convert_to_fast5

Tool for converting pod5 files to the legacy fast5 format

StatusMonitor

StatusMonitor(file_count: int)

Class for monitoring the status / progress of the conversion

formatted_sample_count property

formatted_sample_count: str

Return the sample count as a string with leading Metric prefix if necessary

running property

running: bool

Return true if not all files have finished processing

sample_rate property

sample_rate: float

Return the time averaged sample rate

samples_mb property

samples_mb: float

Return the samples count in megabytes

time_elapsed property

time_elapsed: float

Return the total time elapsed in seconds

increment

increment(
    *,
    files_started: int = 0,
    files_ended: int = 0,
    read_count: int = 0,
    reads_processed: int = 0,
    sample_count: int = 0
) -> None

Incremeent the status counters

print_status

print_status(force: bool = False)

Print the status if the update interval has passed or if forced

convert_pod5_to_fast5

convert_pod5_to_fast5(source: Path, dest: Path, read_ids: List[str]) -> Tuple[int, int]

Open a source pod5 file and write the selected read_ids into the destination fast5 file target.