class WhenParsingIDF(unittest.TestCase):
def setUp(self):
self.parser = MageTabParser()
self.test_path = os.path.join(MAGETAB_DATA_DIR, 'E-MEXP-31.idf.txt')
def test_should_parse_idf_without_error(self):
self.parser.parse_idf(self.test_path)
def test_should_create_ISA(self):
self.parser.parse_idf(self.test_path)
self.assertIsInstance(self.parser.ISA, Investigation)
def test_should_return_ISA(self):
self.assertIsInstance(self.parser.parse_idf(self.test_path),
Investigation)
def convert(idf_file_path, output_path):
""" Converter for MAGE-TAB to ISA-Tab
:param idf_file_path: File descriptor of input IDF file
:param output_path: Path to directory to write output ISA-Tab files to
"""
parser = MageTabParser()
parser.parse_idf(idf_file_path)
sdrf_files = [x.value for x in parser.ISA.studies[-1].comments if 'SDRF File' in x.name]
if len(sdrf_files) == 1:
sdrf_files = sdrf_files[0].split(';')
for sdrf_file in sdrf_files:
table_files = parser.parse_sdrf_to_isa_table_files(os.path.join(os.path.dirname(idf_file_path), sdrf_file))
for in_fp in table_files:
log.info("Writing {0} to {1}".format(in_fp.name, output_path))
with open(os.path.join(output_path, in_fp.name), 'w') as out_fp:
out_fp.write(in_fp.read())
log.info("Writing {0} to {1}".format("i_investigation.txt", output_path))
isatab.dump(parser.ISA, output_path=output_path, skip_dump_tables=True)
class WhenParsedIDF(unittest.TestCase):
""" Test case using E-MEXP-31.idf.txt """
def setUp(self):
self.parser = MageTabParser()
self.test_path = os.path.join(MAGETAB_DATA_DIR, 'E-MEXP-31.idf.txt')
self.parser.parse_idf(self.test_path)
def test_should_load_five_ontology_sources(self):
self.assertEqual(len(self.parser.ISA.ontology_source_references), 5)
def test_should_load_one_study(self):
self.assertEqual(len(self.parser.ISA.studies), 1)
def test_should_load_three_study_designs(self):
self.assertEqual(len(self.parser.ISA.studies[-1].design_descriptors),
3)
def test_should_load_one_study_factor(self):
self.assertEqual(len(self.parser.ISA.studies[-1].factors), 1)
def test_should_load_one_person(self):
self.assertEqual(len(self.parser.ISA.studies[-1].contacts), 1)
def test_should_load_one_publication(self):
self.assertEqual(len(self.parser.ISA.studies[-1].publications), 1)
def test_should_load_six_protocols(self):
self.assertEqual(len(self.parser.ISA.studies[-1].protocols), 6)
def test_should_load_one_assay(self):
self.assertEqual(len(self.parser.ISA.studies[-1].assays), 1)
def test_should_load_assay_with_transcription_micro(self):
self.assertEqual(
self.parser.ISA.studies[-1].assays[-1].measurement_type.term,
"transcription profiling")
self.assertEqual(
self.parser.ISA.studies[-1].assays[-1].technology_type.term,
"DNA microarray")
def setUp(self):
self.parser = MageTabParser()
def setUp(self):
self.parser = MageTabParser()
self.test_path = os.path.join(MAGETAB_DATA_DIR, 'E-MEXP-31.idf.txt')
self.parser.parse_idf(self.test_path)