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""" Helper class for working with 2D basecall type analyses.
"""
import warnings
from ont_fast5_api.analysis_tools.basecall_1d import Basecall1DTools
class Basecall2DTools(Basecall1DTools):
""" Provides helper methods specific to 2D basecall analyses.
"""
group_id = 'Basecall_2D'
analysis_id = 'basecall_2d'
def get_prior_alignment(self):
""" Return the prior alignment that was used for 2D basecalling.
:return: Alignment data table.
"""
data_group = '{}/HairpinAlign'.format(self.group_name)
data = self.handle.get_analysis_dataset(data_group, 'Alignment')
return data
def get_2d_call_alignment(self):
""" Return the alignment and model_states from the 2D basecall.
:return: Alignment data table.
"""
data_group = '{}/BaseCalled_2D'.format(self.group_name)
data = self.handle.get_analysis_dataset(data_group, 'Alignment')
return data
def add_prior_alignment(self, data):
""" Add template or complement basecalled event data.
:param data: Alignment table to be written.
"""
path = 'Analyses/{}'.format(self.group_name)
if 'HairpinAlign' not in self.handle.handle[path]:
self.handle.add_analysis_subgroup(self.group_name, 'HairpinAlign')
path = '{}/HairpinAlign'.format(self.group_name)
self.handle.add_analysis_dataset(path, 'Alignment', data)
def add_2d_call_alignment(self, data):
""" Add the alignment and model_state data table..
:param data: Alignment and model_state table to be written.
"""
path = 'Analyses/{}'.format(self.group_name)
if 'BaseCalled_2D' not in self.handle.handle[path]:
self.handle.add_analysis_subgroup(self.group_name, 'BaseCalled_2D')
path = '{}/BaseCalled_2D'.format(self.group_name)
self.handle.add_analysis_dataset(path, 'Alignment', data)
def get_called_sequence(self, section=None, 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.
"""
if section != "2D":
warnings.warn("Basecall2DTools.get_called_sequence() should specify section='2D'", DeprecationWarning)
# Backwards compatibilty to 0.3.3, if no "2D" section, bump args by 1 and pass to super
if section == None:
# We assume that a named arg or no-arg was given
return super(Basecall2DTools, self).get_called_sequence("2D", fastq)
# We assume that a single unnamed arg was given for fastq
return super(Basecall2DTools, self).get_called_sequence("2D", section)
return super(Basecall2DTools, self).get_called_sequence(section, fastq)
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