#!/usr/bin/env python
__author__ = "Jesse Zaneveld"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Jesse Zaneveld"]
__license__ = "GPL"
__version__ = "1.5.3-dev"
__maintainer__ = "Jesse Zaneveld"
__email__ = "zaneveld@gmail.com"
__status__ = "Production"
"""
Test code for kegg_ko.py in cogent.parse.
"""
from cogent.util.unit_test import TestCase, main
from cogent.parse.kegg_ko import kegg_label_fields,\
parse_kegg_taxonomy, ko_record_iterator, ko_record_splitter,\
ko_default_parser, ko_first_field_parser, delete_comments,\
ko_colon_fields, ko_colon_delimited_parser, _is_new_kegg_rec_group,\
group_by_end_char, class_lines_to_fields, ko_class_parser, parse_ko,\
parse_ko_file, make_tab_delimited_line_parser
class ParseKOTests(TestCase):
def make_tab_delimited_line_parser(self):
"""make_tab_delimited_line_parser should generate line parser"""
line ="good\tbad:good\tgood\tgood\tbad:good\tgood"
parse_fn = make_tab_delimited_line_parser([0,2,3,5])
obs = parse_fn(line)
exp = "good\tgood\tgood\tgood\tgood\tgood"
self.assertEqual(obs,exp)
def test_kegg_label_fields(self):
"""kegg_label_fields should return fields from line"""
# Format is species:gene_id [optional gene_name]; description.
# Note that the '>' should already be stripped by the Fasta Parser
test1 = \
"""stm:STM0001 thrL; thr operon leader peptide ; K08278 thr operon leader peptide"""
test2 = \
"""stm:STM0002 thrA; bifunctional aspartokinase I/homeserine dehydrogenase I (EC:2.7.2.4 1.1.1.13); K00003 homoserine dehydrogenase [EC:1.1.1.3]; K00928 aspartate kinase [EC:2.7.2.4]"""
obs = kegg_label_fields(test1)
exp = ('stm:STM0001','stm','STM0001',\
'thrL','thr operon leader peptide ; K08278 thr operon leader peptide')
self.assertEqual(obs,exp)
obs = kegg_label_fields(test2)
exp = ('stm:STM0002', 'stm', 'STM0002', 'thrA', \
'bifunctional aspartokinase I/homeserine dehydrogenase I (EC:2.7.2.4 1.1.1.13); K00003 homoserine dehydrogenase [EC:1.1.1.3]; K00928 aspartate kinase [EC:2.7.2.4]')
self.assertEqual(obs,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)
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_default_parser(self):
"""ko_default parser should strip out newlines and join lines together"""
# Applies to 'NAME' and 'DEFINITION' lines
default_line_1 = ['NAME E3.8.1.2\n']
obs = ko_default_parser(default_line_1)
self.assertEqual(obs,'E3.8.1.2')
default_line_2 = ['DEFINITION 2-haloacid dehalogenase [EC:3.8.1.2]\n']
obs = ko_default_parser(default_line_2)
self.assertEqual(obs,'2-haloacid dehalogenase [EC:3.8.1.2]')
def test_ko_first_field_parser(self):
"""ko_first_field_parser should strip out newlines and join lines
together (first field only)"""
obs = ko_first_field_parser(\
['ENTRY K01559 KO\n'])
exp = 'K01559'
self.assertEqual(obs,exp)
def test_delete_comments(self):
"""delete_comments should delete parenthetical comments from lines"""
test_line = \
"bifunctional aspartokinase I/homeserine dehydrogenase I (EC:2.7.2.4 1.1.1.13);"
exp = "bifunctional aspartokinase I/homeserine dehydrogenase I ;"
obs = delete_comments(test_line)
self.assertEqual(obs,exp)
nested_test_line = \
"text(comment1(comment2));"
exp = "text;"
obs = delete_comments(nested_test_line)
self.assertEqual(obs,exp)
def test_ko_colon_fields(self):
"""ko_colon_fields should convert lines to (key, [list of values])"""
test_lines =\
[' BXE: Bxe_B0037 Bxe_C0683 Bxe_C1002 Bxe_C1023\n']
obs = ko_colon_fields(test_lines)
exp = ('BXE', ['Bxe_B0037', 'Bxe_C0683', 'Bxe_C1002', 'Bxe_C1023'])
self.assertEqual(obs,exp)
test_lines = [' HMA: rrnAC1925(mhpC)\n']
obs = ko_colon_fields(test_lines, without_comments = True)
exp = ('HMA', ['rrnAC1925'])
self.assertEqual(obs,exp)
test_lines = [' HMA: rrnAC1925(mhpC)\n']
obs = ko_colon_fields(test_lines, without_comments = False)
exp = ('HMA', ['rrnAC1925(mhpC)'])
self.assertEqual(obs,exp)
def test_ko_colon_delimited_parser(self):
"""ko_colon_delimited_parser should return a dict of id: values for
colon delimited lines"""
test_lines =\
['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']
obs = ko_colon_delimited_parser(test_lines, without_comments = True)
self.assertEqual(obs['BXE'],['Bxe_B0037','Bxe_C0683', 'Bxe_C1002','Bxe_C1023'])
self.assertEqual(obs['PHA'],['PSHAa2393'])
# Check that comments are stripped
self.assertEqual(obs['BBA'],['Bd0910'])
obs = ko_colon_delimited_parser(test_lines, without_comments = False)
# Lines without comments shouldn't be affected
self.assertEqual(obs['BXE'],['Bxe_B0037','Bxe_C0683', 'Bxe_C1002','Bxe_C1023'])
self.assertEqual(obs['PHA'],['PSHAa2393'])
# Comments should be preserved
self.assertEqual(obs['BBA'],['Bd0910(catD)'])
def test_is_new_kegg_rec_group(self):
"""_is_new_kegg_rec_group should check for irregular field terminators in KEGG"""
pass
# Handle unusual KEGG fields.
def test_group_by_end_char(self):
"""group_by_end_char should yield successive lines that end with a given
char, plus the last group of lines"""
class_lines=['CLASS Metabolism; Xenobiotics Biodegradation and Metabolism;\n',\
' gamma-Hexachlorocyclohexane degradation [PATH:ko00361]\n',\
' Metabolism; Xenobiotics Biodegradation and Metabolism;\n',\
' 1,2-Dichloroethane degradation [PATH:ko00631]\n']
exp =[['CLASS Metabolism; Xenobiotics Biodegradation and Metabolism;\n',\
' gamma-Hexachlorocyclohexane degradation [PATH:ko00361]\n'],\
[' Metabolism; Xenobiotics Biodegradation and Metabolism;\n',\
' 1,2-Dichloroethane degradation [PATH:ko00631]\n']]
for i,group in enumerate(group_by_end_char(class_lines)):
self.assertEqual(group, exp[i])
def test_class_lines_to_fields(self):
"""class_lines_to_fields should split groups of lines for one KO class
definition"""
class_lines1=['CLASS Metabolism; Xenobiotics Biodegradation and Metabolism;\n',\
' gamma-Hexachlorocyclohexane degradation [PATH:ko00361]\n']
class_lines2=[' Metabolism; Xenobiotics Biodegradation and Metabolism;\n',\
' 1,2-Dichloroethane degradation [PATH:ko00631]\n']
obs = class_lines_to_fields(class_lines1)
exp = ('PATH:ko00361',('Metabolism', 'Xenobiotics Biodegradation and Metabolism', 'gamma-Hexachlorocyclohexane degradation'))
self.assertEqual(obs,exp)
obs = class_lines_to_fields(class_lines2)
exp = ('PATH:ko00631',('Metabolism', 'Xenobiotics Biodegradation and Metabolism','1,2-Dichloroethane degradation'))
self.assertEqual(obs,exp)
def test_ko_class_parser(self):
"""ko_class_parser should return fields"""
class_lines='CLASS Metabolism; Xenobiotics Biodegradation and Metabolism;\n',\
' gamma-Hexachlorocyclohexane degradation [PATH:ko00361]\n',\
' Metabolism; Xenobiotics Biodegradation and Metabolism;\n',\
' 1,2-Dichloroethane degradation [PATH:ko00631]\n'
exp = [('PATH:ko00361',('Metabolism','Xenobiotics Biodegradation and Metabolism',\
'gamma-Hexachlorocyclohexane degradation')),\
('PATH:ko00631',('Metabolism', 'Xenobiotics Biodegradation and Metabolism', '1,2-Dichloroethane degradation'))]
for i,obs in enumerate(ko_class_parser(class_lines)):
self.assertEqual(obs,exp[i])
def test_parse_ko(self):
"""parse_ko should parse a ko record into fields """
lines = TEST_KO_LINES
r = parse_ko(lines)
results = []
for result in r:
results.append(result)
# For each entry we expect a dict
self.assertEqual(results[0]["ENTRY"], "K01559")
self.assertEqual(results[1]["ENTRY"], "K01560")
self.assertEqual(results[2]["ENTRY"], "K01561")
self.assertEqual(results[0]["NAME"], "E3.7.1.-")
self.assertEqual(results[1]["NAME"], "E3.8.1.2")
self.assertEqual(results[2]["NAME"], "E3.8.1.3")
self.assertEqual(results[0].get("DEFINITION"), None) #case 1 has no def
self.assertEqual(results[1]["DEFINITION"],\
"2-haloacid dehalogenase [EC:3.8.1.2]")
self.assertEqual(results[2]["DEFINITION"],\
"haloacetate dehalogenase [EC:3.8.1.3]")
self.assertEqual(len(results[0]["CLASS"]), 5)
self.assertEqual(results[0]["CLASS"][4], \
('PATH:ko00362', ('Metabolism', \
'Xenobiotics Biodegradation and Metabolism',\
'Benzoate degradation via hydroxylation')))
self.assertEqual(results[0]["DBLINKS"], \
{'RN': ['R04488', 'R05100', 'R05363', \
'R05365', 'R06371', 'R07515', \
'R07831']})
self.assertEqual(results[1]["DBLINKS"], \
{'GO': ['0018784'], 'RN': ['R05287'], 'COG': ['COG1011']})
self.assertEqual(results[2]["DBLINKS"], \
{'GO': ['0018785'], 'RN': ['R05287']})
self.assertEqual(results[0]["GENES"], \
{'AFM': ['AFUA_4G13070'], 'FNU': ['FN1345'],\
'GBE': ['GbCGDNIH1_0998', 'GbCGDNIH1_1171'],\
'PHA': ['PSHAa2393'], \
'BBA': ['Bd0910'], \
'ABO': ['ABO_0668'],\
'MPT': ['Mpe_A2274'],\
'RCI': ['RCIX1162', 'RCIX2396'], \
'BXE': ['Bxe_B0037', 'Bxe_C0683', 'Bxe_C1002', 'Bxe_C1023'],\
'HMA': ['rrnAC1925'], \
'RBA': ['RB13257']})
TEST_KO_LINES = ['ENTRY K01559 KO\n', '\
NAME E3.7.1.-\n', '\
PATHWAY ko00351 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT)\n', '\
degradation\n', '\
ko00362 Benzoate degradation via hydroxylation\n', '\
ko00632 Benzoate degradation via CoA ligation\n', '\
ko00903 Limonene and pinene degradation\n', '\
ko00930 Caprolactam degradation\n', '\
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', '\
DBLINKS RN: R04488 R05100 R05363 R05365 R06371 R07515 R07831\n', '\
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', '\
///\n', '\
ENTRY K01560 KO\n', '\
NAME E3.8.1.2\n', '\
DEFINITION 2-haloacid dehalogenase [EC:3.8.1.2]\n', '\
PATHWAY ko00361 gamma-Hexachlorocyclohexane degradation\n', '\
ko00631 1,2-Dichloroethane degradation\n', '\
CLASS Metabolism; Xenobiotics Biodegradation and Metabolism;\n', '\
gamma-Hexachlorocyclohexane degradation [PATH:ko00361]\n', '\
Metabolism; Xenobiotics Biodegradation and Metabolism;\n', '\
1,2-Dichloroethane degradation [PATH:ko00631]\n', '\
DBLINKS RN: R05287\n', '\
COG: COG1011\n', '\
GO: 0018784\n', '\
GENES NCR: NCU03617\n', '\
ANI: AN5830.2 AN7918.2\n', '\
AFM: AFUA_2G07750 AFUA_5G14640 AFUA_8G05870\n', '\
AOR: AO090001000019 AO090003001435 AO090011000921\n', '\
PST: PSPTO_0247(dehII)\n', '\
PSP: PSPPH_1747(dehII1) PSPPH_5028(dehII2)\n', '\
ATU: Atu0797 Atu3405(hadL)\n', '\
ATC: AGR_C_1458 AGR_L_2834\n', '\
RET: RHE_CH00996(ypch00330) RHE_PF00342(ypf00173)\n', '\
MSE: Msed_0732\n', '\
///\n', '\
ENTRY K01561 KO\n', '\
NAME E3.8.1.3\n', '\
DEFINITION haloacetate dehalogenase [EC:3.8.1.3]\n', '\
PATHWAY ko00361 gamma-Hexachlorocyclohexane degradation\n', '\
ko00631 1,2-Dichloroethane degradation\n', '\
CLASS Metabolism; Xenobiotics Biodegradation and Metabolism;\n', '\
gamma-Hexachlorocyclohexane degradation [PATH:ko00361]\n', '\
Metabolism; Xenobiotics Biodegradation and Metabolism;\n', '\
1,2-Dichloroethane degradation [PATH:ko00631]\n', '\
DBLINKS RN: R05287\n', '\
GO: 0018785\n', '\
GENES RSO: RSc0256(dehH)\n', '\
REH: H16_A0197\n', '\
BPS: BPSL0329\n', '\
BPM: BURPS1710b_0537(dehH)\n', '\
BPD: BURPS668_0347\n', '\
STO: ST2570\n', '\
MSE: Msed_1088\n', '\
///\n']
if __name__=="__main__":
main()
