How to use the pomoxis.set_wakeup function in pomoxis

To help you get started, we’ve selected a few pomoxis examples, based on popular ways it is used in public projects.

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github nanoporetech / pomoxis / pomoxis / apps / epi3me.py View on Github external
def run_dealer(args):
    """Entry point handler for server."""
    set_wakeup()
    asyncio.get_event_loop().run_until_complete(main_dealer(args.path, args.outpath, output=args.output, port=args.port))
github nanoporetech / pomoxis / pomoxis / apps / epi3me.py View on Github external
def run_router(args):
    """Entry point handler for client."""
    set_wakeup()
    asyncio.get_event_loop().run_until_complete(main_router(args.addr))
github nanoporetech / pomoxis / pomoxis / apps / read_until_filter.py View on Github external
suffixes).
    :param channels: list of channels to simulate.
    :param start_port: port on which to run .fast5 replay server, bwa alignment
        server will be run on the following numbered port.
    :param targets: list of reference names. If `whitelist` is `False`, reads
        aligning to these references will be ejected. If `whitelist` is `True`
        any read alinging to a reference other than those contained in this
        list will be ejected. Unidentified reads are never ejected.
    :param whitelist: see `target`.
    """

    logger = logging.getLogger('ReadUntil App')
    good_class = 'strand'
    time_warp=2
    event_loop = asyncio.get_event_loop()
    set_wakeup()

    port = start_port
    # Setup replay service
    replay_port = port
    replay_server = event_loop.create_task(replayfast5.replay_server(
        fast5, channels, replay_port, good_class, time_warp=time_warp
    ))
    port += 1
    # Setup alignment service
    align_port = port
    align_server = event_loop.create_task(bwa.align_server(
        bwa_index, align_port
    ))


    identified_reads = {}
github nanoporetech / pomoxis / pomoxis / provider / replayfast5.py View on Github external
def read_until_demo(fast5, channels, port=5555):
    """Simple demo of read until server and client application.

    :param fast5: input .fast5 file.
    :param channels: list of channels to simulate.
    :param port: port on which to run server and cliant.
    """
    logger = logging.getLogger('ReadUntil App')
    good_class = 'strand'
    time_warp=2
    event_loop = asyncio.get_event_loop()
    set_wakeup()
    # Setup replay service
    event_loop.create_task(replay_server(
        fast5, channels, port, good_class, time_warp=time_warp
    ))

    @asyncio.coroutine
    def read_until(port):
        client = yield replay_client(port)
        counter = 0
        while True:
            #This can be mostly rewritten for any real app
            for channel in channels:
                read_block = yield from client.call.get_events(channel)
                if read_block is None:
                    logger.debug("Channel not in '{}' classification".format(good_class))
                else:
github nanoporetech / pomoxis / pomoxis / align / common.py View on Github external
def _run():
        set_wakeup()
        server = yield from align_server(
            args.index, args.port, args.aligner, opts=args.opts
        )
        logger.info('Alignment server running, awaiting requests...')
        yield from server.wait_closed()