pod5_convert_to_fast5

Tool for converting pod5 files to the legacy fast5 format

class StatusMonitor(file_count: int)

Bases: object

Class for monitoring the status / progress of the conversion

__init__(file_count: int)

property formatted_sample_count: str

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

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(force: bool = False)

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

property running: bool

Return true if not all files have finished processing

property sample_rate: float

Return the time averaged sample rate

property samples_mb: float

Return the samples count in megabytes

property time_elapsed: float

Return the total time elapsed in seconds

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.

convert_to_fast5(inputs: List[Path], output: Path, recursive: bool = False, threads: int = 10, force_overwrite: bool = False, file_read_count: int = 4000)

main()

write_pod5_record_to_fast5(read: ReadRecord, fast5: File) → None