Module read5.AbstractFileReader

Classes

class AbstractFileReader (filepath: str)

Abstract file reader class

Attributes

filepath : str

Path to the ONT raw data file

Raises

FileNotFoundError

If the given file does not exist.

Expand source code

class AbstractFileReader():
    '''
    Abstract file reader class

    Attributes
    ----------
    filepath : str
        Path to the ONT raw data file

    Raises
    ------
    FileNotFoundError
        If the given file does not exist.
    '''

    ### abstract methods

    @abstractmethod
    def open(self) -> None:
        '''
        Opens and loads the reads of the raw ONT file.
        '''
        pass
        
    @abstractmethod
    def __getitem__(self, readid : str):
        '''
        Parameter
        ---------
        readid : str

        Returns
        -------
        read
            read dataset
        '''
        pass

    @abstractmethod
    def getAsicID(self, readid : str) -> str:
        '''
        Application Specific Integrated Circuit identifier (ASIC) of the flow cell (unique chip ID, enables tracking of batches of chips).

        Parameter
        ---------
        readid : str

        Returns
        -------
        asic_id : str
        '''
        pass

    @abstractmethod
    def getAsicIDEeprom(self, readid : str) -> str:
        '''
        ID of the ASIC's electrically erasable programmable read-only memory (EEPROM) of the flow cell
        
        Parameter
        ---------
        readid : str

        Returns
        -------
        asic_id_eeprom : str
        '''
        pass

    @abstractmethod
    def getAsicTemp(self, readid : str) -> float:
        '''
        ASIC chip temperature in degrees celsius at start of sequencing
        
        Parameter
        ---------
        readid : str

        Returns
        -------
        asic_temp : float
        '''
        pass

    @abstractmethod
    def getAsicVersion(self, readid : str) -> str:
        '''
        ASIC version

        Parameter
        ---------
        readid : str

        Returns
        -------
        asic_version : str
        '''
        pass

    @abstractmethod
    def isAutoUpdated(self, readid : str) -> bool:
        '''
        Auto update in MinKNOW

        Parameter
        ---------
        readid : str

        Returns
        -------
        status : bool
        '''
        pass

    @abstractmethod
    def getAutoUpdateSource(self, readid : str) -> str:
        '''
        URL to MinKNOW update source

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        url : str
        '''
        pass

    @abstractmethod
    def isBarcodingEnabled(self, readid : str) -> bool:
        '''
        Whether barcoding is enabled or not

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        status : bool
        '''
        pass

    @abstractmethod
    def isBreamStandard(self, readid : str) -> bool:
        '''
        Bream is a sequencing controlling software
        
        Parameter
        ---------
        readid : str
        
        Returns
        -------
        status : bool
        '''
        pass

    @abstractmethod
    def getCalibrationScale(self, readid : str) -> float:
        '''
        Parameter
        ---------
        readid : str

        Returns
        -------
        scale : float
            scale = range / digitisation
        '''
        pass

    @abstractmethod
    def getChannelNumber(self, readid : str) -> int:
        '''
        Parameter
        ---------
        readid : str

        Returns
        -------
        channel : int
            Number of the channel where the read was sequenced
        '''
        pass

    @abstractmethod
    def getConfigurationVersion(self, readid : str) -> str:
        '''
        MinKNOW configuration version including the experiment scripts

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        configuration_version : str
        '''
        pass
    
    @abstractmethod
    def getDeviceID(self, readid : str) -> str:
        '''
        MinION ID or GridION/PromethION device position ID

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        device_id : str
        '''
        pass
    
    @abstractmethod
    def getDeviceType(self, readid : str) -> str:
        '''
        Device type: MinION, PromethION or GridION

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        device_type : str
        '''
        pass

    @abstractmethod
    def getDigitisation(self, readid : str) -> int:
        '''
        Returns read calibration digitisation

        Parameter
        ---------
        readid : str

        Returns
        -------
        digitisation : float
        '''
        pass
    
    @abstractmethod
    def getDistributionStatus(self, readid : str) -> str:
        '''
        stable, dev, alpha or beta

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        distribution_status : str
        '''
        pass
    
    @abstractmethod
    def getDistributionVersion(self, readid : str) -> str:
        '''
        MinKNOW version

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        distribution_version : str
        '''
        pass

    @abstractmethod
    def getDuration(self, readid : str) -> int:
        '''
        Returns
        -------
        duration : int
            length of raw signal, number of signal samples
        '''
        pass
    
    @abstractmethod
    def getEndReason(self, readid : str) -> int:
        '''
        Available since FAST5 v2.2
        ATTENTION: End Reason encoding differs: fast5/slow5/blow5 vs pod5!

        Returns
        -------
        end_reason : int
            0 : unknown
            1 : partial
            2 : mux_change
            3 : unblock_mux_change
            4 : data_service_unblock_mux_change
            5 : signal_positive
            6 : signal_negative
        '''
        pass

    @abstractmethod
    def getExpScriptName(self, readid : str) -> str:
        '''
        Experiment name with selected kits and parameters in MinKNOW.
        Also called protocol name in pod5.

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        exp_script_name : str
        '''
        pass
    
    @abstractmethod
    def getExpScriptPurpose(self, readid : str) -> str:
        '''
        The purpose of the run: sequencing run or simulation playback

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        exp_script_purpose : str
        '''
        pass
    
    @abstractmethod
    def getExpStartTime(self, readid : str) -> str:
        '''
        Start time of the sequencing run in ISO 8601 standard

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        exp_start_time : str
        '''
        pass

    @abstractmethod
    def getExperimentDurationSet(self, readid : str) -> int:
        '''
        Experiment duration set when starting the sequencing run in minutes

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        duration : int
        '''
        pass

    @abstractmethod
    def getExperimentType(self, readid : str) -> str:
        '''
        Type of experiment, like DNA or RNA sequencing

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        experiment_type : str
        '''
        pass

    @abstractmethod
    def getFileVersion(self) -> str:
        '''
        Returns
        -------
        file_version : str
        '''
        pass

    @abstractmethod
    def getFlowCellID(self, readid : str) -> str:
        '''
        Unique flow cell ID

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        flow_cell_id : str
        '''
        pass
    
    @abstractmethod
    def getFlowCellProductCode(self, readid : str) -> str:
        '''
        Product code of the flowcell and pore type

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        production_code : str
        '''
        pass
    
    @abstractmethod
    def getGuppyVersion(self, readid : str) -> str:
        '''
        Guppy version used by MinKNOW

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        version : str
        '''
        pass
    
    @abstractmethod
    def getHeatSinkTemp(self, readid : str) -> float:
        '''
        Start temperature in degress celsius of the ASIC heat sink

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        temperature : float
        '''
        pass
    
    @abstractmethod
    def getHostProductCode(self, readid : str) -> str:
        '''
        Product code of the host computer

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        code : str
        '''
        pass
    
    @abstractmethod
    def getHostProductSerialNumber(self, readid : str) -> str:
        '''
        Serial number of the host computer

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        serial_number : str
        '''
        pass
    
    @abstractmethod
    def getHostname(self, readid : str) -> str:
        '''
        Computer on which the sequencing run is performed

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        hostname : str
        '''
        pass
    
    @abstractmethod
    def getInstallationType(self, readid : str) -> str:
        '''
        MinKNOW installation type

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        installation_type : str
        '''
        pass

    @abstractmethod
    def isLocalBasecalled(self, readid : str) -> bool:
        '''
        Type of experiment, like DNA or RNA sequencing

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        status : bool
        '''
        pass
    
    @abstractmethod
    def getLocalFirmwareFile(self, readid : str) -> int:
        '''
        Parameter
        ---------
        readid : str
        
        Returns
        -------
        firmware_file : int
        '''
        pass
    
    @abstractmethod
    def getMedianBefore(self, readid : str) -> float:
        '''
        Estimated current median preceding the read, can be used as an estimate of the open pore current (no strand inside the pore)
        
        Returns
        -------
        median_before : float
        '''
        pass

    @abstractmethod
    def getOffset(self, readid : str) -> float:
        '''
        Parameter
        ---------
        readid : str

        Returns
        -------
        offset : float
        '''
        pass

    @abstractmethod
    def getOperatingSystem(self, readid : str) -> str:
        '''
        Operating system of the host computer

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        os : str
        '''
        pass

    @abstractmethod
    def getPackage(self, readid : str) -> str:
        '''
        Bream package used during sequencing

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        package : str
        '''
        pass

    @abstractmethod
    def getPackageVersion(self, readid : str) -> str:
        '''
        Bream package version

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        package_version : str
        '''
        pass

    @abstractmethod
    def getpASignal(self, readid :str) -> np.ndarray:
        '''
        Parameter
        ---------
        readid : str

        Returns
        -------
        pASignal : np.ndarray
        '''
        pass

    @abstractmethod
    def getPoreType(self, readid : str) -> str:
        '''
        Parameter
        ---------
        readid : str

        Returns
        -------
        pore_type : str
            can be 'not_set'
        '''
        pass

    @abstractmethod
    def getProtocolGroupID(self, readid : str) -> str:
        '''
        Unique acquisition period ID set by the user, also called 'group id'

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        protocol_id : str
        '''
        pass
    
    @abstractmethod
    def getProtocolRunID(self, readid : str) -> str:
        '''
        Experiment run ID

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        prot_run_id : str
        '''
        pass
    
    @abstractmethod
    def getProtocolStartTime(self, readid : str) -> str:
        '''
        Data acquisition period start time

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        prot_start_time : str
        '''
        pass
    
    @abstractmethod
    def getProtocolVersion(self, readid : str) -> str:
        '''
        Protocol version (barcoding, kits, etc)

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        prot_version : str
        '''
        pass

    @abstractmethod
    def getRange(self, readid : str) -> np.ndarray:
        '''
        Returns read calibration range

        Parameter
        ---------
        readid : str

        Returns
        -------
        range : float
        '''
        pass

    @abstractmethod
    def getReadNumber(self, readid : str) -> int:
        '''
        Parameter
        ---------
        readid : str

        Returns
        -------
        read_number : int
        '''
        pass

    @abstractmethod
    def getRunID(self, readid : str) -> str:
        '''
        Parameter
        ---------
        readid : str

        Returns
        -------
        run_id : str
        '''
        pass

    @abstractmethod
    def getSamplingRate(self, readid) -> int:
        '''
        Measuring rate of the sensor during sequencing in Hz

        Parameter
        ---------
        readid : str

        Returns
        -------
        samplingRate : int
            sampling rate of the sequencing sensor used to sequence the given read
        '''
        pass
    
    @abstractmethod
    def getSampleID(self, readid : str) -> str:
        '''
        Custom user given sample ID

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        sample_id : str
        '''
        pass

    @abstractmethod
    def getSequencingKit(self, readid : str) -> str:
        '''
        Sequencing kit selected by the user

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        kit : str
        '''
        pass

    @abstractmethod
    def getSignal(self, readid : str) -> np.ndarray:
        '''
        Parameter
        ---------
        readid : str

        Returns
        -------
        signal : np.ndarray
            Raw integer signal of readid
        '''
        pass

    @abstractmethod
    def getStartTime(self, readid : str) -> int:
        '''
        Sample number of the sequencing start of the provided read.
        0 = start of sequencing
        
        Parameter
        ---------
        readid : str

        Returns
        -------
        startTime : int
            start of sequencing unconverted
        '''
        pass

    # @abstractmethod
    # def getStartMux(self, readid : str) -> int:
    #     '''
    #     Returns
    #     -------
    #     start_mux : int
    #     '''
    #     pass

    @abstractmethod
    def getUSBConfig(self, readid : str) -> str:
        '''
        Flow cell and host computer connection information

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        config : str
        '''
        pass
    
    @abstractmethod
    def getVersion(self, readid : str) -> str:
        '''
        MinKNOW version

        Parameter
        ---------
        readid : str
        
        Returns
        -------
        version : str
        '''
        pass

    ### explicit functions

    def __init__(self, filepath : str):
        self._file = None
        self._filepath : str = filepath
        self._index : int = -1
        self._nreads : int
        self._reads : list
        self.open()

    def __iter__(self):
        return self
    
    def __len__(self) -> int:
        '''
        Returns
        -------
        length : int
            number of reads in the file
        '''
        return self._nreads
    
    def __next__(self):
        self._index += 1
        if self._index >= self._nreads:
            raise StopIteration
        else:
            return self._reads[self._index]
    
    def close(self) -> None:
        '''
        Close the raw ONT file
        '''
        if self._open:
            self._file.close()
            self._open = False

    def isOpen(self) -> bool:
        '''
        Returns
        -------
        flag : bool
            open status of file
        '''
        return self._open

    def getReads(self) -> list:
        '''
        Returns
        -------
        reads : list
            list of read IDs within the file
        '''
        return self._reads
    
    def getShift(self, readid : str, mode : str = 'median') -> float:
        '''
        Parameter
        ---------
        readid : str
        mode : str
            - 'median': using the median and mad for normalization
            - 'mean': using the mean and std for normalization

        Returns
        -------
        shift : float
        '''
        if mode == 'median':
            return np.median(self.getpASignal(readid))
        elif mode == 'mean':
            return np.mean(self.getpASignal(readid))
        else:
            raise UnknownNormalizationMode

    def getScale(self, readid : str, mode : str = 'median') -> float:
        '''
        Parameter
        ---------
        readid : str
        mode : str
            - 'median': using the median and mad for normalization
            - 'mean': using the mean and std for normalization

        Returns
        -------
        scale : float
        '''
        if mode == 'median':
            return 1.4826 * np.median(np.abs(self.getpASignal(readid) - self.getShift(readid, mode)))
        elif mode == 'mean':
            return np.std(self.getpASignal(readid))
        else:
            raise UnknownNormalizationMode
        
    def getZNormSignal(self, readid : str, mode : str = 'median') -> np.ndarray:
        '''
        Normalize the read signal of the provided read

        Parameter
        ---------
        readid : str
        mode : str
            - 'median': using the median and mad for normalization
            - 'mean': using the mean and std for normalization

        Returns
        -------
        normSignal : np.ndarray
            Z normalized read signal
        '''
        return (self.getpASignal(readid) - self.getShift(readid, mode)) / self.getScale(readid, mode)

    def getPolyAStandardizedSignal(self, readid : str, polyAstart : int, polyAend : int) -> np.ndarray:
        '''
        Standardize the read signal of the provided read with the polyA.
        This function uses the median and mad to standardize the read with the polyA signal.
        After standardization the polyA signal will have a mean of 108.901413 and a stdev of 2.676522.
        
        Parameter
        ---------
        readid : str
        polyAstart : int
            included starting index of the polyA signal in the read
        polyAend : int
            excluded ending index of the polyA signal in the read

        Returns
        -------
        standardizedSignal : np.ndarray
            polyA standardized read signal
        '''
        stdPolyAMean = 108.901413
        stdPolyAStdev = 2.676522
        polyAsignal = self.getpASignal(readid)[polyAstart : polyAend]
        polyAmedian = np.median(polyAsignal)
        polyAmad = 1.4826 * np.median(np.abs(polyAsignal - polyAmedian))
        return ((self.getpASignal(readid) - polyAmedian) / polyAmad) * stdPolyAStdev + stdPolyAMean
    
    def getStartTimeInMinutes(self, readid) -> float:
        '''
        Parameter
        ---------
        readid : str

        Returns
        -------
        startTime : int
            start of sequencing converted to minutes after sequencing start
        '''
        return self.getStartTime(readid) / self.getSamplingRate(readid) / 60
    
    def getFilePath(self) -> str:
        '''
        Returns
        -------
        filepath : str
        '''
        return self._filepath

Subclasses

• Fast5Reader
• Pod5Reader
• Slow5Reader

Methods

def close(self) ‑> None

Close the raw ONT file

Expand source code

def close(self) -> None:
    '''
    Close the raw ONT file
    '''
    if self._open:
        self._file.close()
        self._open = False

def getAsicID(self, readid: str) ‑> str

Application Specific Integrated Circuit identifier (ASIC) of the flow cell (unique chip ID, enables tracking of batches of chips).

Parameter

readid : str

Returns

asic_id : str

 

Expand source code

@abstractmethod
def getAsicID(self, readid : str) -> str:
    '''
    Application Specific Integrated Circuit identifier (ASIC) of the flow cell (unique chip ID, enables tracking of batches of chips).

    Parameter
    ---------
    readid : str

    Returns
    -------
    asic_id : str
    '''
    pass

def getAsicIDEeprom(self, readid: str) ‑> str

ID of the ASIC's electrically erasable programmable read-only memory (EEPROM) of the flow cell

Parameter

readid : str

Returns

asic_id_eeprom : str

 

Expand source code

@abstractmethod
def getAsicIDEeprom(self, readid : str) -> str:
    '''
    ID of the ASIC's electrically erasable programmable read-only memory (EEPROM) of the flow cell
    
    Parameter
    ---------
    readid : str

    Returns
    -------
    asic_id_eeprom : str
    '''
    pass

def getAsicTemp(self, readid: str) ‑> float

ASIC chip temperature in degrees celsius at start of sequencing

Parameter

readid : str

Returns

asic_temp : float

 

Expand source code

@abstractmethod
def getAsicTemp(self, readid : str) -> float:
    '''
    ASIC chip temperature in degrees celsius at start of sequencing
    
    Parameter
    ---------
    readid : str

    Returns
    -------
    asic_temp : float
    '''
    pass

def getAsicVersion(self, readid: str) ‑> str

ASIC version

Parameter

readid : str

Returns

asic_version : str

 

Expand source code

@abstractmethod
def getAsicVersion(self, readid : str) -> str:
    '''
    ASIC version

    Parameter
    ---------
    readid : str

    Returns
    -------
    asic_version : str
    '''
    pass

def getAutoUpdateSource(self, readid: str) ‑> str

URL to MinKNOW update source

Parameter

readid : str

Returns

url : str

 

Expand source code

@abstractmethod
def getAutoUpdateSource(self, readid : str) -> str:
    '''
    URL to MinKNOW update source

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    url : str
    '''
    pass

def getCalibrationScale(self, readid: str) ‑> float

Parameter

readid : str

Returns

scale : float

scale = range / digitisation

Expand source code

@abstractmethod
def getCalibrationScale(self, readid : str) -> float:
    '''
    Parameter
    ---------
    readid : str

    Returns
    -------
    scale : float
        scale = range / digitisation
    '''
    pass

def getChannelNumber(self, readid: str) ‑> int

Parameter

readid : str

Returns

channel : int

Number of the channel where the read was sequenced

Expand source code

@abstractmethod
def getChannelNumber(self, readid : str) -> int:
    '''
    Parameter
    ---------
    readid : str

    Returns
    -------
    channel : int
        Number of the channel where the read was sequenced
    '''
    pass

def getConfigurationVersion(self, readid: str) ‑> str

MinKNOW configuration version including the experiment scripts

Parameter

readid : str

Returns

configuration_version : str

 

Expand source code

@abstractmethod
def getConfigurationVersion(self, readid : str) -> str:
    '''
    MinKNOW configuration version including the experiment scripts

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    configuration_version : str
    '''
    pass

def getDeviceID(self, readid: str) ‑> str

MinION ID or GridION/PromethION device position ID

Parameter

readid : str

Returns

device_id : str

 

Expand source code

@abstractmethod
def getDeviceID(self, readid : str) -> str:
    '''
    MinION ID or GridION/PromethION device position ID

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    device_id : str
    '''
    pass

def getDeviceType(self, readid: str) ‑> str

Device type: MinION, PromethION or GridION

Parameter

readid : str

Returns

device_type : str

 

Expand source code

@abstractmethod
def getDeviceType(self, readid : str) -> str:
    '''
    Device type: MinION, PromethION or GridION

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    device_type : str
    '''
    pass

def getDigitisation(self, readid: str) ‑> int

Returns read calibration digitisation

Parameter

readid : str

Returns

digitisation : float

 

Expand source code

@abstractmethod
def getDigitisation(self, readid : str) -> int:
    '''
    Returns read calibration digitisation

    Parameter
    ---------
    readid : str

    Returns
    -------
    digitisation : float
    '''
    pass

def getDistributionStatus(self, readid: str) ‑> str

stable, dev, alpha or beta

Parameter

readid : str

Returns

distribution_status : str

 

Expand source code

@abstractmethod
def getDistributionStatus(self, readid : str) -> str:
    '''
    stable, dev, alpha or beta

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    distribution_status : str
    '''
    pass

def getDistributionVersion(self, readid: str) ‑> str

MinKNOW version

Parameter

readid : str

Returns

distribution_version : str

 

Expand source code

@abstractmethod
def getDistributionVersion(self, readid : str) -> str:
    '''
    MinKNOW version

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    distribution_version : str
    '''
    pass

def getDuration(self, readid: str) ‑> int

Returns

duration : int

length of raw signal, number of signal samples

Expand source code

@abstractmethod
def getDuration(self, readid : str) -> int:
    '''
    Returns
    -------
    duration : int
        length of raw signal, number of signal samples
    '''
    pass

def getEndReason(self, readid: str) ‑> int

Available since FAST5 v2.2 ATTENTION: End Reason encoding differs: fast5/slow5/blow5 vs pod5!

Returns

end_reason : int

0 : unknown 1 : partial 2 : mux_change 3 : unblock_mux_change 4 : data_service_unblock_mux_change 5 : signal_positive 6 : signal_negative

Expand source code

@abstractmethod
def getEndReason(self, readid : str) -> int:
    '''
    Available since FAST5 v2.2
    ATTENTION: End Reason encoding differs: fast5/slow5/blow5 vs pod5!

    Returns
    -------
    end_reason : int
        0 : unknown
        1 : partial
        2 : mux_change
        3 : unblock_mux_change
        4 : data_service_unblock_mux_change
        5 : signal_positive
        6 : signal_negative
    '''
    pass

def getExpScriptName(self, readid: str) ‑> str

Experiment name with selected kits and parameters in MinKNOW. Also called protocol name in pod5.

Parameter

readid : str

Returns

exp_script_name : str

 

Expand source code

@abstractmethod
def getExpScriptName(self, readid : str) -> str:
    '''
    Experiment name with selected kits and parameters in MinKNOW.
    Also called protocol name in pod5.

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    exp_script_name : str
    '''
    pass

def getExpScriptPurpose(self, readid: str) ‑> str

The purpose of the run: sequencing run or simulation playback

Parameter

readid : str

Returns

exp_script_purpose : str

 

Expand source code

@abstractmethod
def getExpScriptPurpose(self, readid : str) -> str:
    '''
    The purpose of the run: sequencing run or simulation playback

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    exp_script_purpose : str
    '''
    pass

def getExpStartTime(self, readid: str) ‑> str

Start time of the sequencing run in ISO 8601 standard

Parameter

readid : str

Returns

exp_start_time : str

 

Expand source code

@abstractmethod
def getExpStartTime(self, readid : str) -> str:
    '''
    Start time of the sequencing run in ISO 8601 standard

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    exp_start_time : str
    '''
    pass

def getExperimentDurationSet(self, readid: str) ‑> int

Experiment duration set when starting the sequencing run in minutes

Parameter

readid : str

Returns

duration : int

 

Expand source code

@abstractmethod
def getExperimentDurationSet(self, readid : str) -> int:
    '''
    Experiment duration set when starting the sequencing run in minutes

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    duration : int
    '''
    pass

def getExperimentType(self, readid: str) ‑> str

Type of experiment, like DNA or RNA sequencing

Parameter

readid : str

Returns

experiment_type : str

 

Expand source code

@abstractmethod
def getExperimentType(self, readid : str) -> str:
    '''
    Type of experiment, like DNA or RNA sequencing

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    experiment_type : str
    '''
    pass

def getFilePath(self) ‑> str

Returns

filepath : str

 

Expand source code

def getFilePath(self) -> str:
    '''
    Returns
    -------
    filepath : str
    '''
    return self._filepath

def getFileVersion(self) ‑> str

Returns

file_version : str

 

Expand source code

@abstractmethod
def getFileVersion(self) -> str:
    '''
    Returns
    -------
    file_version : str
    '''
    pass

def getFlowCellID(self, readid: str) ‑> str

Unique flow cell ID

Parameter

readid : str

Returns

flow_cell_id : str

 

Expand source code

@abstractmethod
def getFlowCellID(self, readid : str) -> str:
    '''
    Unique flow cell ID

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    flow_cell_id : str
    '''
    pass

def getFlowCellProductCode(self, readid: str) ‑> str

Product code of the flowcell and pore type

Parameter

readid : str

Returns

production_code : str

 

Expand source code

@abstractmethod
def getFlowCellProductCode(self, readid : str) -> str:
    '''
    Product code of the flowcell and pore type

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    production_code : str
    '''
    pass

def getGuppyVersion(self, readid: str) ‑> str

Guppy version used by MinKNOW

Parameter

readid : str

Returns

version : str

 

Expand source code

@abstractmethod
def getGuppyVersion(self, readid : str) -> str:
    '''
    Guppy version used by MinKNOW

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    version : str
    '''
    pass

def getHeatSinkTemp(self, readid: str) ‑> float

Start temperature in degress celsius of the ASIC heat sink

Parameter

readid : str

Returns

temperature : float

 

Expand source code

@abstractmethod
def getHeatSinkTemp(self, readid : str) -> float:
    '''
    Start temperature in degress celsius of the ASIC heat sink

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    temperature : float
    '''
    pass

def getHostProductCode(self, readid: str) ‑> str

Product code of the host computer

Parameter

readid : str

Returns

code : str

 

Expand source code

@abstractmethod
def getHostProductCode(self, readid : str) -> str:
    '''
    Product code of the host computer

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    code : str
    '''
    pass

def getHostProductSerialNumber(self, readid: str) ‑> str

Serial number of the host computer

Parameter

readid : str

Returns

serial_number : str

 

Expand source code

@abstractmethod
def getHostProductSerialNumber(self, readid : str) -> str:
    '''
    Serial number of the host computer

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    serial_number : str
    '''
    pass

def getHostname(self, readid: str) ‑> str

Computer on which the sequencing run is performed

Parameter

readid : str

Returns

hostname : str

 

Expand source code

@abstractmethod
def getHostname(self, readid : str) -> str:
    '''
    Computer on which the sequencing run is performed

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    hostname : str
    '''
    pass

def getInstallationType(self, readid: str) ‑> str

MinKNOW installation type

Parameter

readid : str

Returns

installation_type : str

 

Expand source code

@abstractmethod
def getInstallationType(self, readid : str) -> str:
    '''
    MinKNOW installation type

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    installation_type : str
    '''
    pass

def getLocalFirmwareFile(self, readid: str) ‑> int

Parameter

readid : str

Returns

firmware_file : int

 

Expand source code

@abstractmethod
def getLocalFirmwareFile(self, readid : str) -> int:
    '''
    Parameter
    ---------
    readid : str
    
    Returns
    -------
    firmware_file : int
    '''
    pass

def getMedianBefore(self, readid: str) ‑> float

Estimated current median preceding the read, can be used as an estimate of the open pore current (no strand inside the pore)

Returns

median_before : float

 

Expand source code

@abstractmethod
def getMedianBefore(self, readid : str) -> float:
    '''
    Estimated current median preceding the read, can be used as an estimate of the open pore current (no strand inside the pore)
    
    Returns
    -------
    median_before : float
    '''
    pass

def getOffset(self, readid: str) ‑> float

Parameter

readid : str

Returns

offset : float

 

Expand source code

@abstractmethod
def getOffset(self, readid : str) -> float:
    '''
    Parameter
    ---------
    readid : str

    Returns
    -------
    offset : float
    '''
    pass

def getOperatingSystem(self, readid: str) ‑> str

Operating system of the host computer

Parameter

readid : str

Returns

os : str

 

Expand source code

@abstractmethod
def getOperatingSystem(self, readid : str) -> str:
    '''
    Operating system of the host computer

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    os : str
    '''
    pass

def getPackage(self, readid: str) ‑> str

Bream package used during sequencing

Parameter

readid : str

Returns

package : str

 

Expand source code

@abstractmethod
def getPackage(self, readid : str) -> str:
    '''
    Bream package used during sequencing

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    package : str
    '''
    pass

def getPackageVersion(self, readid: str) ‑> str

Bream package version

Parameter

readid : str

Returns

package_version : str

 

Expand source code

@abstractmethod
def getPackageVersion(self, readid : str) -> str:
    '''
    Bream package version

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    package_version : str
    '''
    pass

def getPolyAStandardizedSignal(self, readid: str, polyAstart: int, polyAend: int) ‑> numpy.ndarray

Standardize the read signal of the provided read with the polyA. This function uses the median and mad to standardize the read with the polyA signal. After standardization the polyA signal will have a mean of 108.901413 and a stdev of 2.676522.

Parameter

readid : str polyAstart : int included starting index of the polyA signal in the read polyAend : int excluded ending index of the polyA signal in the read

Returns

standardizedSignal : np.ndarray

polyA standardized read signal

Expand source code

def getPolyAStandardizedSignal(self, readid : str, polyAstart : int, polyAend : int) -> np.ndarray:
    '''
    Standardize the read signal of the provided read with the polyA.
    This function uses the median and mad to standardize the read with the polyA signal.
    After standardization the polyA signal will have a mean of 108.901413 and a stdev of 2.676522.
    
    Parameter
    ---------
    readid : str
    polyAstart : int
        included starting index of the polyA signal in the read
    polyAend : int
        excluded ending index of the polyA signal in the read

    Returns
    -------
    standardizedSignal : np.ndarray
        polyA standardized read signal
    '''
    stdPolyAMean = 108.901413
    stdPolyAStdev = 2.676522
    polyAsignal = self.getpASignal(readid)[polyAstart : polyAend]
    polyAmedian = np.median(polyAsignal)
    polyAmad = 1.4826 * np.median(np.abs(polyAsignal - polyAmedian))
    return ((self.getpASignal(readid) - polyAmedian) / polyAmad) * stdPolyAStdev + stdPolyAMean

def getPoreType(self, readid: str) ‑> str

Parameter

readid : str

Returns

pore_type : str

can be 'not_set'

Expand source code

@abstractmethod
def getPoreType(self, readid : str) -> str:
    '''
    Parameter
    ---------
    readid : str

    Returns
    -------
    pore_type : str
        can be 'not_set'
    '''
    pass

def getProtocolGroupID(self, readid: str) ‑> str

Unique acquisition period ID set by the user, also called 'group id'

Parameter

readid : str

Returns

protocol_id : str

 

Expand source code

@abstractmethod
def getProtocolGroupID(self, readid : str) -> str:
    '''
    Unique acquisition period ID set by the user, also called 'group id'

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    protocol_id : str
    '''
    pass

def getProtocolRunID(self, readid: str) ‑> str

Experiment run ID

Parameter

readid : str

Returns

prot_run_id : str

 

Expand source code

@abstractmethod
def getProtocolRunID(self, readid : str) -> str:
    '''
    Experiment run ID

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    prot_run_id : str
    '''
    pass

def getProtocolStartTime(self, readid: str) ‑> str

Data acquisition period start time

Parameter

readid : str

Returns

prot_start_time : str

 

Expand source code

@abstractmethod
def getProtocolStartTime(self, readid : str) -> str:
    '''
    Data acquisition period start time

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    prot_start_time : str
    '''
    pass

def getProtocolVersion(self, readid: str) ‑> str

Protocol version (barcoding, kits, etc)

Parameter

readid : str

Returns

prot_version : str

 

Expand source code

@abstractmethod
def getProtocolVersion(self, readid : str) -> str:
    '''
    Protocol version (barcoding, kits, etc)

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    prot_version : str
    '''
    pass

def getRange(self, readid: str) ‑> numpy.ndarray

Returns read calibration range

Parameter

readid : str

Returns

range : float

 

Expand source code

@abstractmethod
def getRange(self, readid : str) -> np.ndarray:
    '''
    Returns read calibration range

    Parameter
    ---------
    readid : str

    Returns
    -------
    range : float
    '''
    pass

def getReadNumber(self, readid: str) ‑> int

Parameter

readid : str

Returns

read_number : int

 

Expand source code

@abstractmethod
def getReadNumber(self, readid : str) -> int:
    '''
    Parameter
    ---------
    readid : str

    Returns
    -------
    read_number : int
    '''
    pass

def getReads(self) ‑> list

Returns

reads : list

list of read IDs within the file

Expand source code

def getReads(self) -> list:
    '''
    Returns
    -------
    reads : list
        list of read IDs within the file
    '''
    return self._reads

def getRunID(self, readid: str) ‑> str

Parameter

readid : str

Returns

run_id : str

 

Expand source code

@abstractmethod
def getRunID(self, readid : str) -> str:
    '''
    Parameter
    ---------
    readid : str

    Returns
    -------
    run_id : str
    '''
    pass

def getSampleID(self, readid: str) ‑> str

Custom user given sample ID

Parameter

readid : str

Returns

sample_id : str

 

Expand source code

@abstractmethod
def getSampleID(self, readid : str) -> str:
    '''
    Custom user given sample ID

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    sample_id : str
    '''
    pass

def getSamplingRate(self, readid) ‑> int

Measuring rate of the sensor during sequencing in Hz

Parameter

readid : str

Returns

samplingRate : int

sampling rate of the sequencing sensor used to sequence the given read

Expand source code

@abstractmethod
def getSamplingRate(self, readid) -> int:
    '''
    Measuring rate of the sensor during sequencing in Hz

    Parameter
    ---------
    readid : str

    Returns
    -------
    samplingRate : int
        sampling rate of the sequencing sensor used to sequence the given read
    '''
    pass

def getScale(self, readid: str, mode: str = 'median') ‑> float

Parameter

readid : str mode : str - 'median': using the median and mad for normalization - 'mean': using the mean and std for normalization

Returns

scale : float

 

Expand source code

def getScale(self, readid : str, mode : str = 'median') -> float:
    '''
    Parameter
    ---------
    readid : str
    mode : str
        - 'median': using the median and mad for normalization
        - 'mean': using the mean and std for normalization

    Returns
    -------
    scale : float
    '''
    if mode == 'median':
        return 1.4826 * np.median(np.abs(self.getpASignal(readid) - self.getShift(readid, mode)))
    elif mode == 'mean':
        return np.std(self.getpASignal(readid))
    else:
        raise UnknownNormalizationMode

def getSequencingKit(self, readid: str) ‑> str

Sequencing kit selected by the user

Parameter

readid : str

Returns

kit : str

 

Expand source code

@abstractmethod
def getSequencingKit(self, readid : str) -> str:
    '''
    Sequencing kit selected by the user

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    kit : str
    '''
    pass

def getShift(self, readid: str, mode: str = 'median') ‑> float

Parameter

readid : str mode : str - 'median': using the median and mad for normalization - 'mean': using the mean and std for normalization

Returns

shift : float

 

Expand source code

def getShift(self, readid : str, mode : str = 'median') -> float:
    '''
    Parameter
    ---------
    readid : str
    mode : str
        - 'median': using the median and mad for normalization
        - 'mean': using the mean and std for normalization

    Returns
    -------
    shift : float
    '''
    if mode == 'median':
        return np.median(self.getpASignal(readid))
    elif mode == 'mean':
        return np.mean(self.getpASignal(readid))
    else:
        raise UnknownNormalizationMode

def getSignal(self, readid: str) ‑> numpy.ndarray

Parameter

readid : str

Returns

signal : np.ndarray

Raw integer signal of readid

Expand source code

@abstractmethod
def getSignal(self, readid : str) -> np.ndarray:
    '''
    Parameter
    ---------
    readid : str

    Returns
    -------
    signal : np.ndarray
        Raw integer signal of readid
    '''
    pass

def getStartTime(self, readid: str) ‑> int

Sample number of the sequencing start of the provided read. 0 = start of sequencing

Parameter

readid : str

Returns

startTime : int

start of sequencing unconverted

Expand source code

@abstractmethod
def getStartTime(self, readid : str) -> int:
    '''
    Sample number of the sequencing start of the provided read.
    0 = start of sequencing
    
    Parameter
    ---------
    readid : str

    Returns
    -------
    startTime : int
        start of sequencing unconverted
    '''
    pass

def getStartTimeInMinutes(self, readid) ‑> float

Parameter

readid : str

Returns

startTime : int

start of sequencing converted to minutes after sequencing start

Expand source code

def getStartTimeInMinutes(self, readid) -> float:
    '''
    Parameter
    ---------
    readid : str

    Returns
    -------
    startTime : int
        start of sequencing converted to minutes after sequencing start
    '''
    return self.getStartTime(readid) / self.getSamplingRate(readid) / 60

def getUSBConfig(self, readid: str) ‑> str

Flow cell and host computer connection information

Parameter

readid : str

Returns

config : str

 

Expand source code

@abstractmethod
def getUSBConfig(self, readid : str) -> str:
    '''
    Flow cell and host computer connection information

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    config : str
    '''
    pass

def getVersion(self, readid: str) ‑> str

MinKNOW version

Parameter

readid : str

Returns

version : str

 

Expand source code

@abstractmethod
def getVersion(self, readid : str) -> str:
    '''
    MinKNOW version

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    version : str
    '''
    pass

def getZNormSignal(self, readid: str, mode: str = 'median') ‑> numpy.ndarray

Normalize the read signal of the provided read

Parameter

readid : str mode : str - 'median': using the median and mad for normalization - 'mean': using the mean and std for normalization

Returns

normSignal : np.ndarray

Z normalized read signal

Expand source code

def getZNormSignal(self, readid : str, mode : str = 'median') -> np.ndarray:
    '''
    Normalize the read signal of the provided read

    Parameter
    ---------
    readid : str
    mode : str
        - 'median': using the median and mad for normalization
        - 'mean': using the mean and std for normalization

    Returns
    -------
    normSignal : np.ndarray
        Z normalized read signal
    '''
    return (self.getpASignal(readid) - self.getShift(readid, mode)) / self.getScale(readid, mode)

def getpASignal(self, readid: str) ‑> numpy.ndarray

Parameter

readid : str

Returns

pASignal : np.ndarray

 

Expand source code

@abstractmethod
def getpASignal(self, readid :str) -> np.ndarray:
    '''
    Parameter
    ---------
    readid : str

    Returns
    -------
    pASignal : np.ndarray
    '''
    pass

def isAutoUpdated(self, readid: str) ‑> bool

Auto update in MinKNOW

Parameter

readid : str

Returns

status : bool

 

Expand source code

@abstractmethod
def isAutoUpdated(self, readid : str) -> bool:
    '''
    Auto update in MinKNOW

    Parameter
    ---------
    readid : str

    Returns
    -------
    status : bool
    '''
    pass

def isBarcodingEnabled(self, readid: str) ‑> bool

Whether barcoding is enabled or not

Parameter

readid : str

Returns

status : bool

 

Expand source code

@abstractmethod
def isBarcodingEnabled(self, readid : str) -> bool:
    '''
    Whether barcoding is enabled or not

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    status : bool
    '''
    pass

def isBreamStandard(self, readid: str) ‑> bool

Bream is a sequencing controlling software

Parameter

readid : str

Returns

status : bool

 

Expand source code

@abstractmethod
def isBreamStandard(self, readid : str) -> bool:
    '''
    Bream is a sequencing controlling software
    
    Parameter
    ---------
    readid : str
    
    Returns
    -------
    status : bool
    '''
    pass

def isLocalBasecalled(self, readid: str) ‑> bool

Type of experiment, like DNA or RNA sequencing

Parameter

readid : str

Returns

status : bool

 

Expand source code

@abstractmethod
def isLocalBasecalled(self, readid : str) -> bool:
    '''
    Type of experiment, like DNA or RNA sequencing

    Parameter
    ---------
    readid : str
    
    Returns
    -------
    status : bool
    '''
    pass

def isOpen(self) ‑> bool

Returns

flag : bool

open status of file

Expand source code

def isOpen(self) -> bool:
    '''
    Returns
    -------
    flag : bool
        open status of file
    '''
    return self._open

def open(self) ‑> None

Opens and loads the reads of the raw ONT file.

Expand source code

@abstractmethod
def open(self) -> None:
    '''
    Opens and loads the reads of the raw ONT file.
    '''
    pass