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 genomics_io.make_read_writer(path) as writer: for read in reads: writer.write(read)
def test_make_read_writer_tfrecords(self): outfile = test_utils.test_tmpfile('test.tfrecord') writer = genomics_io.make_read_writer(outfile=outfile) # 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_make_read_writer_bam_fails_with_not_implemented_error(self): with self.assertRaises(NotImplementedError): genomics_io.make_read_writer('test.bam', contigs=self.contigs)
def test_make_read_writer_bam_fails_without_contigs(self): with self.assertRaisesRegexp(ValueError, 'contigs'): genomics_io.make_read_writer('test.bam')