def set_fastq(self,
destination_root,
data,
section=__default_section__,
overwrite=False):
"""Write new fasta file to file
:param destination_root: root directory; data will be stored in {destination_root}/Basecalled_{section}/Fastq
:param data: fastq file
:param section: name of basecall analysis default (template)
"""
check_fastq_line(data)
# get location and sanity check
path = self._join_path(destination_root,
self.__default_basecall_fastq__.format(section))
if path in self:
if overwrite:
self.delete(path, ignore=True)
else:
raise Exception("Destination {} already exists in {}".format(
path, self.filename))
# save
self._add_string_dataset(data, path)
def set_fastq(self, path, data, section='template'):
"""Write new fasta file to file
:param path: path to fasta file
:param data: fastq file
:param section: name of basecall analysis default (template)
"""
check_fastq_line(data)
path = self._join_path(self.__base_analysis__, path,
"BaseCalled_{}".format(section))
path = self.check_path(path, latest=True)
self._add_string_dataset(data, self._join_path(path, 'Fastq'))
def get_resegment_accuracy(fast5handle, section="template"):
"""Get accuracy comparison between original sequence and resegmented generated sequence
:param fast5handle: Fast5 object with re-segemented read
"""
assert isinstance(fast5handle, Fast5), "fast5handle needs to be a Fast5 instance"
# get fastqs
resegment_fastq = fast5handle.get_fastq(analysis="ReSegmentBasecall", section=section)
original_fastq = bytes.decode(fast5handle.get_fastq(analysis="Basecall_1D", section=section))[:-1]
# make sure the underlying assumption that we can split on newline is ok
check_fastq_line(resegment_fastq)
check_fastq_line(original_fastq)
# get sequence
resegment_seq = resegment_fastq.split('\n')[1]
original_seq = original_fastq.split('\n')[1]
return pairwise_alignment_accuracy(original_seq, resegment_seq, soft_clip=True)
def test_check_fastq_line(self):
with captured_output() as (_, _):
fastq_record = "@asdf\nasdf\n+\nasdf"
self.assertTrue(check_fastq_line(fastq_record))
with self.assertRaises(AssertionError):
check_fastq_line("asdf\nasdf\n+\nasdf")
check_fastq_line("@asdfasdf\n+\nasdf")
check_fastq_line("@asdf\nasdf+\nasdf")
check_fastq_line("@asdf\nasdf\n+\nasdf\n")
check_fastq_line("@asdf\nasdf\n+asdf")
check_fastq_line("@asdf\nasdsf\n+\nasdf")
check_fastq_line("@asdf\nasdf\n+\nassdf")