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_get

Private fn to make the GET call. See the source.

// this callback is fired off when the Promise is resolved
let cb = (resp) => {
    return resp.body;
};

_get(params,cb);

Params:

  • object [params] - optional params to pass to caller.

Return:

  • object json

_post

Private fn to make the POST call. See the source.

Params:

  • object [params] - optional params to pass to caller.

Return:

  • object json

passthru(url)

Passthru query specifiying input and output from a UI, passing in a fully valid service GET url.

Example calls:

var mv = require('myvariantjs');
mv.passthru('http://myvariant.info/v1/variant/chr17:g.40690453T>G?fields=cadd')

Params:

  • string url - fully valid url for a GET service call.

Return:

  • object json

getfields([search])

Return the field metadata available in variant objects.

This is a wrapper to the Variant Fields service.

Example calls:

var mv = require('myvariantjs');
mv.getfields()
mv.getfields('gene')

Params:

  • string [search] - optional case insensitive string to search for in available field names. Leaving this empty returns all fields.

Return:

  • object json

getvariant(vid, [options])

Return the variant object for the given HGVS-based variant id.

This is a wrapper for a GET query of "/variant/{hgvsid}" service.

Example endpoint:

Example calls:

var mv = require('myvariantjs');
mv.getvariant('chr9:g.107620835G>A')
mv.getvariant('chr9:g.107620835G>A', {fields:'dbnsfp.genename'})
mv.getvariant('chr9:g.107620835G>A', {fields:['dbnsfp.genename', 'cadd.phred']})
mv.getvariant('chr9:g.107620835G>A', {fields:'all'})
mv.getvariant('chr9:g.107620835G>A', {fields:['dbnsfp.genename', 'cadd.phred'], from: 0, format:'csv'})
mv.getvariant('chr9:g.107620835G>A', {format:'tsv'})

Notes:

  • The supported field names passed to the fields parameter can be found from any full variant object (without fields, or fields="all").
  • Field name supports dot notation for nested data structure as well, e.g. you can pass "dbnsfp.genename" or "cadd.phred".
  • output formats "table" and "tsv" are the same.
  • API Note: optional params are pased in via named options object

Params:

  • string vid - variantid; hgvs-formatted variant id, e.g. chr9:g.107620835G>A
  • object [options] - optional params are pased in via named options object:
  • [fields] - {string|array} fields to return, a list or a comma-separated string. If not provided or fields="all", all available fields are returned. See here for all available fields.
  • [size] - {number} boost the response size from the default 1000 given by the service api. Default = 10000.
  • [from] - {number} when paging use from as the row offset. Default = 0.
  • [format] - {string} output formats: "json", "csv", "tsv", "table". Default = "json".

Return:

  • object|string json or string

getvariants(vids, [options])

Make variant queries in batch for a list of HGVS name-based ids

Return the list of variant annotation objects for the given list of hgvs-base variant ids.

This is a wrapper for POST query of "/variant" service.

Example endpoint:

Example calls:

var mv = require('myvariantjs');
mv.getvariants("chr1:g.866422C>T,chr1:g.876664G>A,chr1:g.69635G>C")  // string of delimited ids
mv.getvariants(["chr1:g.866422C>T", "chr1:g.876664G>A","chr1:g.69635G>C"])  // array of ids
mv.getvariants(["chr1:g.866422C>T", "chr1:g.876664G>A","chr1:g.69635G>C"], {fields:'cadd.phred'})
mv.getvariants(["chr1:g.866422C>T", "chr1:g.876664G>A","chr1:g.69635G>C"], {fields:'dbnsfp.genename', format:'csv'})
mv.getvariants(["chr1:g.866422C>T", "chr1:g.876664G>A","chr1:g.69635G>C"], {fields:['dbnsfp.genename', 'cadd.phred'], size: 5000, format:'table'})
mv.getvariants(["chr1:g.866422C>T", "chr1:g.876664G>A","chr1:g.69635G>C"], {fields:['dbnsfp.genename', 'cadd.phred'], size: 10000, from: 0, format:'tsv'})

Notes:

  • The supported field names passed to the fields parameter can be found from any full variant object (without fields, or fields="all").
  • Field name supports dot notation for nested data structure as well, e.g. you can pass "dbnsfp.genename" or "cadd.phred".
  • output formats "table" and "tsv" are the same.
  • API Note: optional params are pased in via named options object

Params:

  • string|array vids - string of comma delimited hgvs-formatted variant ids, eg. "chr1:g.866422C>T,chr1:g.876664G>A,chr1:g.69635G>C", or array of ids, eg. ["chr1:g.866422C>T", "chr1:g.876664G>A","chr1:g.69635G>C"],
  • object [options] - optional params are pased in via named options object:
  • [fields] - {string|array} fields to return, a list or a comma-separated string. If not provided or fields="all", all available fields are returned. See here for all available fields.
  • [size] - {number} boost the response size from the default 1000 given by the service api. Default = 10000.
  • [from] - {number} when paging use from as the row offset. Default = 0.
  • [format] - {string} output formats: "json", "csv", "tsv", "table". Default = "json".

Return:

  • object|string json or string

query(query, [options])

Return a variant query result.

This is a wrapper for GET query of "/query?q={query}" service.

Service API here

Example endpoints: * GET [http://myvariant.info/v1/query?q=chr1:69000-70000](http://myvariant.info/v1/query?q=chr1:69000-70000) * GET [http://myvariant.info/v1/query?q=snpeff.ann.hgvs_p:p.Ala681Val AND snpeff.ann.gene_name:NAGLU&size=10](http://myvariant.info/v1/query?q=snpeff.ann.hgvs_p:p.Ala681Val AND snpeff.ann.gene_name:NAGLU&size=10)

Example calls:

var mv = require('myvariantjs');
// var mv = require('./public/index');
mv.query("chr1:69000-70000", {fields:'dbnsfp.genename'})
mv.query("dbsnp.rsid:rs58991260", {fields:'dbnsfp'})
mv.query("snpeff.ann.gene_name:cdk2 AND dbnsfp.polyphen2.hdiv.pred:D", , {fields:'dbnsfp.polyphen2.hdiv'})
mv.query("snpeff.ann.gene_name:naglu", {fields:["snpeff.ann.gene_name","dbnsfp"], size:10, format:"csv"})

Paging

q=cdk*&size=50                     first 50 hits
q=cdk*&size=50&from=50             the next 50 hits

Range queries

q=dbnsfp.polyphen2.hdiv.score:>0.99
q=dbnsfp.polyphen2.hdiv.score:>=0.99
q=exac.af:<0.00001
q=exac.af:<=0.00001

q=exac.ac.ac_adj:[76640 TO 80000]        # bounded (including 76640 and 80000)
q=exac.ac.ac_adj:{76640 TO 80000}        # unbounded

Wildcard queries

q=cdk*
q=dbnsfp.genename:CDK?
q=dbnsfp.genename:CDK*

Notes:

  • The combination of “size” and “from” parameters can be used to get paging for large queries.
  • Wildcard characters “*” and ”?” are supported in either simple queries or fielded queries.
  • API Note: optional params are pased in via named options object

Params:

  • string query - case insensitive string to search.
  • object [options] - optional params are pased in via named options object:
  • [fields] - {string|array} fields to return, a list or a comma-separated string. If not provided or fields="all", all available fields are returned. See here for all available fields.
  • [size] - {number} boost the response size from the default 1000 given by the service api. Default = 10000.
  • [from] - {number} when paging use from as the row offset. Default = 0.
  • [format] - {string} output formats: "json", "csv", "tsv", "table". Default = "json".

Return:

  • object|string json or string

querymany(query, [options])

Return the batch query result.

This is a wrapper for POST query of "/query" service.

Example calls:

var mv = require('myvariantjs');
mv.querymany('chr1:g.218631822G>A, chr11:g.66397320A>G'])
mv.querymany(['RCV000083620', 'RCV000083611', 'RCV000083584'], {scopes:'clinvar.rcv_accession'})
mv.querymany(['COSM1362966', 'COSM990046', 'COSM1392449'], {scopes:['dbsnp.rsid', 'cosmic.cosmic_id'], fields:['dbsnp','cosmic']})

Notes:

  • API Note: optional params are pased in via named options object

Params:

  • string query - csv formatted search terms.
  • object [options] - optional params are pased in via named options object:
  • [scopes] - {string|array} string or array of field names to scope the search to
  • [fields] - {string|array} fields to return, a list or a comma-separated string. If not provided or fields="all", all available fields are returned. See here for all available fields.
  • [size] - {number} boost the response size from the default 1000 given by the service api. Default = 10000.
  • [from] - {number} when paging use from as the row offset. Default = 0.
  • [format] - {string} output formats: "json", "csv", "tsv", "table". Default = "json".

Return:

  • object|string json or string