def test_sampletab_load_dump_round_trip_GSB_537(self):
with open(os.path.join(self._sampletab_data_dir, 'GSB-537.txt')) as fp:
ISA = sampletab.load(fp) # load into ISA objects
with open(os.path.join(self._tmp_dir, "out.txt"), "w") as out_fp:
sampletab.dump(ISA, out_fp) # dump out to SampleTab from ISA objects
with open(os.path.join(self._tmp_dir, "out.txt"), "r") as in_fp:
ISA = sampletab.load(in_fp) # load into ISA objects again from dumped SampleTab and check contents
self.assertEqual(len(ISA.studies), 1)
sources = ISA.studies[0].sources
samples = ISA.studies[0].samples
self.assertEqual(len(sources), 4)
self.assertEqual(len(samples), 80)
self.assertEqual(len(ISA.studies[0].process_sequence), 8)
def convert(source_sampletab_fp, target_dir):
""" Converter for ISA-JSON to SampleTab.
:param source_sampletab_fp: File descriptor of input SampleTab file
:param target_dir: Path to write out ISA-Tab files to
"""
ISA = sampletab.load(source_sampletab_fp)
isatab.dump(ISA, target_dir)
def convert(source_sampletab_fp, target_json_fp):
""" Converter for ISA-JSON to SampleTab.
:param source_sampletab_fp: File descriptor of input SampleTab file
:param target_json_fp: File descriptor to write output ISA JSON (must be writeable)
"""
ISA = sampletab.load(source_sampletab_fp)
json.dump(ISA, fp=target_json_fp, cls=ISAJSONEncoder)
def test_sampletab_load_GSB_718(self):
with open(os.path.join(self._sampletab_data_dir, 'GSB-718.txt')) as fp:
ISA = sampletab.load(fp)
self.assertEqual(len(ISA.studies), 1)
sources = ISA.studies[0].sources
samples = ISA.studies[0].samples
self.assertEqual(len(sources), 51)
self.assertEqual(len(samples), 2409)
self.assertEqual(len(ISA.studies[0].process_sequence), 109)
def test_sampletab_load_GSB_3(self):
with open(os.path.join(self._sampletab_data_dir, 'GSB-3.txt')) as fp:
ISA = sampletab.load(fp)
self.assertEqual(len(ISA.studies), 1)
sources = ISA.studies[0].sources
samples = ISA.studies[0].samples
self.assertEqual(len(sources), 1157)
self.assertEqual(len(samples), 3858)
self.assertEqual(len(ISA.studies[0].process_sequence), 1747)
def test_sampletab_load_GSB_537(self):
with open(os.path.join(self._sampletab_data_dir, 'GSB-537.txt')) as fp:
ISA = sampletab.load(fp)
self.assertEqual(len(ISA.studies), 1)
sources = ISA.studies[0].materials['sources']
samples = ISA.studies[0].materials['samples']
self.assertEqual(len(sources), 4)
self.assertEqual(len(samples), 80)
self.assertEqual(len(ISA.studies[0].process_sequence), 8)
def test_sampletab_load_test1(self):
with open(os.path.join(self._sampletab_data_dir, 'test1.txt')) as fp:
ISA = sampletab.load(fp)
self.assertEqual(len(ISA.studies), 1)
sources = ISA.studies[0].sources
samples = ISA.studies[0].samples
self.assertEqual(len(sources), 1)
self.assertEqual(len(samples), 1)
process = ISA.studies[0].process_sequence[0]
for source in sources:
self.assertIn(source, process.inputs)
for sample in samples:
self.assertIn(sample, process.outputs)
