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HgvsApi.md

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HgvsApi

All URIs are relative to https://api.ncbi.nlm.nih.gov/variation/v0

Method HTTP request Description
hgvsBatchContextualsPost POST /hgvs/batch/contextuals Retrieve contextual alleles for each input
hgvsHgvsContextualsGet GET /hgvs/{hgvs}/contextuals Retrieve the contextual alleles equivalent to the HGVS notation input

hgvsBatchContextualsPost

HgvsBatchSuccess hgvsBatchContextualsPost(body, assembly)

Retrieve contextual alleles for each input

For the input HGVS notation, retrieve all contextual alleles in SPDI syntax. (There can be more than one because of differences in the way the two models represent variation. For example, NC_012920.1:m.961delTinsC(2_7) requires one SPDI for each number of cytosines inserted).

Example

// Import classes:
//import org.pharmgkb.io.ncbi.ApiException;
//import org.pharmgkb.io.ncbi.api.HgvsApi;


HgvsApi apiInstance = new HgvsApi();
List<String> body = Arrays.asList("body_example"); // List<String> | JSON object containing a single field "hgvs" which contains an array of the variants to process, each in HGVS notation. Up to 50,000 expressions may be included in a single request.
String assembly = "assembly_example"; // String | GenColl assembly accession for provided list of HGVS. Used only if the hgvs uses a chr location like chr1:g.12345A>T or chrX:g.234C>G
try {
    HgvsBatchSuccess result = apiInstance.hgvsBatchContextualsPost(body, assembly);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling HgvsApi#hgvsBatchContextualsPost");
    e.printStackTrace();
}

Parameters

Name Type Description Notes
body List<String> JSON object containing a single field "hgvs" which contains an array of the variants to process, each in HGVS notation. Up to 50,000 expressions may be included in a single request.
assembly String GenColl assembly accession for provided list of HGVS. Used only if the hgvs uses a chr location like chr1:g.12345A>T or chrX:g.234C>G [optional]

Return type

HgvsBatchSuccess

Authorization

No authorization required

HTTP request headers

  • Content-Type: application/json
  • Accept: application/json

hgvsHgvsContextualsGet

SpdisSuccess hgvsHgvsContextualsGet(hgvs, assembly)

Retrieve the contextual alleles equivalent to the HGVS notation input

For the input HGVS notation, retrieve all contextual alleles in SPDI syntax. (There can be more than one because of differences in the way the two models represent variation. For example, NC_012920.1:m.961delTinsC(2_7) requires one SPDI for each number of cytosines inserted.)

Example

// Import classes:
//import org.pharmgkb.io.ncbi.ApiException;
//import org.pharmgkb.io.ncbi.api.HgvsApi;


HgvsApi apiInstance = new HgvsApi();
String hgvs = "hgvs_example"; // String | Allele in HGVS notation
String assembly = "assembly_example"; // String | GenColl assembly accession for provided list of HGVS. Required only if the hgvs uses a chr location like chr1:g.12345A>T or chrX:g.234C>G
try {
    SpdisSuccess result = apiInstance.hgvsHgvsContextualsGet(hgvs, assembly);
    System.out.println(result);
} catch (ApiException e) {
    System.err.println("Exception when calling HgvsApi#hgvsHgvsContextualsGet");
    e.printStackTrace();
}

Parameters

Name Type Description Notes
hgvs String Allele in HGVS notation
assembly String GenColl assembly accession for provided list of HGVS. Required only if the hgvs uses a chr location like chr1:g.12345A>T or chrX:g.234C>G [optional]

Return type

SpdisSuccess

Authorization

No authorization required

HTTP request headers

  • Content-Type: Not defined
  • Accept: application/json