def test_indexing_to_custom_location_works(self):
'''test indexing a file with a non-default location.'''
index_path = get_temp_filename(suffix='custom.tbi')
pysam.tabix_index(self.tmpfilename,
preset="gff",
index=index_path,
force=True)
self.assertTrue(checkGZBinaryEqual(index_path, self.filename_idx))
os.unlink(index_path)
def test_indexing_with_lineskipping_works(self):
'''test indexing via preset and lineskip.'''
pysam.tabix_index(self.tmpfilename,
seq_col=0,
start_col=3,
end_col=4,
line_skip=1,
zerobased=False)
self.assertFalse(
checkGZBinaryEqual(self.tmpfilename + ".tbi", self.filename_idx))
def test_indexing_with_preset_works(self):
'''test indexing via preset.'''
pysam.tabix_index(self.tmpfilename, preset="gff")
self.assertTrue(
checkGZBinaryEqual(self.tmpfilename + ".tbi", self.filename_idx))