def test_run_hisat2_sampleset_ok(self):
res = self.get_impl().run_hisat2(self.get_context(), {
"ws_name": self.ws_name,
"sampleset_ref": self.single_end_sampleset,
"genome_ref": self.genome_ref,
"alignmentset_suffix": "_sampleset_alignments",
"alignment_suffix": "_sampleset_alignment",
"num_threads": 2,
"quality_score": "phred33",
"skip": 0,
"trim3": 0,
"trim5": 0,
"np": 1,
"min_intron_length": 20,
"max_intron_length": 500000,
"no_spliced_alignment": 0,
"transcriptome_mapping_only": 0,
"build_report": 1
})[0]
self.assertIsNotNone(res)
print("Done with HISAT2 run! {}".format(res))
self.assertIn("report_ref", res)
self.assertTrue(check_reference(res["report_ref"]))
self.assertIn("report_name", res)
self.assertIn("alignmentset_ref", res)
self.assertTrue(check_reference(res["alignmentset_ref"]))
self.assertTrue(get_object_names([res["alignmentset_ref"]], self.wsURL)[res["alignmentset_ref"]].endswith("_sampleset_alignments"))
self.assertIn("alignment_objs", res)
self.assertTrue(len(res["alignment_objs"].keys()) == 2)
for reads_ref in res["alignment_objs"]:
ref_from_refpath = reads_ref.split(';')[-1]
self.assertIn(ref_from_refpath, self.reads_refs)
self.assertTrue(res["alignment_objs"][reads_ref]["name"].endswith("_sampleset_alignment"))
self.assertTrue(check_reference(res["alignment_objs"][reads_ref]["ref"]))
def test_run_hisat2_single_end_lib_ok(self):
res = self.get_impl().run_hisat2(
self.get_context(), {
"ws_name": self.ws_name,
"sampleset_ref": self.single_end_ref_wt_1,
"condition": "wt",
"genome_ref": self.genome_ref,
"alignmentset_suffix": "_alignment_set",
"alignment_suffix": "_alignment",
"num_threads": 2,
"quality_score": "phred33",
"skip": 0,
"trim3": 0,
"trim5": 0,
"np": 1,
"min_intron_length": 20,
"max_intron_length": 500000,
"no_spliced_alignment": 0,
"build_report": 1
})[0]
self.assertIsNotNone(res)
print("Done with HISAT2 run! {}".format(res))
self.assertIn("report_ref", res)
self.assertTrue(check_reference(res["report_ref"]))
self.assertIn("report_name", res)
self.assertIn("alignmentset_ref", res)
self.assertIsNone(res["alignmentset_ref"])
self.assertIn("alignment_objs", res)
self.assertTrue(len(res["alignment_objs"].keys()) == 1)
for reads_ref in res["alignment_objs"]:
ref_from_refpath = reads_ref.split(';')[-1]
self.assertIn(ref_from_refpath, self.reads_refs)
self.assertTrue(res["alignment_objs"][reads_ref]["name"].endswith(
"_alignment"))
alignment_ref = res["alignment_objs"][reads_ref]["ref"]
self.assertTrue(check_reference(alignment_ref))
alignment_data = self.dfu.get_objects(
{"object_refs": [alignment_ref]})['data'][0]['data']
align_stats = alignment_data.get('alignment_stats')
self.assertEqual(align_stats.get('total_reads'), 15254)
self.assertEqual(align_stats.get('mapped_reads'), 15081)
self.assertEqual(align_stats.get('unmapped_reads'), 173)
self.assertEqual(align_stats.get('singletons'), 11044)
self.assertEqual(align_stats.get('multiple_alignments'), 4037)