1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
|
"""
Unit tests for Annotation module
"""
# Info
__author__ = 'Jason Anthony Vander Heiden'
# Imports
import os
import sys
import time
import unittest
from collections import OrderedDict
# Presto imports
from presto.Annotation import collapseAnnotation, mergeAnnotation, renameAnnotation, getCoordKey
# Paths
test_path = os.path.dirname(os.path.realpath(__file__))
class TestAnnotation(unittest.TestCase):
"""
Notes:
illumina @MISEQ:132:000000000-A2F3U:1:1101:14340:1555 2:N:0:ATCACG
@HWI-EAS209_0006_FC706VJ:5:58:5894:21141#ATCACG/1
@MS6_33112:1:1101:18371:1066/1
sra @SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36
@SRR001666.1.2 1 length=250
454 @000034_0199_0169 length=437 uaccno=GNDG01201ARRCR
pesto @AATCGGATTTGC|COUNT=2|PRIMER=IGHJ_RT|PRFREQ=1.0
"""
def setUp(self):
print('-> %s()' % self._testMethodName)
# Annotation dictionaries
self.ann_dict_1 = OrderedDict([('ID', 'SEQ1'),
('TEST1', 'A,B'),
('TEST2', [1, 2]),
('TEST3', ['First','Second'])])
self.ann_dict_2 = OrderedDict([('ID', 'SEQ2'),
('TEST1', 'C,C'),
('TEST2', 3)])
# SRA, ENA
self.desc_sra = ['SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36',
'SRR735691.1 GXGJ56Z01AE06X length=222',
'SRR1383326.1 1 length=250',
'SRR1383326.1.2 1 length=250',
'ERR346596.6 BS-DSFCONTROL04:4:000000000-A3F0Y:1:1101:13220:1649/1']
self.id_sra = ['SRR001666.1',
'SRR735691.1',
'SRR1383326.1',
'SRR1383326.1',
'ERR346596.6']
# 454
self.desc_454 = ['000034_0199_0169 length=437 uaccno=GNDG01201ARRCR',
'GXGJ56Z01AE06X length=222']
self.id_454 = ['000034_0199_0169',
'GXGJ56Z01AE06X']
# Illumina, Solexa
self.desc_illumina = ['MISEQ:132:000000000-A2F3U:1:1101:14340:1555 1:N:0:ATCACG',
'HWI-EAS209_0006_FC706VJ:5:58:5894:21141#ATCACG/1',
'MS6_33112:1:1101:18371:1066/1']
self.id_illumina = ['MISEQ:132:000000000-A2F3U:1:1101:14340:1555',
'HWI-EAS209_0006_FC706VJ:5:58:5894:21141',
'MS6_33112:1:1101:18371:1066']
# Start clock
self.start = time.time()
def tearDown(self):
# End clock
t = time.time() - self.start
print('<- %s() %.3f' % (self._testMethodName, t))
#@unittest.skip('-> mergeAnnotation() skipped\n')
def test_mergeAnnotation(self):
result = mergeAnnotation(self.ann_dict_1, self.ann_dict_2)
print(result)
self.assertEqual('SEQ1', result['ID'])
self.assertEqual('A,B,C,C', result['TEST1'])
self.assertEqual('1,2,3', result['TEST2'])
result = mergeAnnotation(self.ann_dict_1, self.ann_dict_2, prepend=True)
print(result)
self.assertEqual('SEQ1', result['ID'])
self.assertEqual('C,C,A,B', result['TEST1'])
self.assertEqual('3,1,2', result['TEST2'])
#@unittest.skip('-> renameAnnotation() skipped\n')
def test_renameAnnotation(self):
result = renameAnnotation(self.ann_dict_1, 'TEST1', 'RENAMED1')
print(result)
self.assertEqual('A,B', result['RENAMED1'])
self.assertEqual(None, result.get('TEST1', None))
result = renameAnnotation(self.ann_dict_1, 'TEST1', 'RENAMED2')
print(result)
self.assertEqual('A,B', result['RENAMED2'])
self.assertEqual(None, result.get('TEST1', None))
result = renameAnnotation(self.ann_dict_1, 'TEST2', 'TEST1')
print(result)
self.assertEqual('A,B,1,2', result['TEST1'])
self.assertEqual(None, result.get('TEST2', None))
result = renameAnnotation(self.ann_dict_1, 'TEST2', 'TEST1')
result = renameAnnotation(result, 'TEST3', 'TEST1')
print(result)
self.assertEqual('A,B,1,2,First,Second', result['TEST1'])
self.assertEqual(None, result.get('TEST2', None))
self.assertEqual(None, result.get('TEST3', None))
#@unittest.skip('-> collapseAnnotation() skipped\n')
def test_collapseAnnotation(self):
result = collapseAnnotation(self.ann_dict_1, 'first')
print(result)
self.assertEqual('SEQ1', result['ID'])
self.assertEqual('A', result['TEST1'])
self.assertEqual(1, result['TEST2'])
result = collapseAnnotation(self.ann_dict_1, 'last')
print(result)
self.assertEqual('SEQ1', result['ID'])
self.assertEqual('B', result['TEST1'])
self.assertEqual(2, result['TEST2'])
result = collapseAnnotation(self.ann_dict_1, 'set')
self.assertEqual('SEQ1', result['ID'])
self.assertEqual(['A' ,'B'], result['TEST1'])
self.assertEqual([1, 2], result['TEST2'])
print(result)
result = collapseAnnotation(self.ann_dict_1, 'cat')
self.assertEqual('SEQ1', result['ID'])
self.assertEqual('AB', result['TEST1'])
self.assertEqual('12', result['TEST2'])
print(result)
# TODO: may be better for min/max/sum to return float/int
result = collapseAnnotation(self.ann_dict_1, 'min', fields='TEST2')
self.assertEqual('1', result['TEST2'])
print(result)
result = collapseAnnotation(self.ann_dict_1, 'max', fields='TEST2')
self.assertEqual('2', result['TEST2'])
print(result)
result = collapseAnnotation(self.ann_dict_1, 'sum', fields='TEST2')
self.assertEqual('3', result['TEST2'])
print(result)
#@unittest.skip('-> getCoordKey() skipped\n')
def test_getCoordKey(self):
result = [getCoordKey(x, coord_type='illumina') for x in self.desc_illumina]
self.assertListEqual(result, self.id_illumina)
print(result)
result = [getCoordKey(x, coord_type='sra') for x in self.desc_sra]
self.assertListEqual(result, self.id_sra)
print(result)
result = [getCoordKey(x, coord_type='454') for x in self.desc_454]
self.assertListEqual(result, self.id_454)
print(result)
if __name__ == '__main__':
unittest.main()
|
