Example #1
0
def getGa2VcfParser():
    parser = cli.createArgumentParser((
        "GA4GH VCF conversion tool. Converts variant information "
        "stored in a GA4GH repository into VCF format."))
    cli_client.addClientGlobalOptions(parser)
    cli.addOutputFileArgument(parser)
    cli_client.addUrlArgument(parser)
    parser.add_argument("variantSetId", help="The variant set to convert")
    parser.add_argument(
        "--outputFormat", "-O", choices=['vcf', 'bcf'], default="vcf",
        help=(
            "The format for object output. Currently supported are "
            "'vcf' (default), which is a text-based format and "
            "'bcf', which is the binary equivalent"))
    cli_client.addReferenceNameArgument(parser)
    cli_client.addCallSetIdsArgument(parser)
    cli_client.addStartArgument(parser)
    cli_client.addEndArgument(parser)
    cli_client.addPageSizeArgument(parser)
    return parser
Example #2
0
def getGa2SamParser():
    parser = cli.createArgumentParser("GA4GH SAM conversion tool")
    cli_client.addClientGlobalOptions(parser)
    cli_client.addUrlArgument(parser)
    parser.add_argument(
        "readGroupId",
        help="The ReadGroup to convert to SAM/BAM format.")
    cli_client.addPageSizeArgument(parser)
    cli_client.addStartArgument(parser)
    cli_client.addEndArgument(parser)
    parser.add_argument(
        "--referenceId", default=None,
        help="The referenceId to search over")
    parser.add_argument(
        "--outputFormat", "-O", default="sam", choices=["sam", "bam"],
        help=(
            "The format for object output. Currently supported are "
            "'sam' (default), which is a text-based format and "
            "'bam', which is the binary equivalent"))
    cli.addOutputFileArgument(parser)
    return parser
Example #3
0
def getGa2SamParser():
    parser = cli.createArgumentParser("GA4GH SAM conversion tool")
    cli_client.addClientGlobalOptions(parser)
    cli_client.addUrlArgument(parser)
    parser.add_argument("readGroupId",
                        help="The ReadGroup to convert to SAM/BAM format.")
    cli_client.addPageSizeArgument(parser)
    cli_client.addStartArgument(parser)
    cli_client.addEndArgument(parser)
    parser.add_argument("--referenceId",
                        default=None,
                        help="The referenceId to search over")
    parser.add_argument(
        "--outputFormat",
        "-O",
        default="sam",
        choices=["sam", "bam"],
        help=("The format for object output. Currently supported are "
              "'sam' (default), which is a text-based format and "
              "'bam', which is the binary equivalent"))
    cli.addOutputFileArgument(parser)
    return parser