def log_realigned_reads(self, region, reads, shared_header=None):
"""Logs, if enabled, the realigned reads for region."""
if self.enabled and self.config.emit_realigned_reads and shared_header is not None:
path = self._file_for_region(region, self.realigned_reads_filename)
with sam.SamWriter(path, header=shared_header) as writer:
for read in reads:
writer.write(read)
def log_realigned_reads(self, region, reads):
"""Logs, if enabled, the realigned reads for region."""
if self.enabled and self.config.emit_realigned_reads:
path = self._file_for_region(region, self.realigned_reads_filename)
with sam.SamWriter(path) as writer:
for read in reads:
writer.write(read)
def test_roundtrip_writer(self, filename):
output_path = test_utils.test_tmpfile(filename)
original_reader = sam.SamReader(test_utils.genomics_core_testdata(filename))
original_records = list(original_reader.iterate())
with sam.SamWriter(output_path, header=original_reader.header) as writer:
for record in original_records:
writer.write(record)
with sam.SamReader(output_path) as new_reader:
self.assertEqual(original_records, list(new_reader.iterate()))
def log_realigned_reads(self, region, reads, shared_header=None):
"""Logs, if enabled, the realigned reads for region."""
if self.enabled and self.config.emit_realigned_reads and shared_header is not None:
path = self._file_for_region(region, self.realigned_reads_filename)
with sam.SamWriter(path, header=shared_header) as writer:
# For realigned reads, sorting by just looking at starting position is
# enough.
for read in sorted(
reads,
key=lambda read: read.alignment.position.position):
writer.write(read)
def test_make_read_writer_tfrecords(self):
outfile = test_utils.test_tmpfile('test.tfrecord')
writer = sam.SamWriter(outfile, header=self.header)
# Test that the writer is a context manager and that we can write a read to
# it.
with writer:
writer.write(self.read1)
writer.write(self.read2)
# Our output should have exactly one read in it.
self.assertEqual([self.read1, self.read2],
list(
io_utils.read_tfrecords(outfile,
proto=reads_pb2.Read)))
def test_roundtrip_cram_writer(self, filename, has_embedded_ref):
output_path = test_utils.test_tmpfile(filename)
writer_ref_path = test_utils.genomics_core_testdata('test.fasta')
reader_ref_path = ''
if not has_embedded_ref:
reader_ref_path = writer_ref_path
original_reader = sam.SamReader(
test_utils.genomics_core_testdata(filename), ref_path=reader_ref_path)
original_records = list(original_reader.iterate())
with sam.SamWriter(
output_path,
header=original_reader.header,
ref_path=writer_ref_path,
embed_ref=has_embedded_ref) as writer:
for record in original_records:
writer.write(record)
with sam.SamReader(output_path, ref_path=reader_ref_path) as new_reader:
self.assertEqual(original_records, list(new_reader.iterate()))
def test_make_read_writer_bam_fails_with_not_implemented_error(self):
with self.assertRaises(NotImplementedError):
sam.SamWriter('test.bam', header=self.header)