def test_2_compare_hits_2(self):
# test 2 hits with 1 function, case 1.2
hit = DiamondHit()
hit.import_hit('NS500496_240_HYN75BGXX:1:11101:10772:2071#CTCTCT/1 fig|485913.3.peg.8591 87.9 33 4 101 100 2 1 33 1.1e-09 58.5 UreA'.split('\t'))
read = AnnotatedRead('NS500496_240_HYN75BGXX:1:11101:10772:2071#CTCTCT/1')
old_hit_list = DiamondHitList('NS500496_240_HYN75BGXX:1:11101:10772:2071#CTCTCT/1')
old_hit_list.add_hit(hit)
read.hit_list = old_hit_list
print ('*test_2_compare_hits_2: test 2 hits with 1 function, case 1.2 *')
new_hits = ['NS500496_240_HYN75BGXX:1:11101:10772:2071#CTCTCT/1|100|2 fig|316274.7.peg.2519 87.9 33 4 101 99 1 1 33 2.1e-07 58.9'
]
hit_list = DiamondHitList('NS500496_240_HYN75BGXX:1:11101:10772:2071#CTCTCT/1|100|2')
for new_hit in new_hits:
hit = DiamondHit()
hit.create_hit(new_hit.split('\t'))
hit.annotate_hit(self.parser.ref_data)
hit_list.add_hit(hit)
self.assertEqual(read.functions['UreA'], 0.0)
compare_hits_erpk_lca(read, 100, 2, hit_list, self.parser.config.get_biscore_range_cutoff(self.parser.collection), 15, 150, self.parser.taxonomy_data, self.parser.ref_data)
# print('Read status:', read.status)
# print('Read function:', read.functions)
self.assertEqual(read.status, STATUS_GOOD)
self.assertEqual(len(read.functions), 1)
self.assertEqual(read.functions['UreA'], get_erpk_score(101, 150, 15))
self.assertEqual(read.taxonomy, '65')
def import_hit_list(self):
"""Imports tab-separated table of DAIMOND hits. Use for resuming
analysis after Fama restart
Returns:
:obj:dict[str, :obj:AnnotatedRead]
"""
infile = os.path.join(os.path.join(self.sample.work_directory,
self.sample.sample_id + '_'
+ self.end + '_'
+ self.options.ref_hits_list_name))
ret_val = {}
hit_list = None
current_read_id = None
with open(infile, 'r', newline='') as infile:
tsvin = csv.reader(infile, delimiter='\t')
for row in tsvin:
if current_read_id is None:
# initialize
current_read_id = row[0]
hit_list = DiamondHitList(current_read_id)
elif current_read_id != row[0]:
ret_val[current_read_id] = AnnotatedRead(current_read_id)
ret_val[current_read_id].hit_list = hit_list
current_read_id = row[0]
hit_list = DiamondHitList(current_read_id)
hit = DiamondHit()
hit.import_hit(row)
hit_list.add_hit(hit)
ret_val[current_read_id] = AnnotatedRead(current_read_id)
ret_val[current_read_id].hit_list = hit_list
return ret_val
def test_2_compare_hits_5(self):
# test 7 hits, two functions, case 2.1
hit = DiamondHit()
hit.import_hit('NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1 fig|1121378.3.peg.2960 76.0 50 12 231 150 1 23 72 9.0e-15 75.5 UreA|UreB'.split('\t'))
read = AnnotatedRead('NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1')
old_hit_list = DiamondHitList('NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1')
old_hit_list.add_hit(hit)
read.hit_list = old_hit_list
print ('* test_2_compare_hits_5: test 7 hits with 2 functions, case 2.1*')
new_hits = ['NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1|150|1 fig|1121378.3.peg.2960 76.0 50 12 231 150 1 23 72 3.3e-12 75.5',
'NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1|150|1 kegg|hco:LOKO_03690 72.0 50 14 100 150 1 23 72 4.3e-12 75.1',
'NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1|150|1 fig|1160705.3.peg.7402 72.0 50 14 236 150 1 159 208 4.3e-12 75.1',
'NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1|150|1 fig|1156841.3.peg.6425 74.0 50 13 100 150 1 23 72 4.3e-12 75.1',
'NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1|150|1 kegg|masw:AM586_12165 74.0 50 13 100 150 1 23 72 5.6e-12 74.7',
'NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1|150|1 fig|1203460.3.peg.2591 72.0 50 14 100 150 1 23 72 5.6e-12 74.7',
'NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1|150|1 fig|1121943.4.peg.3735 72.0 50 14 100 150 1 23 72 5.6e-12 74.7',
]
hit_list = DiamondHitList('NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1|150|1')
for new_hit in new_hits:
hit = DiamondHit()
hit.create_hit(new_hit.split('\t'))
hit.annotate_hit(self.parser.ref_data)
hit_list.add_hit(hit)
compare_hits_erpk_lca(read, 150, 1, hit_list, self.parser.config.get_biscore_range_cutoff(self.parser.collection), 15, 150, self.parser.taxonomy_data, self.parser.ref_data)
# print('Read status:', read.get_status())
# print('Read function:', read.get_functions())
self.assertEqual(read.status, STATUS_GOOD)
self.assertEqual(len(read.functions), 1)
self.assertEqual(read.functions['UreA'], get_erpk_score(231, 150, 15))
self.assertEqual(read.taxonomy, '2')
def test_2_compare_hits_12(self):
# test 20 hits, one function, case 2.5
hit = DiamondHit()
hit.import_hit('NS500496_240_HYN75BGXX:1:11112:25043:18797#CTCTCT/2 kegg|nio:NITINOP_1721 58.5 41 17 311 3 125 271 311 4.2e-05 44.3 RP-L22'.split('\t'))
read = AnnotatedRead('NS500496_240_HYN75BGXX:1:11112:25043:18797#CTCTCT/2')
old_hit_list = DiamondHitList('NS500496_240_HYN75BGXX:1:11112:25043:18797#CTCTCT/2')
old_hit_list.add_hit(hit)
read.hit_list = old_hit_list
# print ('* test2_10: 17 hits with 1 function, case 2.5*')
new_hits = ['NS500496_240_HYN75BGXX:1:11112:25043:18797#CTCTCT/2|3|125 kegg|nio:NITINOP_1721 58.5 41 17 311 1 123 271 311 1.0e-02 43.9',
'NS500496_240_HYN75BGXX:1:11112:25043:18797#CTCTCT/2|3|125 kegg|mgot:MgSA37_03614 58.5 41 17 128 1 123 88 128 1.4e-02 43.5',
'NS500496_240_HYN75BGXX:1:11112:25043:18797#CTCTCT/2|3|125 kegg|lfc:LFE_0874 58.5 41 17 127 1 123 87 127 1.4e-02 43.5',
'NS500496_240_HYN75BGXX:1:11112:25043:18797#CTCTCT/2|3|125 fig|269799.8.peg.645 53.7 41 19 127 1 123 87 127 1.8e-02 43.1',
'NS500496_240_HYN75BGXX:1:11112:25043:18797#CTCTCT/2|3|125 fig|653733.4.peg.1965 58.5 41 17 126 1 123 86 126 1.8e-02 43.1',
'NS500496_240_HYN75BGXX:1:11112:25043:18797#CTCTCT/2|3|125 kegg|gbe:GbCGDNIH1_0546 56.1 41 18 125 1 123 85 125 1.8e-02 43.1'
]
hit_list = DiamondHitList('NS500496_240_HYN75BGXX:1:11112:25043:18797#CTCTCT/2|3|125')
for new_hit in new_hits:
hit = DiamondHit()
hit.create_hit(new_hit.split('\t'))
hit.annotate_hit(self.parser.ref_data)
hit_list.add_hit(hit)
compare_hits_erpk_lca(read, 3, 125, hit_list, self.parser.config.get_biscore_range_cutoff(self.parser.collection), 15, 150, self.parser.taxonomy_data, self.parser.ref_data)
# print('Read status:', read.status)
# print('Read function:', read.functions)
self.assertEqual(read.status, STATUS_BAD)
self.assertEqual(len(read.functions), 0)
self.assertEqual(read.taxonomy, None)
def test_2_compare_hits_11(self):
# read with two hits
hit1 = DiamondHit()
hit1.import_hit('NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1 fig|363754.4.peg.84 88.0 50 6 570 1 150 270 319 7.6e-22 99.0 UreC'.split('\t'))
hit2 = DiamondHit()
hit2.import_hit('NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1 fig|485913.3.peg.8591 87.9 33 4 101 100 2 1 33 1.1e-09 58.5 UreA'.split('\t'))
read = AnnotatedRead('NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1')
old_hit_list = DiamondHitList('NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1')
old_hit_list.add_hit(hit1)
old_hit_list.add_hit(hit2)
read.hit_list = old_hit_list
print ('* test read with 2 hits *')
new_hits = ['NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|100|2 fig|485913.3.peg.8591 87.9 33 4 101 99 1 1 33 2.1e-07 58.9',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|100|2 kegg|cap:CLDAP_03170 81.8 33 6 100 99 1 1 33 1.4e-06 56.2',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|100|2 fig|316274.7.peg.2519 78.8 33 7 100 99 1 1 33 6.8e-06 53.9'
]
hit_list = DiamondHitList('NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|100|2')
for new_hit in new_hits:
hit = DiamondHit()
hit.create_hit(new_hit.split('\t'))
hit.annotate_hit(self.parser.ref_data)
hit_list.add_hit(hit)
compare_hits_erpk_lca(read, 100, 2, hit_list, self.parser.config.get_biscore_range_cutoff(self.parser.collection), 15, 150, self.parser.taxonomy_data, self.parser.ref_data)
new_hits = ['NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|266835.9.peg.3902 88.0 50 6 570 1 150 270 319 2.8e-19 99.0',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|363754.4.peg.84 90.0 50 5 590 1 150 290 339 4.7e-19 98.2',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|411684.3.peg.2730 88.0 50 6 570 1 150 270 319 6.2e-19 97.8',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|176299.10.peg.2410 90.0 50 5 569 1 150 269 318 6.2e-19 97.8',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 kegg|maad:AZF01_14085 86.0 50 7 570 1 150 270 319 6.2e-19 97.8',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|266834.11.peg.3959 88.0 50 6 570 1 150 270 319 6.2e-19 97.8',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 kegg|six:BSY16_122 88.0 50 6 568 1 150 269 318 6.2e-19 97.8',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|1144306.3.peg.717 86.0 50 7 569 1 150 269 318 6.2e-19 97.8',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 kegg|meso:BSQ44_05880 88.0 50 6 570 1 150 270 319 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|244592.3.peg.2201 90.0 50 5 570 1 150 270 319 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|1150469.3.peg.1765 90.0 50 5 583 1 150 270 319 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 kegg|don:BSK21_03675 90.0 50 5 566 1 150 269 318 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|1048680.4.peg.3848 86.0 50 7 569 1 150 269 318 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|311402.9.peg.5014 86.0 50 7 570 1 150 270 319 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 kegg|hoe:IMCC20628_02897 88.0 50 6 570 1 150 270 319 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|744979.4.peg.2070 88.0 50 6 570 1 150 270 319 8.1e-19 97.4'
]
hit_list = DiamondHitList('NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150')
for new_hit in new_hits:
hit = DiamondHit()
hit.create_hit(new_hit.split('\t'))
hit.annotate_hit(self.parser.ref_data)
hit_list.add_hit(hit)
compare_hits_erpk_lca(read, 1, 150, hit_list, self.parser.config.get_biscore_range_cutoff(self.parser.collection), 15, 150, self.parser.taxonomy_data, self.parser.ref_data)
# print('Read status:', read.status)
# print('Read function:', read.functions)
# print('Read hits:', read.show_hits())
self.assertEqual(read.status, STATUS_GOOD)
self.assertEqual(len(read.functions), 2)
self.assertEqual(read.functions['UreA'], get_erpk_score(101, 150, 15))
self.assertEqual(read.taxonomy, '28211')
def test_6_annotate_hit(self):
print ('Test hit annotation')
hit_line = 'NS500496_240_HYN75BGXX:1:11101:10772:2071#CTCTCT/1 fig|485913.3.peg.8591 87.9 33 4 101 100 2 1 33 1.1e-09 58.5 UreA'
hit = DiamondHit()
hit.import_hit(hit_line.split('\t'))
hit.annotate_hit(self.parser.ref_data)
self.assertEqual(len(hit.functions), 1)
self.assertEqual(hit.functions[0], 'UreA')
hit_line = 'NS500496_240_HYN75BGXX:1:11101:10772:2071#CTCTCT/1|100|2 kegg|cap:CLDAP_03170 81.8 33 6 100 99 1 1 33 1.4e-06 56.2 UreA'
hit = DiamondHit()
hit.import_hit(hit_line.split('\t'))
hit.annotate_hit(self.parser.ref_data)
self.assertEqual(len(hit.functions), 1)
self.assertEqual(hit.functions[0], 'UreA')
def test_2_compare_hits_4(self):
# test hit with two functions
hit = DiamondHit()
hit.import_hit('NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1 fig|1121378.3.peg.2960 76.0 50 12 231 150 1 23 72 9.0e-15 75.5 UreA|UreB'.split('\t'))
read = AnnotatedRead('NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1')
old_hit_list = DiamondHitList('NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1')
old_hit_list.add_hit(hit)
read.hit_list = old_hit_list
# test 20 hits, one function
print ('*test_2_compare_hits_4: test 20 hits with 2 functions, case 2.1*')
new_hits = ['NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1|150|1 fig|1121378.3.peg.2960 76.0 50 12 231 150 1 23 72 3.3e-12 75.5',
'NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1|150|1 kegg|hco:LOKO_03690 72.0 50 14 100 150 1 23 72 4.3e-12 75.1',
'NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1|150|1 fig|1160705.3.peg.7402 72.0 50 14 236 150 1 159 208 4.3e-12 75.1',
'NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1|150|1 fig|1156841.3.peg.6425 74.0 50 13 100 150 1 23 72 4.3e-12 75.1',
'NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1|150|1 kegg|masw:AM586_12165 74.0 50 13 100 150 1 23 72 5.6e-12 74.7',
'NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1|150|1 fig|1203460.3.peg.2591 72.0 50 14 100 150 1 23 72 5.6e-12 74.7',
'NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1|150|1 fig|1121943.4.peg.3735 72.0 50 14 100 150 1 23 72 5.6e-12 74.7',
'NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1|150|1 kegg|samb:SAM23877_1321 72.0 50 14 100 150 1 23 72 7.3e-12 74.3',
'NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1|150|1 fig|100226.15.peg.1235 72.0 50 14 100 150 1 23 72 7.3e-12 74.3',
'NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1|150|1 fig|290398.11.peg.2325 72.0 50 14 100 150 1 23 72 7.3e-12 74.3',
'NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1|150|1 fig|1000565.3.peg.3274 72.0 50 14 100 150 1 23 72 9.6e-12 73.9',
'NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1|150|1 kegg|hhu:AR456_08480 68.0 50 16 100 150 1 23 72 1.3e-11 73.6',
'NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1|150|1 fig|1126229.3.peg.323 70.0 50 15 100 150 1 23 72 1.3e-11 73.6',
'NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1|150|1 fig|1155714.3.peg.3022 70.0 50 15 100 150 1 23 72 1.3e-11 73.6',
'NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1|150|1 fig|1155716.3.peg.3618 72.0 50 14 100 150 1 23 72 1.3e-11 73.6',
'NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1|150|1 fig|1155718.3.peg.3182 68.0 50 16 100 150 1 23 72 1.3e-11 73.6',
'NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1|150|1 fig|591167.6.peg.5739 70.0 50 15 100 150 1 23 72 1.3e-11 73.6',
'NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1|150|1 fig|1054862.3.peg.1097 72.0 50 14 103 150 1 26 75 1.3e-11 73.6'
]
hit_list = DiamondHitList('NS500496_240_HYN75BGXX:1:11101:9189:2106#CTCTCT/1|150|1')
for new_hit in new_hits:
hit = DiamondHit()
hit.create_hit(new_hit.split('\t'))
hit.annotate_hit(self.parser.ref_data)
hit_list.add_hit(hit)
compare_hits_erpk_lca(read, 150, 1, hit_list, self.parser.config.get_biscore_range_cutoff(self.parser.collection), 15, 150, self.parser.taxonomy_data, self.parser.ref_data)
# print('268 Read status:', read.get_status())
# print('269 Read function:', read.get_functions())
self.assertEqual(read.status, STATUS_GOOD)
self.assertEqual(len(read.functions), 1)
self.assertEqual(read.functions['UreA'], get_erpk_score(231, 150, 15))
self.assertEqual(read.taxonomy, '2')
def test_2_compare_hits_7(self):
# test hit with one function and many close homologs, case 2.2
hit = DiamondHit()
hit.import_hit('NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1 fig|363754.4.peg.84 88.0 50 6 570 1 150 270 319 7.6e-22 99.0 UreC'.split('\t'))
read = AnnotatedRead('NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1')
old_hit_list = DiamondHitList('NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1')
old_hit_list.add_hit(hit)
read.hit_list = old_hit_list
# test 20 hits, one function
print ('* test 17 hits with 1 function, case 2.2*')
new_hits = ['NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|266835.9.peg.3902 88.0 50 6 570 1 150 270 319 2.8e-19 99.0',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|363754.4.peg.84 90.0 50 5 590 1 150 290 339 4.7e-19 98.2',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|411684.3.peg.2730 88.0 50 6 570 1 150 270 319 6.2e-19 97.8',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|176299.10.peg.2410 90.0 50 5 569 1 150 269 318 6.2e-19 97.8',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 kegg|maad:AZF01_14085 86.0 50 7 570 1 150 270 319 6.2e-19 97.8',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|266834.11.peg.3959 88.0 50 6 570 1 150 270 319 6.2e-19 97.8',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 kegg|six:BSY16_122 88.0 50 6 568 1 150 269 318 6.2e-19 97.8',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|1144306.3.peg.717 86.0 50 7 569 1 150 269 318 6.2e-19 97.8',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 kegg|meso:BSQ44_05880 88.0 50 6 570 1 150 270 319 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|118163.3.peg.2804 90.0 50 5 565 1 150 266 315 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|244592.3.peg.2201 90.0 50 5 570 1 150 270 319 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|1150469.3.peg.1765 90.0 50 5 583 1 150 270 319 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 kegg|don:BSK21_03675 90.0 50 5 566 1 150 269 318 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|1048680.4.peg.3848 86.0 50 7 569 1 150 269 318 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|311402.9.peg.5014 86.0 50 7 570 1 150 270 319 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 kegg|hoe:IMCC20628_02897 88.0 50 6 570 1 150 270 319 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|744979.4.peg.2070 88.0 50 6 570 1 150 270 319 8.1e-19 97.4'
]
hit_list = DiamondHitList('NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150')
for new_hit in new_hits:
hit = DiamondHit()
hit.create_hit(new_hit.split('\t'))
hit.annotate_hit(self.parser.ref_data)
hit_list.add_hit(hit)
compare_hits_erpk_lca(read, 1, 150, hit_list, self.parser.config.get_biscore_range_cutoff(self.parser.collection), 15, 150, self.parser.taxonomy_data, self.parser.ref_data)
# print('Read status:', read.get_status())
# print('Read function:', read.get_functions())
self.assertEqual(read.status, STATUS_GOOD)
self.assertEqual(len(read.functions), 1)
self.assertEqual(read.functions['UreC'], get_erpk_score(570, 150, 15))
self.assertEqual(read.taxonomy, '28211')
def test_2_compare_hits_8(self):
# test hit with one function and many close homologs, case 2.4
hit = DiamondHit()
hit.import_hit('NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1 fig|363754.4.peg.84 88.0 50 6 570 1 150 270 319 7.6e-22 99.0 UreC'.split('\t'))
read = AnnotatedRead('NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1')
old_hit_list = DiamondHitList('NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1')
old_hit_list.add_hit(hit)
read.hit_list = old_hit_list
# test 20 hits, one function, case 2.4
print ('* test2_8: 17 hits with 1 function, case 2.4*')
new_hits = ['NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fake_id1 88.0 50 6 570 1 150 270 319 2.8e-19 99.0',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fake_id2 90.0 50 5 590 1 150 290 339 4.7e-19 98.2',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fake_id3 88.0 50 6 570 1 150 270 319 6.2e-19 97.8',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fake_id4 90.0 50 5 569 1 150 269 318 6.2e-19 97.8',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fake_id5 86.0 50 7 570 1 150 270 319 6.2e-19 97.8',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fake_id6 88.0 50 6 570 1 150 270 319 6.2e-19 97.8',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fake_id7 88.0 50 6 568 1 150 269 318 6.2e-19 97.8',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fake_id8 86.0 50 7 569 1 150 269 318 6.2e-19 97.8',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fake_id9 88.0 50 6 570 1 150 270 319 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fake_id10 90.0 50 5 565 1 150 266 315 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fake_id11 90.0 50 5 570 1 150 270 319 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fake_id12 90.0 50 5 583 1 150 270 319 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fake_id13 90.0 50 5 566 1 150 269 318 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fake_id14 86.0 50 7 569 1 150 269 318 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fake_id15 86.0 50 7 570 1 150 270 319 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fake_id16 88.0 50 6 570 1 150 270 319 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fake_id17 88.0 50 6 570 1 150 270 319 8.1e-19 97.4'
]
hit_list = DiamondHitList('NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150')
for new_hit in new_hits:
hit = DiamondHit()
hit.create_hit(new_hit.split('\t'))
hit.annotate_hit(self.parser.ref_data)
hit_list.add_hit(hit)
compare_hits_erpk_lca(read, 1, 150, hit_list, self.parser.config.get_biscore_range_cutoff(self.parser.collection), 15, 150, self.parser.taxonomy_data, self.parser.ref_data)
# print('Read status:', read.get_status())
# print('Read function:', read.get_functions())
self.assertEqual(read.status, STATUS_BAD)
self.assertEqual(len(read.functions), 0)
self.assertEqual(read.taxonomy, None)
def test_2_compare_hits_3(self):
# test 3 hits with 1 function, case 1.3
hit = DiamondHit()
hit.import_hit('NS500496_240_HYN75BGXX:1:11101:10772:2071#CTCTCT/1 fig|485913.3.peg.8591 87.9 33 4 101 100 2 1 33 1.1e-09 58.5 UreA'.split('\t'))
read = AnnotatedRead('NS500496_240_HYN75BGXX:1:11101:10772:2071#CTCTCT/1')
old_hit_list = DiamondHitList('NS500496_240_HYN75BGXX:1:11101:10772:2071#CTCTCT/1')
old_hit_list.add_hit(hit)
read.hit_list = old_hit_list
print ('* test 1 hit with 1 function, case 1.3 *')
new_hits = ['NS500496_240_HYN75BGXX:1:11101:10772:2071#CTCTCT/1|100|2 fake_id 87.9 33 4 101 99 1 1 33 2.1e-07 58.9'
]
hit_list = DiamondHitList('NS500496_240_HYN75BGXX:1:11101:10772:2071#CTCTCT/1|100|2')
for new_hit in new_hits:
hit = DiamondHit()
hit.create_hit(new_hit.split('\t'))
hit.annotate_hit(self.parser.ref_data)
hit_list.add_hit(hit)
compare_hits_erpk_lca(read, 100, 2, hit_list, self.parser.config.get_biscore_range_cutoff(self.parser.collection), 15, 150, self.parser.taxonomy_data, self.parser.ref_data)
# print('Read status:', read.get_status())
# print('Read function:', read.get_functions())
self.assertEqual(read.status, STATUS_BAD)
self.assertEqual(len(read.functions), 0)
self.assertEqual(read.taxonomy, None)
def test_2_compare_hits_6(self):
# test hit with one function and many close homologs, case 2.1
hit = DiamondHit()
hit.import_hit('NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1 fig|363754.4.peg.84 88.0 50 6 570 1 150 270 319 7.6e-22 99.0 UreC'.split('\t'))
read = AnnotatedRead('NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1')
old_hit_list = DiamondHitList('NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1')
old_hit_list.add_hit(hit)
read.hit_list = old_hit_list
# test 20 hits, one function
print ('* test_2_compare_hits_6: test 40 hits with 1 function, case 2.1*')
new_hits = ['NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|363754.4.peg.84 88.0 50 6 570 1 150 270 319 2.8e-19 99.0',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|266835.9.peg.3902 90.0 50 5 590 1 150 290 339 4.7e-19 98.2',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|411684.3.peg.2730 88.0 50 6 570 1 150 270 319 6.2e-19 97.8',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|176299.10.peg.2410 90.0 50 5 569 1 150 269 318 6.2e-19 97.8',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 kegg|maad:AZF01_14085 86.0 50 7 570 1 150 270 319 6.2e-19 97.8',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|266834.11.peg.3959 88.0 50 6 570 1 150 270 319 6.2e-19 97.8',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 kegg|six:BSY16_122 88.0 50 6 568 1 150 269 318 6.2e-19 97.8',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|1144306.3.peg.717 86.0 50 7 569 1 150 269 318 6.2e-19 97.8',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 kegg|meso:BSQ44_05880 88.0 50 6 570 1 150 270 319 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|118163.3.peg.2804 90.0 50 5 565 1 150 266 315 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|244592.3.peg.2201 90.0 50 5 570 1 150 270 319 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|1150469.3.peg.1765 90.0 50 5 583 1 150 270 319 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 kegg|don:BSK21_03675 90.0 50 5 566 1 150 269 318 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|1048680.4.peg.3848 86.0 50 7 569 1 150 269 318 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|311402.9.peg.5014 86.0 50 7 570 1 150 270 319 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 kegg|hoe:IMCC20628_02897 88.0 50 6 570 1 150 270 319 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|744979.4.peg.2070 88.0 50 6 570 1 150 270 319 8.1e-19 97.4',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|1123256.3.peg.2564 90.0 50 5 570 1 150 270 319 1.1e-18 97.1',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 kegg|labr:CHH27_19355 90.0 50 5 570 1 150 270 319 1.1e-18 97.1',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|1156935.5.peg.1846 86.0 50 7 570 1 150 270 319 1.1e-18 97.1',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|314231.3.peg.911 90.0 50 5 570 1 150 270 319 1.1e-18 97.1',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|216596.11.peg.5042 86.0 50 7 570 1 150 270 319 1.1e-18 97.1',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|292564.3.peg.2428 88.0 50 6 574 1 150 270 319 1.1e-18 97.1',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|1122218.3.peg.2653 88.0 50 6 570 1 150 270 319 1.4e-18 96.7',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|633131.3.peg.1456 88.0 50 6 586 1 150 287 336 1.4e-18 96.7',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|375451.14.peg.3633 88.0 50 6 569 1 150 270 319 1.4e-18 96.7',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|391593.3.peg.1570 88.0 50 6 569 1 150 270 319 1.4e-18 96.7',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|1120961.3.peg.1492 86.0 50 7 570 1 150 270 319 1.8e-18 96.3',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|756067.3.peg.5652 88.0 50 6 581 1 150 266 315 1.8e-18 96.3',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|640510.4.peg.718 88.0 50 6 568 1 150 269 318 1.8e-18 96.3',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|272129.4.peg.175 88.0 50 6 452 1 150 266 315 1.8e-18 96.3',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|197221.4.peg.4 88.0 50 6 572 1 150 270 319 1.8e-18 96.3',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|314256.5.peg.1029 88.0 50 6 569 1 150 270 319 1.8e-18 96.3',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|313624.3.peg.4907 88.0 50 6 568 1 150 270 319 1.8e-18 96.3',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|402777.3.peg.1444 88.0 50 6 601 1 150 270 319 1.8e-18 96.3',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|179408.3.peg.7446 88.0 50 6 603 1 150 266 315 1.8e-18 96.3',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|643473.3.peg.1780 88.0 50 6 564 1 150 266 315 1.8e-18 96.3',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|1173263.3.peg.2622 86.0 50 7 565 1 150 266 315 2.4e-18 95.9',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|391038.7.peg.2407 88.0 50 6 568 1 150 269 318 2.4e-18 95.9',
'NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150 fig|103690.10.peg.4352 88.0 50 6 568 1 150 270 319 2.4e-18 95.9'
]
hit_list = DiamondHitList('NS500496_240_HYN75BGXX:1:11101:9460:3085#CTCTCT/1|1|150')
for new_hit in new_hits:
hit = DiamondHit()
hit.create_hit(new_hit.split('\t'))
hit.annotate_hit(self.parser.ref_data)
hit_list.add_hit(hit)
compare_hits_erpk_lca(read, 1, 150, hit_list, self.parser.config.get_biscore_range_cutoff(self.parser.collection), 15, 150, self.parser.taxonomy_data, self.parser.ref_data)
# print('Read status:', read.get_status())
# print('Read function:', read.get_functions())
self.assertEqual(read.status, STATUS_GOOD)
self.assertEqual(len(read.functions), 1)
self.assertEqual(read.functions['UreC'], get_erpk_score(570, 150, 15))
self.assertEqual(read.taxonomy, '2')