def convert(source_inv_fp, target_fp):
""" Converter for ISA-Tab to SampleTab.
:param source_inv_fp: File descriptor of input investigation file
:param target_fp: File descriptor to write output SampleTab to (must be writeable)
"""
ISA = isatab.load(source_inv_fp)
sampletab.dump(ISA, target_fp)
def convert(source_json_fp, target_fp):
""" Converter for ISA-JSON to SampleTab.
:param source_json_fp: File descriptor of input ISA JSON file
:param target_fp: File descriptor to write output SampleTab to (must be writeable)
"""
ISA = isajson.load(source_json_fp)
sampletab.dump(ISA, target_fp)
def convert(source_inv_fp, target_fp):
""" Converter for ISA-Tab to SampleTab.
:param source_inv_fp: File descriptor of input investigation file
:param target_fp: File descriptor to write output SampleTab to (must be writeable)
"""
log.info("loading isatab %s", source_inv_fp.name)
ISA = isatab.load(source_inv_fp)
log.info("dumping sampletab %s", target_fp.name)
sampletab.dump(ISA, target_fp)
def convert(source_json_fp, target_fp):
""" Converter for ISA-JSON to SampleTab.
:param source_json_fp: File descriptor of input ISA JSON file
:param target_fp: File descriptor to write output SampleTab to (must be writeable)
"""
log.info("loading isajson %s", source_json_fp.name)
ISA = isajson.load(source_json_fp)
log.info("dumping sampletab %s", target_fp.name)
sampletab.dump(ISA, target_fp)
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)