "reference_genome": "<string>",
  "dataset_note": "<string>"
}

Full parameters and usage notes

4) Find gnomAD structural variants by genomic interval¶

Purpose: Find gnomAD structural variants by genomic interval.
Method: Use gnomADGraphQLQuery to query or submit the supplied input and parse the response.
API： dnakit.databases.gnomad_get_sv_by_region(*, chrom, start, stop=None, reference_genome=None, end=None, verbose=True)
Input: Provide chrom, start.
Output: Returns a mapping with region, dataset, reference_genome, dataset_note and related fields.
Example code:

import dnakit

result = dnakit.databases.gnomad_get_sv_by_region(
    chrom='17',
    start=43044295,
    stop=43070295,
    reference_genome='GRCh38',
    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.

{
  "region": {
    "chrom": "<string>",
    "start": "<integer>",
    "stop": "<integer>",
    "genes": [
      "<object>"
    ],
    "structural_variants": [
      "<object>"
    ]
  },
  "dataset": "<string>",
  "reference_genome": "<string>",
  "dataset_note": "<string>"
}

Full parameters and usage notes

5) Retrieve gnomAD structural variant details¶

Purpose: Retrieve gnomAD structural variant details.
Method: Use gnomADGraphQLQuery to query or submit the supplied input and parse the response.
API： dnakit.databases.gnomad_get_sv_detail(*, variant_id=None, dataset=None, sv_id=None, verbose=True)
Input: Choose filters as shown in the example; omitted options use the operation defaults.
Output: Returns a mapping with structural_variant, dataset, reference_genome, dataset_note and related fields.
Example code:

import dnakit

result = dnakit.databases.gnomad_get_sv_detail(
    variant_id='DEL_chr17_24e4872b',
    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.

{
  "structural_variant": {
    "variant_id": "<string>",
    "chrom": "<string>",
    "pos": "<integer>",
    "end": "<integer>",
    "type": "<string>",
    "length": "<integer>",
    "ac": "<integer>",
    "an": "<integer>"
  },
  "dataset": "<string>",
  "reference_genome": "<string>",
  "dataset_note": "<string>"
}

Full parameters and usage notes