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