Python get_sequence_data Examples

Example #1

File: main.py Project: Arabidopsis-Information-Portal/Get_Sequence_API

def search(args):
    """
    Return the sequence provided a coordinate
    """
    # Validate the coordinates
    tools.validate_coordinates(args['start'], args['end'])

    # Build the XML path query
    query_xml = tools.create_xml(args['chromosome'])

    # Request the sequence data
    tools.get_sequence_data(args['start'], args['end'], args['chromosome'], query_xml, args['flank'])

Example #2

File: main.py Project: Arabidopsis-Information-Portal/Get_Sequence_API

def search(args):
    """
    Return the sequence of a gene
    """

    # Get the gene coordinates
    coordinate = tools.get_gene_data(args["identifier"])
    if not coordinate:
        raise Exception(
            "Identifier '%s' could not be found! Please make sure to use a valid AGI locus identifier."
            % args["identifier"]
        )

    # Validate the coordinates
    tools.validate_coordinates(coordinate["start"], coordinate["end"])

    # Build the XML path query
    query_xml = tools.create_xml(coordinate["chromosome"])

    # Request the sequence data
    tools.get_sequence_data(coordinate["start"], coordinate["end"], coordinate["chromosome"], query_xml, args["flank"])