POD5 API Types Reference

Container class for a pod5 Read object

BaseRead `dataclass`

BaseRead(
    read_id: UUID,
    pore: Pore,
    calibration: Calibration,
    read_number: int,
    start_sample: int,
    median_before: float,
    end_reason: EndReason,
    run_info: RunInfo,
    num_minknow_events: int = 0,
    tracked_scaling: ShiftScalePair = ShiftScalePair(),
    predicted_scaling: ShiftScalePair = ShiftScalePair(),
    num_reads_since_mux_change: int = 0,
    time_since_mux_change: float = 0.0,
    open_pore_level: float = float("nan"),
)

Base class for POD5 Read Data

Parameters:

Name	Type	Description	Default
`read_id`	`UUID`	The read_id of this read as UUID.	required
`pore`	`Pore`	Pore data.	required
`calibration`	`Calibration`	Calibration data.	required
`read_number`	`int`	The read number on channel. This is increasing but typically not necessarily consecutive.	required
`start_sample`	`int`	The number samples recorded on this channel before the read started.	required
`median_before`	`float`	The level of current in the well before this read.	required
`end_reason`	`EndReason`	EndReason data.	required
`run_info`	`RunInfo`	RunInfo data.	required
`num_minknow_events`	`int`	Number of minknow events that the read contains	`0`
`tracked_scaling`	`ShiftScalePair`	Shift and Scale for tracked read scaling values (based on previous reads shift)	`ShiftScalePair()`
`predicted_scaling`	`ShiftScalePair`	Shift and Scale for predicted read scaling values (based on this read's raw signal)	`ShiftScalePair()`
`num_reads_since_mux_change`	`int`	Number of selected reads since the last mux change on this reads channel	`0`
`time_since_mux_change`	`float`	Time in seconds since the last mux change on this reads channel	`0.0`
`open_pore_level`	`float`	The tracked open pore level for the read.	`float('nan')`

Calibration `dataclass`

Calibration(offset: float, scale: float)

Parameters to convert the signal data to picoamps.

Parameters:

Name	Type	Description	Default
`offset`	`float`	Calibration offset used to convert raw ADC data into pA readings.	required
`scale`	`float`	Calibration scale factor used to convert raw ADC data into pA readings.	required

from_range `classmethod`

from_range(offset: float, adc_range: float, digitisation: float) -> Calibration

Create a Calibration instance from offset, adc_range and digitisation

CompressedRead `dataclass`

CompressedRead(
    read_id: UUID,
    pore: Pore,
    calibration: Calibration,
    read_number: int,
    start_sample: int,
    median_before: float,
    end_reason: EndReason,
    run_info: RunInfo,
    num_minknow_events: int = 0,
    tracked_scaling: ShiftScalePair = ShiftScalePair(),
    predicted_scaling: ShiftScalePair = ShiftScalePair(),
    num_reads_since_mux_change: int = 0,
    time_since_mux_change: float = 0.0,
    open_pore_level: float = float("nan"),
    signal_chunks: List[NDArray[uint8]] = list(),
    signal_chunk_lengths: List[int] = list(),
)

Bases: BaseRead

POD5 Read Data with a compressed signal.

Parameters:

Name	Type	Description	Default
`read_id`	`UUID`	The read_id of this read as UUID.	required
`pore`	`Pore`	Pore data.	required
`calibration`	`Calibration`	Calibration data.	required
`read_number`	`int`	The read number on channel. This is increasing but typically not necessarily consecutive.	required
`start_sample`	`int`	The number samples recorded on this channel before the read started.	required
`median_before`	`float`	The level of current in the well before this read.	required
`end_reason`	`EndReason`	EndReason data.	required
`run_info`	`RunInfo`	RunInfo data.	required
`signal_chunks`	`List[array[uint8]]`	Compressed signal data in chunks.	`list()`
`signal_chunk_lengths`	`List[int]`	Chunk lengths (number of samples) of signal data before compression.	`list()`

decompressed_signal `property`

decompressed_signal: NDArray[int16]

Decompress and return the chunked signal data as a contiguous numpy array.

Returns:

Name	Type	Description
`decompressed_signal`	`array[int16]`	Decompressed signal data

sample_count `property`

sample_count: int

Return the total number of samples in the uncompressed signal.

EndReason `dataclass`

EndReason(reason: EndReasonEnum, forced: bool)

Data on why the Read ended.

Parameters:

Name	Type	Description	Default
`reason`	`EndReasonEnum`	The end reason enumeration.	required
`forced`	`bool`	True if it is a 'forced' read break.	required

name `property`

name: str

Return the reason name as a lower string

from_reason_with_default_forced `classmethod`

from_reason_with_default_forced(reason: EndReasonEnum) -> EndReason

Return a new EndReason instance with the 'forced' flag set to the expected default for the given reason

EndReasonEnum

Bases: Enum

EndReason Enumeration

Pore `dataclass`

Pore(channel: int, well: int, pore_type: str)

Data for the pore that the Read was acquired on

Parameters:

Name	Type	Description	Default
`channel`	`int`	1-indexed channel.	required
`well`	`int`	1-indexed well.	required
`pore_type`	`str`	The pore type present in the well.	required

Read `dataclass`

Read(
    read_id: UUID,
    pore: Pore,
    calibration: Calibration,
    read_number: int,
    start_sample: int,
    median_before: float,
    end_reason: EndReason,
    run_info: RunInfo,
    num_minknow_events: int = 0,
    tracked_scaling: ShiftScalePair = ShiftScalePair(),
    predicted_scaling: ShiftScalePair = ShiftScalePair(),
    num_reads_since_mux_change: int = 0,
    time_since_mux_change: float = 0.0,
    open_pore_level: float = float("nan"),
    signal: NDArray[int16] = (lambda: array([], dtype=int16))(),
)

Bases: BaseRead

POD5 Read Data with an uncompressed signal

Parameters:

Name	Type	Description	Default
`read_id`	`UUID`	The read_id of this read as UUID.	required
`pore`	`Pore`	Pore data.	required
`calibration`	`Calibration`	Calibration data.	required
`read_number`	`int`	The read number on channel. This is increasing but typically not necessarily consecutive.	required
`start_sample`	`int`	The number samples recorded on this channel before the read started.	required
`median_before`	`float`	The level of current in the well before this read.	required
`end_reason`	`EndReason`	EndReason data.	required
`run_info`	`RunInfo`	RunInfo data.	required
`signal`	`array[int16]`	Uncompressed signal data.	`(lambda: array([], dtype=int16))()`

sample_count `property`

sample_count: int

Return the total number of samples in the uncompressed signal.

RunInfo `dataclass`

RunInfo(
    acquisition_id: str,
    acquisition_start_time: datetime,
    adc_max: int,
    adc_min: int,
    context_tags: Dict[str, str],
    experiment_name: str,
    flow_cell_id: str,
    flow_cell_product_code: str,
    protocol_name: str,
    protocol_run_id: str,
    protocol_start_time: datetime,
    sample_id: str,
    sample_rate: int,
    sequencing_kit: str,
    sequencer_position: str,
    sequencer_position_type: str,
    software: str,
    system_name: str,
    system_type: str,
    tracking_id: Dict[str, str],
)

Higher-level information about the Reads that correspond to a part of an experiment, protocol or acquisition

Parameters:

Name	Type	Description	Default
`acquisition_id`	`str`	A unique identifier for the acquisition.	required
`acquisition_start_time`	`datetime`	This is the clock time for sample 0	required
`adc_max`	`int`	The maximum ADC value that might be encountered.	required
`adc_min`	`int`	The minimum ADC value that might be encountered.	required
`context_tags`	`Dict[str, str]`	The context tags for the run. (For compatibility with fast5).	required
`experiment_name`	`str`	The user-supplied name for the experiment being run.	required
`flow_cell_id`	`str`	Uniquely identifies the flow cell the data was captured on.	required
`flow_cell_product_code`	`str`	Identifies the type of flow cell the data was captured on.	required
`protocol_name`	`str`	The name of the protocol that was run.	required
`protocol_run_id`	`str`	The unique identifier for the protocol run that produced this data.	required
`protocol_start_time`	`datetime`	When the protocol that the acquisition was part of started.	required
`sample_id`	`str`	A user-supplied name for the sample being analysed.	required
`sample_rate`	`int`	The number of samples acquired each second on each channel.	required
`sequencing_kit`	`str`	The type of sequencing kit used to prepare the sample.	required
`sequencer_position`	`str`	The sequencer position the data was collected on.	required
`sequencer_position_type`	`str`	The type of sequencing hardware the data was collected on.	required
`software`	`str`	A description of the software that acquired the data.	required
`system_name`	`str`	The name of the system the data was collected on.	required
`system_type`	`str`	The type of system the data was collected on.	required
`tracking_id`	`Dict[str, str]`	The tracking id for the run. (For compatibility with fast5).	required

ShiftScalePair `dataclass`

ShiftScalePair(shift: float = float('nan'), scale: float = float('nan'))

A pair of floating point shift and scale values.

POD5 API Types Reference

BaseRead dataclass

Calibration dataclass

from_range classmethod

CompressedRead dataclass

decompressed_signal property

sample_count property

EndReason dataclass

name property

from_reason_with_default_forced classmethod

EndReasonEnum

Pore dataclass

Read dataclass

sample_count property

RunInfo dataclass

ShiftScalePair dataclass

BaseRead `dataclass`

Calibration `dataclass`

from_range `classmethod`

CompressedRead `dataclass`

decompressed_signal `property`

sample_count `property`

EndReason `dataclass`

name `property`

from_reason_with_default_forced `classmethod`

Pore `dataclass`

Read `dataclass`

sample_count `property`

RunInfo `dataclass`

ShiftScalePair `dataclass`