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)