def test_wrong_peptides_onlypept(self): """ When onlypept file has wrong peptides """ path_ = path.join(wrong_pepts_dir, "wrong_pepts_onlypept.xls") p = proteomic_xls.sequest_onlypept_parser() a_d = dict(fileName=path_) self.assertRaises(data_input.bad_format_peptide, p.parse, **a_d)
def test_bad_format_real_discoverer(self): """ Should fail with format no data_discoverer using wrong data_discoverer analysis files """ p = proteomic_xls.sequest_onlypept_parser() self.match_format_parser(p.parse, protpept_dir) self.match_format_parser(p.parse, discoverer_dir)
def test_file_source_store_op(self): """ testing the original seq storage """ p = proteomic_xls.sequest_onlypept_parser(mode=True) for f in self.files: try: p.parse(path.join(onlypept_dir, f)) except proteomic_xls.EmptyCell: pass self.assertListEqual([path.join(onlypept_dir, f) for f in self.files], p.sources)
def test_proteins_onlypept(self): """ proteins occurrence during parsing the five file """ p = proteomic_xls.sequest_onlypept_parser() for i, f in enumerate(self.files): try: p.parse(path.join(onlypept_dir, f)) except proteomic_xls.EmptyCell: pass for acc, occs in self.prots: self.assertEqual(occs[i], p.proteins[acc], "%d != %d @prot: %s, @time: %d"\ %(occs[i], p.proteins[acc], acc, i))
def test_peptides_onlypept_red(self): """ peptides occurrence during parsing the five file Spectral Count True """ p = proteomic_xls.sequest_onlypept_parser(mode=True) for i, f in enumerate(self.files): try: p.parse(path.join(onlypept_dir, f)) except proteomic_xls.EmptyCell: pass for acc, pepts in self.onlypepts: for seq, occs_nr, occs_r in pepts: self.assertEqual(occs_r[i], p.peptides[acc][seq], "%d, %s, %s" %(i, acc, seq))
def test_spectral_count_false_onlypept(self): """ Using a onlypept file with peptides no-distinct, the frequencies must be equal to one. """ chase2 = path.join(redundants_dir, "redundant_onlypept.xls") p = proteomic_xls.sequest_onlypept_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)