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""" Helper class for working with 1D basecall type analyses.
"""
import numpy as np
from ont_fast5_api.analysis_tools.base_tool import BaseTool
class Basecall1DTools(BaseTool):
""" Provides helper methods specific to 1D basecall analyses.
"""
group_id = 'Basecall_1D'
analysis_id = 'basecall_1d'
def get_event_data(self, section):
""" Return either the template or complement event data, if present.
:param section: Either template or complement.
:return: Event data table.
"""
event_group = '{}/BaseCalled_{}'.format(self.group_name, section)
data = self.handle.get_analysis_dataset(event_group, 'Events')
return data
def add_event_data(self, section, data):
""" Add template or complement basecalled event data.
:param section: Either template or complement.
:param data: Event data table to be written.
"""
event_group = 'BaseCalled_{}'.format(section)
if not event_group in self.handle.handle['Analyses/{}'.format(self.group_name)]:
self.handle.add_analysis_subgroup(self.group_name, event_group)
self.handle.add_analysis_dataset('{}/{}'.format(self.group_name, event_group), 'Events', data)
def get_called_sequence(self, section, fastq=False):
""" Return either the called sequence data, if present.
:param section: ['template', 'complement' or '2D']
:param fastq: If True, return a single, multiline fastq string. If
False, return a tuple of (name, sequence, qstring).
:return: Either the fastq string or the (name, sequence, qstring) tuple.
"""
event_group = '{}/BaseCalled_{}'.format(self.group_name, section)
data = self.handle.get_analysis_dataset(event_group, 'Fastq')
if data is None:
raise KeyError("No fastq data in: {} {}".format(event_group, self.filename))
if fastq:
return data
name, sequence, _, qstring = data.strip().split('\n')
name = name[1:]
return name, sequence, qstring
def add_called_sequence(self, section, name, sequence, qstring):
""" Add basecalled sequence data
:param section: ['template', 'complement' or '2D']
:param name: The record ID to use for the fastq.
:param sequence: The called sequence.
:param qstring: The quality string.
"""
event_group = 'BaseCalled_{}'.format(section)
if not event_group in self.handle.handle['Analyses/{}'.format(self.group_name)]:
self.handle.add_analysis_subgroup(self.group_name, event_group)
fastq_text = '@{}\n{}\n+\n{}\n'.format(name, sequence, qstring)
fastq_arr = np.array(fastq_text, dtype=str)
self.handle.add_analysis_dataset('{}/{}'.format(self.group_name, event_group), 'Fastq', fastq_arr)
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