def test_ko_record_splitter(self):
"""ko_record_splitter should split ko lines into a dict of groups"""
recs = [rec for rec in ko_record_iterator(TEST_KO_LINES)]
split_recs = ko_record_splitter(recs[0])
exp = ['GENES AFM: AFUA_4G13070\n',\
' PHA: PSHAa2393\n',\
' ABO: ABO_0668\n',\
' BXE: Bxe_B0037 Bxe_C0683 Bxe_C1002 Bxe_C1023\n',\
' MPT: Mpe_A2274\n',\
' BBA: Bd0910(catD)\n',\
' GBE: GbCGDNIH1_0998 GbCGDNIH1_1171\n',\
' FNU: FN1345\n', \
' RBA: RB13257\n',\
' HMA: rrnAC1925(mhpC)\n',\
' RCI: RCIX1162 RCIX2396\n']
self.assertEqual(exp, split_recs["GENES"])
exp = [
'CLASS Metabolism; Biosynthesis of Secondary Metabolites; Limonene and\n',
' pinene degradation [PATH:ko00903]\n',
' Metabolism; Xenobiotics Biodegradation and Metabolism; Caprolactam\n',
' degradation [PATH:ko00930]\n',
' Metabolism; Xenobiotics Biodegradation and Metabolism;\n',
' 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation\n',
' [PATH:ko00351]\n',
' Metabolism; Xenobiotics Biodegradation and Metabolism; Benzoate\n',
' degradation via CoA ligation [PATH:ko00632]\n',
' Metabolism; Xenobiotics Biodegradation and Metabolism; Benzoate\n',
' degradation via hydroxylation [PATH:ko00362]\n'
]
def test_ko_record_splitter(self):
"""ko_record_splitter should split ko lines into a dict of groups"""
recs=[rec for rec in ko_record_iterator(TEST_KO_LINES)]
split_recs = ko_record_splitter(recs[0])
exp = ['GENES AFM: AFUA_4G13070\n',\
' PHA: PSHAa2393\n',\
' ABO: ABO_0668\n',\
' BXE: Bxe_B0037 Bxe_C0683 Bxe_C1002 Bxe_C1023\n',\
' MPT: Mpe_A2274\n',\
' BBA: Bd0910(catD)\n',\
' GBE: GbCGDNIH1_0998 GbCGDNIH1_1171\n',\
' FNU: FN1345\n', \
' RBA: RB13257\n',\
' HMA: rrnAC1925(mhpC)\n',\
' RCI: RCIX1162 RCIX2396\n']
self.assertEqual(exp,split_recs["GENES"])
exp = ['CLASS Metabolism; Biosynthesis of Secondary Metabolites; Limonene and\n', ' pinene degradation [PATH:ko00903]\n', ' Metabolism; Xenobiotics Biodegradation and Metabolism; Caprolactam\n', ' degradation [PATH:ko00930]\n', ' Metabolism; Xenobiotics Biodegradation and Metabolism;\n', ' 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation\n', ' [PATH:ko00351]\n', ' Metabolism; Xenobiotics Biodegradation and Metabolism; Benzoate\n', ' degradation via CoA ligation [PATH:ko00632]\n', ' Metabolism; Xenobiotics Biodegradation and Metabolism; Benzoate\n', ' degradation via hydroxylation [PATH:ko00362]\n']
def test_ko_record_iterator(self):
"""ko_record_iterator should iterate over KO records"""
recs = []
for rec in ko_record_iterator(TEST_KO_LINES):
recs.append(rec)
self.assertEqual(len(recs),3)
self.assertEqual(len(recs[0]),31)
exp = 'ENTRY K01559 KO\n'
self.assertEqual(recs[0][0],exp)
exp = ' RCI: RCIX1162 RCIX2396\n'
self.assertEqual(recs[0][-1],exp)
exp = 'ENTRY K01561 KO\n'
self.assertEqual(recs[-1][0],exp)
exp = ' MSE: Msed_1088\n'
self.assertEqual(recs[-1][-1],exp)
def test_ko_record_iterator(self):
"""ko_record_iterator should iterate over KO records"""
recs = []
for rec in ko_record_iterator(TEST_KO_LINES):
recs.append(rec)
self.assertEqual(len(recs), 3)
self.assertEqual(len(recs[0]), 31)
exp = 'ENTRY K01559 KO\n'
self.assertEqual(recs[0][0], exp)
exp = ' RCI: RCIX1162 RCIX2396\n'
self.assertEqual(recs[0][-1], exp)
exp = 'ENTRY K01561 KO\n'
self.assertEqual(recs[-1][0], exp)
exp = ' MSE: Msed_1088\n'
self.assertEqual(recs[-1][-1], exp)
