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_run_analysis():
tmp_control = idr.tagalign_split(_copy_file_to_testdir(control_file))
tmp_exp = idr.tagalign_split(_copy_file_to_testdir(exp_file))
with cluster_view(scheduler, queue, jobs) as view:
plots, filtered_files = idr.run_analysis(tmp_control, tmp_exp,
spp_path, idr_runner_path,
idr_plotter_path, view.map,
caller)
all(map(idr.file_exists, filtered_files))
def test_pooled_pseudo_replicate_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)
with cluster_view(scheduler, queue, jobs) as view:
peaks = idr.call_peaks_on_pooled_pseudoreplicates(control_replicates,
experimental_replicates,
peak_caller, view.map)
self.assertTrue(all(map(idr.file_exists, peaks)))
self.assertTrue(all(map(idr.is_peak_file, peaks)))
def test_tagalign_split(self):
tagalign_split_files = idr.tagalign_split(self.tagalign_file)
self.assertTrue(all(map(idr.is_tagalign, tagalign_split_files)))
self.assertTrue(all(map(idr.file_exists, tagalign_split_files)))
