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AbstractFileReader.html
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<article id="content">
<header>
<h1 class="title">Module <code>read5.AbstractFileReader</code></h1>
</header>
<section id="section-intro">
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">#!/usr/bin/env python
# author: Jannes Spangenberg
# e-mail: [email protected]
# github: https://github.com/JannesSP
# website: https://jannessp.github.io
from abc import abstractmethod
import numpy as np
from read5.Exceptions import UnknownNormalizationMode
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
'''