def test_pooled_caller(self):
peak_caller = idr.spp_peak_caller(spp_path)
control_replicates = idr.tagalign_split(self.control, nfiles=2)
experimental_replicates = idr.tagalign_split(self.experimental,
nfiles=2)
peaks = idr.call_peaks_on_pooled_replicates(control_replicates,
experimental_replicates,
peak_caller)
self.assertTrue(idr.file_exists(peaks))
self.assertTrue(idr.is_peak_file(peaks))
def test_spp_caller(self):
peak_caller = idr.spp_peak_caller(spp_path, cores=1)
peaks = peak_caller(self.control, self.experimental)
self.assertTrue(idr.file_exists(peaks))
self.assertTrue(idr.is_peak_file(peaks))
def test_tagalign_pool(self):
pooled_file = idr.tagalign_pool(self.split_files)
self.assertTrue(idr.is_tagalign(pooled_file))
self.assertTrue(idr.file_exists(pooled_file))
def test_bam_to_tagalign(self):
tagalign_file = idr.bam_to_tagalign(self.bam_file)
self.assertTrue(idr.is_tagalign(tagalign_file))
self.assertTrue(idr.file_exists(tagalign_file))
def test_idr_plotter():
prefixes = _prepare_idr_files(os.path.join(peak_dir, "idr", "reps"))
idr_plotter = idr.idr_plotter(idr_plotter_path)
plot_out = idr_plotter(prefixes)
assert idr.file_exists(plot_out)
def test_idr_runner():
tmp_peak_files = map(_copy_file_to_testdir, peak_files)
idr_runner = idr.idr_runner(idr_runner_path)
idr_out = idr_runner(tmp_peak_files)
assert idr.file_exists(idr_out)
def setUp(self):
idr.safe_makedir(test_dir)
if not idr.file_exists(control_file):
idr.download_to_dir(DATA_URL, os.curdir)