vatvs_API

• List annotation databases, their types, and their fields.

  This API will be called from VAT for users to find out which databases in variant server are available for query.

  @app.route('/vatvs/variants/list_fields',methods=['GET'])
  def list_fields()
  

• Given varaints information, return variantIDs

  This API will be called from vatdp to get variantIDs for variants in the VCF file.

  @app.route('/vatvs/variants/variantsID', methods=['POST'])
  def get_variantIDs()
  

• Given chromosome and range, return variantIDs

  This API will be called from VAT to get variantIDs for variants in the specified range on a chromosome.

  @app.route('/vatvs/variants/<string:chromosome,range>', methods=['GET'])
  def get_variants_by_chromosome_range(chr,range)
  

• Given fields and range, return variantIDs

  This API will be called from VAT to get variantIDs for variants in the specified range of a field.

  @app.route('/vatvs/variants/<string:field,range>', methods=['GET'])
  def get_variants_by_field_range(field,range)
  

• Given gene name, return variantIDs

  This API will be called from VAT to get variantIDs for a gene. The gene name could be a string specifying which database will be searched, for example ‘refGene.name=”ASD”’.

  @app.route('/vatvs/variants/gene/<string:geneName>', methods=['GET'])
  def get_variants_in_gene(geneName)
  

• Given search criteria, return variantIDs

  This API will be called from VAT to get variantIDs for certain search criteria .

  @app.route('/vatvs/variants/search', methods=['POST'])
  def search_variants()
  

• Given gene name, return annotations

  This API will be called from VAT to get annotation for a gene.

  @app.route('/vatvs/annotation/gene/<string:geneName>', methods=['GET'])
  def get_annotations_by_gene(geneName)
  

• Given variantID, return annotations

  This API will be called from VAT to get annotation for a variant.

  @app.route('/vatvs/annotation/variant/<string:variantID>', methods=['GET'])
  def get_annotations_by_variantID(variantID)
  

• Given variantIDs, return annotations

  This API will be called from VAT to get annotations for a batch query of variantIDs.

  @app.route('/vatvs/annotation/variant', methods=['POST'])
  def get_annotations_by_variantIDs([variantIDs])