def setUp(self):
self.isa = Investigation()
self.isa.ontology_source_references = [
OntologySource('A', 'f1', '1', 'd1'),
OntologySource('B', 'f2', '2', 'd2')
]
self.parser = isatab.AssayTableParser(self.isa)
self.assay_table = \
u'Sample Name\tExtract Name\tLabeled Extract Name\tRaw Data File\n' \
u'sample1\textract1\t\tfile1.txt\n' \
u'sample2\t\tlabeled1\tfile2.txt'
self.assay_table_with_process = \
u'Sample Name\tProtocol REF\tExtract Name\tProtocol REF\tLabeled Extract Name\tProtocol REF\tRaw Data File\n' \
u'sample1\tsample extraction\textract1\tlabeling\tlabeled1\tscanning\tfile1.txt\n' \
u'sample2\tsample extraction\textract1\tlabeling\tlabeled1\tscanning\tfile2.txt'
self.sample_list = [Sample(name='sample1'), Sample(name='sample2')]
self.data_file_list = [
DataFile(filename='file2.txt', label='Raw Data File'),
DataFile(filename='file1.txt', label='Raw Data File')
]
self.other_material_list = [
LabeledExtract(name='labeled1'),
Extract(name='extract1')
]
def test_isatab_parse_bii_s_1_proteome(self):
with io.open(
os.path.join(self._tab_data_dir, 'BII-I-1',
'i_investigation.txt')) as fp:
investigation_parser = isatab.InvestigationParser()
investigation_parser.parse(fp)
self.parser = isatab.AssayTableParser(investigation_parser.isa)
self.parser.parse(
os.path.join(self._tab_data_dir, 'BII-I-1', 'a_proteome.txt'))
self.assertEqual(len(self.parser.samples), 8)
self.assertEqual(len(self.parser.data_files), 7)
self.assertEqual(len(self.parser.other_material), 19)
self.assertEqual(len(self.parser.process_sequence), 16)
def test_isatab_parse_bii_s_7_Gx(self):
with io.open(
os.path.join(self._tab_data_dir, 'BII-S-7',
'i_matteo.txt')) as fp:
investigation_parser = isatab.InvestigationParser()
investigation_parser.parse(fp)
self.parser = isatab.AssayTableParser(investigation_parser.isa)
self.parser.parse(
os.path.join(self._tab_data_dir, 'BII-S-7',
'a_matteo-assay-Gx.txt'))
self.assertEqual(len(self.parser.samples), 29)
self.assertEqual(len(self.parser.data_files), 29)
self.assertEqual(len(self.parser.other_material), 29)
self.assertEqual(len(self.parser.process_sequence), 116)