def test_real_redundant_discoverer(self): """ When there aren't redundancy data_discoverer """ path_ = path.join(redundants_dir, "redundant_accessions_discoverer.xls") p = proteomic_xls.discoverer_parser() a_d = dict(fileName=path_) self.assertRaises(proteomic_xls.Same_Accession, p.parse, **a_d)
def test_file_source_store(self): """ testing the original seq storage """ p = proteomic_xls.discoverer_parser(mode=True) for f in self.files: try: p.parse(path.join(discoverer_dir, f)) except proteomic_xls.EmptyCell: pass self.assertListEqual([path.join(discoverer_dir, f)\ for f in self.files], p.sources)
def test_proteins(self): """ proteins occurrence during parsing the five file """ p = proteomic_xls.discoverer_parser() msg = "{0}: predicted {1} != counted {2}" for i, f in enumerate(self.files): try: p.parse(path.join(discoverer_dir, f)) except proteomic_xls.EmptyCell: pass for acc, occs in self.prots: self.assertEqual(occs[i], p.proteins[acc], msg.format(acc, occs[i], p.proteins[acc]))
def test_spectral_count_false_discoverer(self): """ Using a data_discoverer file with peptides no-distinct, the frequencies must be equal to one. """ chase2 = path.join(redundants_dir, "redundant_discoverer.xls") p = proteomic_xls.discoverer_parser() try: p.parse(chase2) except proteomic_xls.EmptyCell: pass finally: for acc, pepts in p.peptides.iteritems(): for seq, occ in pepts.iteritems(): self.assertEqual(occ, 1)
def test_peptides_protpept_nored(self): """ peptides occurrence during parsing the five file Spectral count False """ p = proteomic_xls.discoverer_parser() for i, f in enumerate(self.files): try: p.parse(path.join(discoverer_dir, f)) except proteomic_xls.EmptyCell: pass for acc, pepts in self.pepts: for seq, occs_nr, occs_r in pepts: self.assertEqual(occs_nr[i], p.peptides[acc][seq], "{0} - {1}:{2} aspected {3} != retrived {4}".format( f, acc, seq, occs_nr[i], p.peptides[acc][seq]))
def test_wrong_peptides_discoverer(self): path_ = path.join(wrong_pepts_dir, "wrong_pepts_discoverer.xls") p = proteomic_xls.discoverer_parser() a_d = dict(fileName=path_) self.assertRaises(data_input.bad_format_peptide, p.parse, **a_d)