def setUp(self): self.records = [ bed_pb2.BedRecord(reference_name='chr1', start=30, end=40, name='first', score=55.5), bed_pb2.BedRecord(reference_name='chr2', start=32, end=38, name='second', score=0), bed_pb2.BedRecord(reference_name='chr3', start=40, end=50, name='third', score=99), ] self.tokens = [ [ 'chr1', '30', '40', 'first', '55.5', '+', '35', '38', '128,242,16', '2', '5,3', '30,37' ], [ 'chr2', '32', '38', 'second', '0', '.', '32', '38', '128,128,128', '1', '6', '32' ], [ 'chr3', '40', '50', 'third', '99', '-', '40', '44', '0,0,0', '3', '40,43,48', '3,2,2' ], ]
def setUp(self): out_fname = test_utils.test_tmpfile('output.bed') self.writer = bed_writer.BedWriter.to_file( out_fname, bed_pb2.BedHeader(num_fields=12), bed_pb2.BedWriterOptions()) self.expected_bed_content = [ 'chr1\t10\t20\tfirst\t100\t+\t12\t18\t255,124,1\t3\t2,6,2\t10,12,18\n', 'chr1\t100\t200\tsecond\t250\t.\t120\t180\t252,122,12\t2\t35,40\t' '100,160\n' ] self.record = bed_pb2.BedRecord( reference_name='chr1', start=20, end=30, name='r')
def setUp(self): self.bed = test_utils.genomics_core_testdata('test_regions.bed') self.zipped_bed = test_utils.genomics_core_testdata( 'test_regions.bed.gz') self.options = bed_pb2.BedReaderOptions() self.first = bed_pb2.BedRecord(reference_name='chr1', start=10, end=20, name='first', score=100, strand=bed_pb2.BedRecord.FORWARD_STRAND, thick_start=12, thick_end=18, item_rgb='255,124,1', block_count=3, block_sizes='2,6,2', block_starts='10,12,18')
def _raw_next(self): record = bed_pb2.BedRecord() not_done = self._cc_iterable.PythonNext(record) return record, not_done