def __init__(self, output_path, header):
"""Initializer for NativeGffWriter.
Args:
output_path: str. The path to which to write the GFF file.
header: nucleus.genomics.v1.GffHeader. The header that defines all
information germane to the constituent GFF records.
"""
super(NativeGffWriter, self).__init__()
writer_options = gff_pb2.GffWriterOptions()
self._writer = gff_writer.GffWriter.to_file(output_path, header,
writer_options)
def setUp(self):
out_fname = test_utils.test_tmpfile('output.gff')
self.writer = gff_writer.GffWriter.to_file(out_fname,
gff_pb2.GffHeader(),
gff_pb2.GffWriterOptions())
self.expected_gff_content = open(
test_utils.genomics_core_testdata(
'test_features.gff')).readlines()
self.header = gff_pb2.GffHeader(
sequence_regions=[ranges.make_range('ctg123', 0, 1497228)])
self.record = gff_pb2.GffRecord(
range=ranges.make_range('ctg123', 1000, 1100))
def test_writing_canned_records(self):
"""Tests writing all the records that are 'canned' in our tfrecord file."""
# This file is in TFRecord format.
tfrecord_file = test_utils.genomics_core_testdata(
'test_features.gff.tfrecord')
writer_options = gff_pb2.GffWriterOptions()
gff_records = list(
io_utils.read_tfrecords(tfrecord_file, proto=gff_pb2.GffRecord))
out_fname = test_utils.test_tmpfile('output.gff')
with gff_writer.GffWriter.to_file(out_fname, self.header,
writer_options) as writer:
for record in gff_records:
writer.write(record)
with open(out_fname) as f:
self.assertEqual(f.readlines(), self.expected_gff_content)