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Pod5Reader.html
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<!doctype html>
<html lang="en">
<head>
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<title>read5.Pod5Reader API documentation</title>
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<body>
<main>
<article id="content">
<header>
<h1 class="title">Module <code>read5.Pod5Reader</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: jannes.spangenberg@uni-jena.de
# github: https://github.com/JannesSP
# website: https://jannessp.github.io
import uuid
from read5.AbstractFileReader import AbstractFileReader
import pod5
import datetime
import numpy as np
class Pod5Reader(AbstractFileReader):
'''
File reader for pod5 files
Attributes
----------
filepath : str
Path to the ONT raw data file
Raises
------
FileNotFoundError
If the given file does not exist.
'''
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
def open(self) -> None:
self._file = pod5.Reader(self._filepath)
self._reads = self._file.read_ids
self._nreads = self._file.num_reads
self._open = True
def getReads(self) -> list:
return self._reads
def __getitem__(self, readid : str):
'''
Returns the ReadRecord for the provided readid.
'''
return next(self._file.reads([readid]))
def getAsicID(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['asic_id']
def getAsicIDEeprom(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['asic_id_eeprom']
def getAsicTemp(self, readid : str) -> float:
return float(self.getTrackingIDDict(readid)['asic_temp'])
def getAsicVersion(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['asic_version']
def getAutoUpdateSource(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['auto_update_source']
def isAutoUpdated(self, readid : str) -> bool:
return bool(int(self.getTrackingIDDict(readid)['auto_update']))
def isBarcodingEnabled(self, readid : str) -> bool:
return bool(int(self.getContextTagsDict(readid)['barcoding_enabled']))
def isBreamStandard(self, readid : str) -> bool:
return bool(int(self.getTrackingIDDict(readid)['bream_is_standard']))
def getCalibration(self, readid : str) -> float:
return self.__getitem__(readid).calibration
def getCalibrationScale(self, readid : str) -> float:
return self.getCalibration(readid).scale
def getChannelNumber(self, readid : str) -> int:
return self.getPoreObject(readid).channel
def getConfigurationVersion(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['configuration_version']
def getContextTagsDict(self, readid : str) -> dict:
'''
Returns
-------
context_tags : dict
'''
return self.getRunInfoObject(readid).context_tags
def getDeviceID(self, readid : str) -> str:
return self.getRunInfoObject(readid).sequencer_position
def getDeviceType(self, readid : str) -> str:
return self.getRunInfoObject(readid).sequencer_position_type
def getDigitisation(self, readid : str) -> int:
return self.__getitem__(readid).calibration_digitisation
def getDistributionStatus(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['distribution_status']
def getDistributionVersion(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['distribution_version']
def getDuration(self, readid : str) -> int:
return self.__getitem__(readid).num_samples
def getEndReason(self, readid: str) -> int:
'''
ATTENTION: End Reason encoding differs: fast5/slow5/blow5 vs pod5!
Returns
-------
end_reason : int
0 : unknown
1 : mux_change
2 : unblock_mux_change
3 : data_service_unblock_mux_change
4 : signal_positive
5 : signal_negative
'''
return self.__getitem__(readid).end_reason_index
def getEndReasonObject(self, readid: str) -> pod5.pod5_types.EndReason:
'''
Returns
-------
end_reason : pod5.pod5_types.EndReason
'''
return self.__getitem__(readid).end_reason
def getExperimentDurationSet(self, readid : str) -> int:
return int(self.getContextTagsDict(readid)['experiment_duration_set'])
def getExperimentType(self, readid : str) -> str:
return self.getContextTagsDict(readid)['experiment_type']
def getExpScriptPurpose(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['exp_script_purpose']
def getExpScriptName(self, readid : str) -> str:
return self.getRunInfoObject(readid).protocol_name
def getExpStartTime(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['exp_start_time']
def getFileID(self) -> uuid.UUID:
return self._file.file_identifier
# file_version : packagin.version.Version
# contains more (& detailed) information if needed in the future
def getFileVersion(self) -> str:
return str(self._file.file_version)
def getLocalFirmwareFile(self, readid : str) -> int:
return int(self.getTrackingIDDict(readid)['local_firmware_file'])
def getFlowCellID(self, readid : str) -> str:
return self.getRunInfoObject(readid).flow_cell_id
def getFlowCellProductCode(self, readid : str) -> str:
return self.getRunInfoObject(readid).flow_cell_product_code
def getGuppyVersion(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['guppy_version']
def getHeatSinkTemp(self, readid : str) -> float:
return float(self.getTrackingIDDict(readid)['heatsink_temp'])
def getHostname(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['hostname']
def getHostProductCode(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['host_product_code']
def getHostProductSerialNumber(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['host_product_serial_number']
def getInstallationType(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['installation_type']
def isLocalBasecalled(self, readid : str) -> bool:
return bool(int(self.getContextTagsDict(readid)['local_basecalling']))
def getMedianBefore(self, readid : str) -> float:
return self.__getitem__(readid).median_before
def getNumMinknowEvents(self, readid : str) -> int:
'''
Number of minknow events that the read contains.
Returns
-------
num_minknow_events : int
np.nan, if attribute not available
'''
return self.__getitem__(readid).num_minknow_events
def getNumReadsSinceMuxChange(self, readid : str) -> int:
'''
Number of selected reads since the last mux change on this reads channel
Returns
-------
num_reads_since_mux_change : int
'''
return self.__getitem__(readid).num_reads_since_mux_change
def getTimeSinceMuxChange(self, readid : str) -> float:
'''
Returns
-------
time_since_mux_change : float
'''
return self.__getitem__(readid).time_since_mux_change
def getOffset(self, readid : str) -> float:
return self.getCalibration(readid).offset
def getOperatingSystem(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['operating_system']
def getPackage(self, readid : str) -> str:
return self.getContextTagsDict(readid)['package']
def getPackageVersion(self, readid : str) -> str:
return self.getContextTagsDict(readid)['package_version']
def getProtocolGroupID(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['protocol_group_id']
def getProtocolStartTime(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['protocol_start_time']
def getProtocolStartTime_fromRunInfo(self, readid : str) -> str:
return self.getRunInfoObject(readid).protocol_start_time.isoformat()
# TODO the following function works and is correct, but the converted time seems to be wrong -> error in pod5 converter?
def getProtocolStartTime_datetime(self, readid : str) -> datetime.datetime:
'''
Parameters
----------
readid : str
Returns
-------
protocol_start_time : datetime.datetime
'''
return self.getRunInfoObject(readid).protocol_start_time
def getProtocolRunID(self, readid : str) -> str:
return self.getRunInfoObject(readid).protocol_run_id
def getProtocolVersion(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['protocols_version']
def getpASignal(self, readid : str) -> np.ndarray:
return self.__getitem__(readid).signal_pa
def getPoreObject(self, readid : str) -> pod5.pod5_types.Pore:
'''
Returns
-------
pore : pod5.pod5_types.Pore
'''
return self.__getitem__(readid).pore
def getPoreType(self, readid : str) -> str:
return self.getPoreObject(readid).pore_type
def getPredictedScaling(self, readid : str) -> tuple:
'''
Shift and Scale for predicted read scaling values (based on this read's raw signal)
Returns
-------
(shift, scale) : tuple[float, float]
(nan, nan), if attributes not available
'''
ShScPair = self.__getitem__(readid).predicted_scaling
return (ShScPair.shift, ShScPair.scale)
def getRange(self, readid : str) -> float:
return self.__getitem__(readid).calibration_range
def getReadNumber(self, readid : str) -> int:
return self.__getitem__(readid).read_number
def getRunID(self, readid : str) -> str:
return self.getRunInfoObject(readid).acquisition_id
def getReadObject(self, readid : str) -> pod5.pod5_types.Read:
return self.__getitem__(readid).to_read()
def getRunInfoObject(self, readid : str) -> pod5.pod5_types.RunInfo:
'''
Returns
-------
run_info : pod5.pod5_types.RunInfo
'''
return self.__getitem__(readid).run_info
def getSampleID(self, readid : str) -> str:
return self.getRunInfoObject(readid).sample_id
def getSamplingRate(self, readid : str) -> int:
return self.getRunInfoObject(readid).sample_rate
def getSequencingKit(self, readid : str) -> str:
return self.getRunInfoObject(readid).sequencing_kit
def getSignal(self, readid : str) -> np.ndarray:
return self.__getitem__(readid).signal
def getStartTime(self, readid : str) -> int:
return self.__getitem__(readid).start_sample
def getTrackingIDDict(self, readid : str) -> dict:
'''
Returns
-------
tracking_id : dict
'''
return self.getRunInfoObject(readid).tracking_id
def isVBZCompressed(self) -> bool:
'''
Returns
-------
flag : bool
if file is VBZ compressed or not
'''
return self._file.is_vbz_compressed
def getVersion(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['version']
def getWellNumber(self, readid : str) -> int:
'''
Returns
-------
well : int
Number of the well in the channel used for sequencing
'''
return self.getPoreObject(readid).well
def getUSBConfig(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['usb_config']</code></pre>
</details>
</section>
<section>
</section>
<section>
</section>
<section>
</section>
<section>
<h2 class="section-title" id="header-classes">Classes</h2>
<dl>
<dt id="read5.Pod5Reader.Pod5Reader"><code class="flex name class">
<span>class <span class="ident">Pod5Reader</span></span>
<span>(</span><span>*args, **kwargs)</span>
</code></dt>
<dd>
<div class="desc"><p>File reader for pod5 files</p>
<h2 id="attributes">Attributes</h2>
<dl>
<dt><strong><code>filepath</code></strong> : <code>str</code></dt>
<dd>Path to the ONT raw data file</dd>
</dl>
<h2 id="raises">Raises</h2>
<dl>
<dt><code>FileNotFoundError</code></dt>
<dd>If the given file does not exist.</dd>
</dl></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">class Pod5Reader(AbstractFileReader):
'''
File reader for pod5 files
Attributes
----------
filepath : str
Path to the ONT raw data file
Raises
------
FileNotFoundError
If the given file does not exist.
'''
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
def open(self) -> None:
self._file = pod5.Reader(self._filepath)
self._reads = self._file.read_ids
self._nreads = self._file.num_reads
self._open = True
def getReads(self) -> list:
return self._reads
def __getitem__(self, readid : str):
'''
Returns the ReadRecord for the provided readid.
'''
return next(self._file.reads([readid]))
def getAsicID(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['asic_id']
def getAsicIDEeprom(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['asic_id_eeprom']
def getAsicTemp(self, readid : str) -> float:
return float(self.getTrackingIDDict(readid)['asic_temp'])
def getAsicVersion(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['asic_version']
def getAutoUpdateSource(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['auto_update_source']
def isAutoUpdated(self, readid : str) -> bool:
return bool(int(self.getTrackingIDDict(readid)['auto_update']))
def isBarcodingEnabled(self, readid : str) -> bool:
return bool(int(self.getContextTagsDict(readid)['barcoding_enabled']))
def isBreamStandard(self, readid : str) -> bool:
return bool(int(self.getTrackingIDDict(readid)['bream_is_standard']))
def getCalibration(self, readid : str) -> float:
return self.__getitem__(readid).calibration
def getCalibrationScale(self, readid : str) -> float:
return self.getCalibration(readid).scale
def getChannelNumber(self, readid : str) -> int:
return self.getPoreObject(readid).channel
def getConfigurationVersion(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['configuration_version']
def getContextTagsDict(self, readid : str) -> dict:
'''
Returns
-------
context_tags : dict
'''
return self.getRunInfoObject(readid).context_tags
def getDeviceID(self, readid : str) -> str:
return self.getRunInfoObject(readid).sequencer_position
def getDeviceType(self, readid : str) -> str:
return self.getRunInfoObject(readid).sequencer_position_type
def getDigitisation(self, readid : str) -> int:
return self.__getitem__(readid).calibration_digitisation
def getDistributionStatus(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['distribution_status']
def getDistributionVersion(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['distribution_version']
def getDuration(self, readid : str) -> int:
return self.__getitem__(readid).num_samples
def getEndReason(self, readid: str) -> int:
'''
ATTENTION: End Reason encoding differs: fast5/slow5/blow5 vs pod5!
Returns
-------
end_reason : int
0 : unknown
1 : mux_change
2 : unblock_mux_change
3 : data_service_unblock_mux_change
4 : signal_positive
5 : signal_negative
'''
return self.__getitem__(readid).end_reason_index
def getEndReasonObject(self, readid: str) -> pod5.pod5_types.EndReason:
'''
Returns
-------
end_reason : pod5.pod5_types.EndReason
'''
return self.__getitem__(readid).end_reason
def getExperimentDurationSet(self, readid : str) -> int:
return int(self.getContextTagsDict(readid)['experiment_duration_set'])
def getExperimentType(self, readid : str) -> str:
return self.getContextTagsDict(readid)['experiment_type']
def getExpScriptPurpose(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['exp_script_purpose']
def getExpScriptName(self, readid : str) -> str:
return self.getRunInfoObject(readid).protocol_name
def getExpStartTime(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['exp_start_time']
def getFileID(self) -> uuid.UUID:
return self._file.file_identifier
# file_version : packagin.version.Version
# contains more (& detailed) information if needed in the future
def getFileVersion(self) -> str:
return str(self._file.file_version)
def getLocalFirmwareFile(self, readid : str) -> int:
return int(self.getTrackingIDDict(readid)['local_firmware_file'])
def getFlowCellID(self, readid : str) -> str:
return self.getRunInfoObject(readid).flow_cell_id
def getFlowCellProductCode(self, readid : str) -> str:
return self.getRunInfoObject(readid).flow_cell_product_code
def getGuppyVersion(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['guppy_version']
def getHeatSinkTemp(self, readid : str) -> float:
return float(self.getTrackingIDDict(readid)['heatsink_temp'])
def getHostname(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['hostname']
def getHostProductCode(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['host_product_code']
def getHostProductSerialNumber(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['host_product_serial_number']
def getInstallationType(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['installation_type']
def isLocalBasecalled(self, readid : str) -> bool:
return bool(int(self.getContextTagsDict(readid)['local_basecalling']))
def getMedianBefore(self, readid : str) -> float:
return self.__getitem__(readid).median_before
def getNumMinknowEvents(self, readid : str) -> int:
'''
Number of minknow events that the read contains.
Returns
-------
num_minknow_events : int
np.nan, if attribute not available
'''
return self.__getitem__(readid).num_minknow_events
def getNumReadsSinceMuxChange(self, readid : str) -> int:
'''
Number of selected reads since the last mux change on this reads channel
Returns
-------
num_reads_since_mux_change : int
'''
return self.__getitem__(readid).num_reads_since_mux_change
def getTimeSinceMuxChange(self, readid : str) -> float:
'''
Returns
-------
time_since_mux_change : float
'''
return self.__getitem__(readid).time_since_mux_change
def getOffset(self, readid : str) -> float:
return self.getCalibration(readid).offset
def getOperatingSystem(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['operating_system']
def getPackage(self, readid : str) -> str:
return self.getContextTagsDict(readid)['package']
def getPackageVersion(self, readid : str) -> str:
return self.getContextTagsDict(readid)['package_version']
def getProtocolGroupID(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['protocol_group_id']
def getProtocolStartTime(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['protocol_start_time']
def getProtocolStartTime_fromRunInfo(self, readid : str) -> str:
return self.getRunInfoObject(readid).protocol_start_time.isoformat()
# TODO the following function works and is correct, but the converted time seems to be wrong -> error in pod5 converter?
def getProtocolStartTime_datetime(self, readid : str) -> datetime.datetime:
'''
Parameters
----------
readid : str
Returns
-------
protocol_start_time : datetime.datetime
'''
return self.getRunInfoObject(readid).protocol_start_time
def getProtocolRunID(self, readid : str) -> str:
return self.getRunInfoObject(readid).protocol_run_id
def getProtocolVersion(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['protocols_version']
def getpASignal(self, readid : str) -> np.ndarray:
return self.__getitem__(readid).signal_pa
def getPoreObject(self, readid : str) -> pod5.pod5_types.Pore:
'''
Returns
-------
pore : pod5.pod5_types.Pore
'''
return self.__getitem__(readid).pore
def getPoreType(self, readid : str) -> str:
return self.getPoreObject(readid).pore_type
def getPredictedScaling(self, readid : str) -> tuple:
'''
Shift and Scale for predicted read scaling values (based on this read's raw signal)
Returns
-------
(shift, scale) : tuple[float, float]
(nan, nan), if attributes not available
'''
ShScPair = self.__getitem__(readid).predicted_scaling
return (ShScPair.shift, ShScPair.scale)
def getRange(self, readid : str) -> float:
return self.__getitem__(readid).calibration_range
def getReadNumber(self, readid : str) -> int:
return self.__getitem__(readid).read_number
def getRunID(self, readid : str) -> str:
return self.getRunInfoObject(readid).acquisition_id
def getReadObject(self, readid : str) -> pod5.pod5_types.Read:
return self.__getitem__(readid).to_read()
def getRunInfoObject(self, readid : str) -> pod5.pod5_types.RunInfo:
'''
Returns
-------
run_info : pod5.pod5_types.RunInfo
'''
return self.__getitem__(readid).run_info
def getSampleID(self, readid : str) -> str:
return self.getRunInfoObject(readid).sample_id
def getSamplingRate(self, readid : str) -> int:
return self.getRunInfoObject(readid).sample_rate
def getSequencingKit(self, readid : str) -> str:
return self.getRunInfoObject(readid).sequencing_kit
def getSignal(self, readid : str) -> np.ndarray:
return self.__getitem__(readid).signal
def getStartTime(self, readid : str) -> int:
return self.__getitem__(readid).start_sample
def getTrackingIDDict(self, readid : str) -> dict:
'''
Returns
-------
tracking_id : dict
'''
return self.getRunInfoObject(readid).tracking_id
def isVBZCompressed(self) -> bool:
'''
Returns
-------
flag : bool
if file is VBZ compressed or not
'''
return self._file.is_vbz_compressed
def getVersion(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['version']
def getWellNumber(self, readid : str) -> int:
'''
Returns
-------
well : int
Number of the well in the channel used for sequencing
'''
return self.getPoreObject(readid).well
def getUSBConfig(self, readid : str) -> str:
return self.getTrackingIDDict(readid)['usb_config']</code></pre>
</details>
<h3>Ancestors</h3>
<ul class="hlist">
<li><a title="read5.AbstractFileReader.AbstractFileReader" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader">AbstractFileReader</a></li>
</ul>
<h3>Methods</h3>
<dl>
<dt id="read5.Pod5Reader.Pod5Reader.getCalibration"><code class="name flex">
<span>def <span class="ident">getCalibration</span></span>(<span>self, readid: str) ‑> float</span>
</code></dt>
<dd>
<div class="desc"></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def getCalibration(self, readid : str) -> float:
return self.__getitem__(readid).calibration</code></pre>
</details>
</dd>
<dt id="read5.Pod5Reader.Pod5Reader.getContextTagsDict"><code class="name flex">
<span>def <span class="ident">getContextTagsDict</span></span>(<span>self, readid: str) ‑> dict</span>
</code></dt>
<dd>
<div class="desc"><h2 id="returns">Returns</h2>
<dl>
<dt><strong><code>context_tags</code></strong> : <code>dict</code></dt>
<dd> </dd>
</dl></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def getContextTagsDict(self, readid : str) -> dict:
'''
Returns
-------
context_tags : dict
'''
return self.getRunInfoObject(readid).context_tags</code></pre>
</details>
</dd>
<dt id="read5.Pod5Reader.Pod5Reader.getEndReason"><code class="name flex">
<span>def <span class="ident">getEndReason</span></span>(<span>self, readid: str) ‑> int</span>
</code></dt>
<dd>
<div class="desc"><p>ATTENTION: End Reason encoding differs: fast5/slow5/blow5 vs pod5!</p>
<h2 id="returns">Returns</h2>
<dl>
<dt><strong><code>end_reason</code></strong> : <code>int</code></dt>
<dd>0 : unknown
1 : mux_change
2 : unblock_mux_change
3 : data_service_unblock_mux_change
4 : signal_positive
5 : signal_negative</dd>
</dl></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def getEndReason(self, readid: str) -> int:
'''
ATTENTION: End Reason encoding differs: fast5/slow5/blow5 vs pod5!
Returns
-------
end_reason : int
0 : unknown
1 : mux_change
2 : unblock_mux_change
3 : data_service_unblock_mux_change
4 : signal_positive
5 : signal_negative
'''
return self.__getitem__(readid).end_reason_index</code></pre>
</details>
</dd>
<dt id="read5.Pod5Reader.Pod5Reader.getEndReasonObject"><code class="name flex">
<span>def <span class="ident">getEndReasonObject</span></span>(<span>self, readid: str) ‑> pod5.pod5_types.EndReason</span>
</code></dt>
<dd>
<div class="desc"><h2 id="returns">Returns</h2>
<dl>
<dt><strong><code>end_reason</code></strong> : <code>pod5.pod5_types.EndReason</code></dt>
<dd> </dd>
</dl></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def getEndReasonObject(self, readid: str) -> pod5.pod5_types.EndReason:
'''
Returns
-------
end_reason : pod5.pod5_types.EndReason
'''
return self.__getitem__(readid).end_reason</code></pre>
</details>
</dd>
<dt id="read5.Pod5Reader.Pod5Reader.getFileID"><code class="name flex">
<span>def <span class="ident">getFileID</span></span>(<span>self) ‑> uuid.UUID</span>
</code></dt>
<dd>
<div class="desc"></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def getFileID(self) -> uuid.UUID:
return self._file.file_identifier</code></pre>
</details>
</dd>
<dt id="read5.Pod5Reader.Pod5Reader.getNumMinknowEvents"><code class="name flex">
<span>def <span class="ident">getNumMinknowEvents</span></span>(<span>self, readid: str) ‑> int</span>
</code></dt>
<dd>
<div class="desc"><p>Number of minknow events that the read contains.</p>
<h2 id="returns">Returns</h2>
<dl>
<dt><strong><code>num_minknow_events</code></strong> : <code>int</code></dt>
<dd>np.nan, if attribute not available</dd>
</dl></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def getNumMinknowEvents(self, readid : str) -> int:
'''
Number of minknow events that the read contains.
Returns
-------
num_minknow_events : int
np.nan, if attribute not available
'''
return self.__getitem__(readid).num_minknow_events</code></pre>
</details>
</dd>
<dt id="read5.Pod5Reader.Pod5Reader.getNumReadsSinceMuxChange"><code class="name flex">
<span>def <span class="ident">getNumReadsSinceMuxChange</span></span>(<span>self, readid: str) ‑> int</span>
</code></dt>
<dd>
<div class="desc"><p>Number of selected reads since the last mux change on this reads channel</p>
<h2 id="returns">Returns</h2>
<dl>
<dt><strong><code>num_reads_since_mux_change</code></strong> : <code>int</code></dt>
<dd> </dd>
</dl></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def getNumReadsSinceMuxChange(self, readid : str) -> int:
'''
Number of selected reads since the last mux change on this reads channel
Returns
-------
num_reads_since_mux_change : int
'''
return self.__getitem__(readid).num_reads_since_mux_change</code></pre>
</details>
</dd>
<dt id="read5.Pod5Reader.Pod5Reader.getPoreObject"><code class="name flex">
<span>def <span class="ident">getPoreObject</span></span>(<span>self, readid: str) ‑> pod5.pod5_types.Pore</span>
</code></dt>
<dd>
<div class="desc"><h2 id="returns">Returns</h2>
<dl>
<dt><strong><code>pore</code></strong> : <code>pod5.pod5_types.Pore</code></dt>
<dd> </dd>
</dl></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def getPoreObject(self, readid : str) -> pod5.pod5_types.Pore:
'''
Returns
-------
pore : pod5.pod5_types.Pore
'''
return self.__getitem__(readid).pore</code></pre>
</details>
</dd>
<dt id="read5.Pod5Reader.Pod5Reader.getPredictedScaling"><code class="name flex">
<span>def <span class="ident">getPredictedScaling</span></span>(<span>self, readid: str) ‑> tuple</span>
</code></dt>
<dd>
<div class="desc"><p>Shift and Scale for predicted read scaling values (based on this read's raw signal)</p>
<h2 id="returns">Returns</h2>
<p>(shift, scale) : tuple[float, float]
(nan, nan), if attributes not available</p></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def getPredictedScaling(self, readid : str) -> tuple:
'''
Shift and Scale for predicted read scaling values (based on this read's raw signal)
Returns
-------
(shift, scale) : tuple[float, float]
(nan, nan), if attributes not available
'''
ShScPair = self.__getitem__(readid).predicted_scaling
return (ShScPair.shift, ShScPair.scale)</code></pre>
</details>
</dd>
<dt id="read5.Pod5Reader.Pod5Reader.getProtocolStartTime_datetime"><code class="name flex">
<span>def <span class="ident">getProtocolStartTime_datetime</span></span>(<span>self, readid: str) ‑> datetime.datetime</span>
</code></dt>
<dd>
<div class="desc"><h2 id="parameters">Parameters</h2>
<dl>
<dt><strong><code>readid</code></strong> : <code>str</code></dt>
<dd> </dd>
</dl>
<h2 id="returns">Returns</h2>
<dl>
<dt><strong><code>protocol_start_time</code></strong> : <code>datetime.datetime</code></dt>
<dd> </dd>
</dl></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def getProtocolStartTime_datetime(self, readid : str) -> datetime.datetime:
'''
Parameters
----------
readid : str
Returns
-------
protocol_start_time : datetime.datetime
'''
return self.getRunInfoObject(readid).protocol_start_time</code></pre>
</details>
</dd>
<dt id="read5.Pod5Reader.Pod5Reader.getProtocolStartTime_fromRunInfo"><code class="name flex">
<span>def <span class="ident">getProtocolStartTime_fromRunInfo</span></span>(<span>self, readid: str) ‑> str</span>
</code></dt>
<dd>
<div class="desc"></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def getProtocolStartTime_fromRunInfo(self, readid : str) -> str:
return self.getRunInfoObject(readid).protocol_start_time.isoformat()</code></pre>
</details>
</dd>
<dt id="read5.Pod5Reader.Pod5Reader.getReadObject"><code class="name flex">
<span>def <span class="ident">getReadObject</span></span>(<span>self, readid: str) ‑> pod5.pod5_types.Read</span>
</code></dt>
<dd>