forked from biopython/biopython
/
test_SeqIO_AbiIO.py
147 lines (125 loc) · 17.8 KB
/
test_SeqIO_AbiIO.py
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
# Copyright 2011 by Wibowo Arindrarto (w.arindrarto@gmail.com)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
import unittest
from os.path import join, basename
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio._py3k import _bytes_to_string, _as_bytes
test_data = {
'data_empty': {
'path': ['Abi', 'empty.ab1'],
'seq': 'NNNNN',
'qual': [0, 0, 0, 0, 0],
'sample': '226041_C-ME-19_pCAGseqF',
'sample_well': 'C10',
'machine_model': '3730',
'run_start': '2009-12-12 09:56:53',
'run_finish': '2009-12-12 11:44:49',
},
'data_3730': {
'path': ['Abi', '3730.ab1'],
'seq':
'GGGCGAGCKYYAYATTTTGGCAAGAATTGAGCTCTATGGCCACAACCATGGTGAGCAAGGGCGAGGAGGATAACATGGCCATCATCAAGGAGTTCATGCGCTTCAAGGTGCACATGGAGGGCTCCGTGAACGGCCACGAGTTCGAGATCGAGGGCGAGGGCGAGGGCCGCCCCTACGAGGGCACCCAGACCGCCAAGCTGAAGGTGACCAAGGGTGGCCCCCTGCCCTTCGCCTGGGACATCCTGTCCCCTCAGTTCATGTACGGCTCCAAGGCCTACGTGAAGCACCCCGCCGACATCCCCGACTACTTGAAGCTGTCCTTCCCCGAGGGCTTCAAGTGGGAGCGCGTGATGAACTTCGAGGACGGCGGCGTGGTGACCGTGACCCAGGACTCCTCCCTGCAGGACGGCGAGTTCATCTACAAGGTGAAGCTGCGCGGCACCAACTTCCCCTCCGACGGCCCCGTAATGCAGAAGAAGACCATGGGCTGGGAGGCCTCCTCCGAGCGGATGTACCCCGAGGACGGCGCCCTGAAGGGCGAGATCAAGCAGAGGCTGAAGCTGAAGGACGGCGGCCACTACGACGCTGAGGTCAAGACCACCTACAAGGCCAAGAAGCCCGTGCAGCTGCCCGGCGCCTACAACGTCAACATCAAGTTGGACATCACCTCCCACAACGAGGACTACACCATCGTGGAACAGTACGAACGCGCCGAGGGCCGCCACTCCACCGGCGGCATGGACGAGCTGTACAAGGGCGGCAGCGGCATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAARACCCGCGCCGAGGTGAARTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAAGGGGCAYCGCACCTTTC',
'qual':
[20, 3, 4, 4, 4, 6, 4, 4, 0, 0, 0, 6, 0, 10, 20, 26, 22, 17, 21, 31, 29, 32, 28, 18, 23, 17, 19, 35, 36, 50, 39, 50, 50, 50, 50, 50, 25, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 39, 33, 20, 35, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 50, 35, 31, 23, 28, 31, 21, 43, 39, 35, 24, 30, 26, 35, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 31, 24, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 43, 43, 50, 50, 50, 50, 50, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 35, 50, 50, 50, 50, 31, 36, 55, 55, 55, 55, 36, 55, 55, 55, 55, 55, 36, 55, 55, 55, 55, 55, 36, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 40, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 36, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 40, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 50, 43, 43, 50, 43, 43, 50, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 50, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 28, 28, 35, 28, 28, 35, 28, 28, 35, 28, 28, 35, 28, 28, 35, 28, 21, 28, 35, 28, 28, 35, 35, 35, 35, 35, 37, 38, 21, 28, 35, 28, 28, 35, 35, 35, 35, 35, 35, 35, 36, 36, 21, 39, 35, 35, 35, 39, 35, 37, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 28, 28, 35, 35, 28, 28, 35, 35, 35, 36, 36, 22, 39, 35, 35, 35, 35, 35, 35, 37, 38, 28, 35, 21, 36, 36, 37, 35, 35, 20, 39, 39, 35, 35, 35, 35, 37, 38, 28, 35, 37, 34, 35, 24, 24, 27, 25, 20, 24, 37, 35, 27, 21, 20, 21, 27, 17, 20, 24, 32, 26, 20, 12, 20, 10, 20, 24, 25, 23, 20, 32, 24, 24, 23, 20, 24, 23, 18, 34, 34, 34, 22, 26, 24, 24, 18, 22, 22, 23, 25, 20, 12, 20, 24, 23, 24, 23, 22, 20, 20, 0, 20, 24, 23, 20, 8, 10, 4, 20, 20, 3, 7, 19, 20, 4, 4, 7, 7, 0, 7, 11, 18, 8, 3, 23, 23, 20, 11, 4, 20, 18, 12, 20, 20, 20, 4, 20, 4, 2, 3, 21, 21, 21, 21, 10, 15, 14, 15, 19, 2, 4, 3, 6, 11, 3, 4, 6, 21, 16, 20, 11, 1, 4, 12, 0, 15, 8, 1, 3, 3, 12, 1, 11, 20, 4],
'sample': '226032_C-ME-18_pCAGseqF',
'sample_well': 'B9',
'dye': 'Z-BigDyeV3',
'polymer': 'POP7 ',
'machine_model': '3730',
'run_start': '2009-12-12 09:56:53',
'run_finish': '2009-12-12 11:44:49',
},
'data_3100': {
'path': ['Abi', '3100.ab1'],
'seq':
'CAAGATTGCATTCATGATCTACGATTACTAGCGATTCCAGCTTCATATAGTCGAGTTGCAGACTACAATCCGAACTGAGAACAACTTTATGGGATTTGCTTGACCTCGCGGTTTCGCTGCCCTTTGTATTGTCCATTGTAGCACGTGTGTAGCCCAAATCATAAGGGGCATGATGATTTGACGTCATCCCCACCTTCCTCCGGTTTGTCACCGGCAGTCAACTTAGAGTGCCCAACTTAATGATGGCAACTAAGCTTAAGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAACCATGCACCACCTGTCACTCTGTCCCCCGAAGGGGAAAACTCTATCTCTAGAGGAGTCAGAGGATGTCAAGATTTGGTAAGGTTCTTCGCGTTGCTTCGAATTAAACCACATGCTCCACCGCTTGTGCGGGTCCCCGTCAATTCCTTTGAGTTTCAACCTTGCGGTCGTACTCCCCAGGCGGAGTGCTTAATGCGTTAGCTGCAGCACTAAGGGGCGGAAACCCCCTAACACTTAGCACTCATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGATCCCCACGCTTTCGCACATCAGCGTCAGTTACAGACCAGAAAGTCGCCTTCGCCACTGGTGTTCCTCCATATCTCTGCGCATTTCACCGCTACACATGGAAATTCCACTTTCCTCTTCTGCACTCAAGTTTTCCAGATTTCGATGAACCTTCAACGATGGAGGCCCGTGGCTTTTCACCATTCAAGGAACCTTTTA',
'qual':
[5, 3, 4, 4, 4, 5, 9, 4, 4, 4, 5, 4, 4, 4, 4, 4, 6, 13, 23, 20, 15, 17, 10, 9, 13, 23, 18, 14, 19, 34, 15, 24, 34, 18, 30, 35, 41, 34, 22, 39, 53, 58, 35, 46, 24, 42, 46, 46, 54, 42, 53, 58, 52, 41, 22, 62, 52, 62, 52, 62, 41, 38, 16, 42, 62, 56, 62, 62, 62, 62, 62, 62, 54, 56, 39, 62, 49, 35, 19, 44, 44, 42, 62, 62, 62, 62, 54, 62, 62, 62, 62, 49, 49, 43, 39, 62, 62, 62, 62, 62, 62, 62, 59, 43, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 49, 59, 62, 62, 59, 59, 62, 62, 62, 62, 62, 59, 62, 62, 62, 62, 62, 62, 59, 59, 62, 62, 62, 62, 62, 59, 62, 62, 59, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 59, 59, 62, 59, 59, 62, 62, 62, 59, 59, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 50, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 59, 59, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 54, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 59, 59, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 59, 59, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 49, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 42, 31, 31, 26, 18, 24, 33, 56, 56, 62, 56, 62, 47, 39, 62, 62, 62, 62, 62, 62, 49, 47, 62, 62, 62, 49, 62, 62, 62, 62, 49, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 58, 58, 58, 58, 58, 58, 58, 58, 58, 54, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 54, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 53, 58, 58, 58, 51, 49, 58, 58, 58, 58, 50, 58, 58, 58, 58, 58, 58, 51, 32, 58, 58, 42, 58, 51, 58, 49, 39, 58, 58, 51, 58, 53, 58, 50, 58, 58, 58, 53, 54, 53, 58, 54, 53, 58, 53, 58, 32, 58, 44, 46, 50, 58, 54, 58, 58, 49, 41, 58, 58, 58, 54, 54, 54, 51, 52, 53, 51, 54, 54, 54, 38, 52, 53, 47, 54, 54, 53, 54, 54, 54, 52, 54, 42, 47, 35, 42, 54, 45, 54, 53, 54, 23, 34, 24, 51, 52, 33, 46, 44, 33, 49, 51, 45, 53, 32, 52, 53, 52, 51, 36, 52, 53, 52, 52, 37, 53, 52, 40, 27, 24, 46, 16, 33, 45, 51, 43, 51, 51, 46, 46, 45, 42, 31, 43, 41, 43, 35, 43, 43, 42, 31, 46, 46, 32, 46, 35, 42, 46, 42, 31, 31, 43, 42, 35, 21, 42, 35, 28, 46, 47, 37, 41, 29, 39, 31, 32, 39, 31, 41, 43, 34, 43, 36, 27, 31, 27, 35, 36, 24, 44, 33, 31, 32, 38, 35, 31, 32, 29, 31, 31, 31, 38, 38, 36, 31, 34, 30, 21, 28, 32, 32, 47, 31, 33, 30, 23, 22, 25, 25, 26, 30, 30, 21, 28, 31, 21, 14, 5, 3, 16, 9, 18, 27, 8, 19, 4, 5, 13, 47, 27, 14, 21, 9, 17, 21, 17, 27, 14, 23, 23, 14, 15, 28, 15, 12, 8, 5, 3, 17, 28, 16, 13, 17, 11, 2, 2, 3, 29, 7, 3, 1, 3, 3, 8, 7, 7, 24, 12, 3, 4, 15, 3, 4, 7, 5, 1, 2, 2, 8, 24, 6, 4, 11, 23, 9, 6, 4, 3, 5, 3, 5, 17, 17, 22, 11, 4, 5, 8, 16, 10, 6, 11, 6, 11, 5, 5, 27, 18, 7, 15, 16, 30, 21, 14, 7],
'sample': '16S_S2_1387R',
'sample_well': 'H3',
'dye': 'Z-BigDyeV3',
'polymer': 'POP7 ',
'machine_model': '3100',
'run_start': '2010-01-27 09:52:45',
'run_finish': '2010-01-27 10:41:07',
},
'data_310': {
'path': ['Abi', '310.ab1'],
'seq':
'TGATNTTNACNNTTTTGAANCANTGAGTTAATAGCAATNCTTTACNAATAAGAATATACACTTTCTGCTTAGGGATGATAATTGGCAGGCAAGTGAATCCCTGAGCGTGNATTTGATAATGACCTAAATAATGGATGGGGTTTTAATTCCCAGACCTTCCCCTTTTTAANNGGNGGATTANTGGGGGNNNAACNNGGGGGGCCCTTNCCNAAGGGGGAAAAAATTTNAAACCCCCCNAGGNNGGGNAAAAAAAAATTTCCAAATTNCCGGGGTNNCCCCCAANTTTTTNCCGCNGGGAAAANNNNCCCCCCCNGGGNCCCCCCCCNNAAAAAAAAAAAAAAAAACCCCCCCCCCNTTGGGGNGGTNTNCNCCCCCNNANAANNGGGGGNNAAAAAAAAAGGCCCCCCCCAAAAAAAACCCNCNTTCTNNCNNNNNGNNCNGNNCCCCCNNCCNTNTNGGGGGGGGGGGNGGAAAAAAAACCCCTTTNTGNNNANANNAACCCNCTCNTNTTTTTTTTTTTANGNNNNCNNNNCAAAAAAAAANCNCCCCCNNCNNNCNNNCNCCCCNNNNTNAAAANANNAANNNNTTTTTTTNGGGGGGGTGNGCGNCCCNNANCNNNNNNNNGCGNGGNCNCCNNCCCNCNANAAANNNTNTTTTTTTTTTTTTTTNTNNTCNNCCCNNNCCCCNNCCCCCCCCCCCCCNCCNCNNNNNGGGGNNNCGGNNCNNNNNNNCCNTNCTNNANATNCCNTTNNNNNNNNGNNNNNNNNACNNNNNTNNTNNNCNNNNNNNNNNNNNNCNNNNNNCNNCCCNNCANNNNNNNCNNNNNNNNNNNNNNNNNNNNNTCNCTNCNCNCCCCNCCCNNNNNNNG',
'qual':
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
'sample': 'D11F',
'sample_well': 'C5',
'dye': None,
'polymer': None,
'machine_model': '310 ',
'run_start': '2009-02-19 01:19:30',
'run_finish': '2009-02-19 04:04:15',
},
}
test_data_fake = {
'fake': {
'path': ['Abi', 'fake.ab1'],
}
}
def open_files(test_array):
for trace in test_array:
test_array[trace]['handle'] = open(join(*test_array[trace]['path']), 'rb')
def open_files_wrong_mode(test_array):
for trace in test_array:
test_array[trace]['handle'] = open(join(*test_array[trace]['path']))
def close_files(test_array):
for trace in test_array:
test_array[trace]['handle'].close()
class TestAbi(unittest.TestCase):
def setUp(self):
open_files(test_data)
def tearDown(self):
close_files(test_data)
def test_file_type(self):
"""Test if filetype is ABIF."""
for trace in test_data:
self.assertEqual(test_data[trace]['handle'].read(4), _as_bytes('ABIF'))
def test_seqrecord(self):
"""Test if the extracted seqrecords data are equal to expected values."""
for trace in test_data:
record = SeqIO.read(test_data[trace]['handle'], 'abi')
self.assertEqual(basename(test_data[trace]["path"][-1]).replace('.ab1',''), record.name)
self.assertEqual(test_data[trace]['seq'], str(record.seq))
self.assertEqual(test_data[trace]['qual'], record.letter_annotations['phred_quality'])
self.assertEqual(test_data[trace]['sample'], record.id)
self.assertEqual(test_data[trace]['sample_well'], record.annotations['sample_well'])
self.assertEqual(test_data[trace]['machine_model'], record.annotations['machine_model'])
self.assertEqual(test_data[trace]['run_start'], record.annotations['run_start'])
self.assertEqual(test_data[trace]['run_finish'], record.annotations['run_finish'])
def test_trim(self):
"""Test if trim works."""
for trace in test_data:
record = SeqIO.read(test_data[trace]['handle'], 'abi-trim')
if trace != 'data_empty':
self.assertNotEqual(str(record.seq), test_data[trace]['seq'])
self.assertTrue(str(record.seq) in test_data[trace]['seq'])
else:
self.assertEqual(str(record.seq), test_data[trace]['seq'])
class TestAbiWrongMode(unittest.TestCase):
def test_file_mode(self):
"""Test if exception is raised if file is not opened in 'rb' mode."""
open_files_wrong_mode(test_data)
for trace in test_data:
self.assertRaises(ValueError, SeqIO.read, test_data[trace]['handle'], 'abi')
close_files(test_data)
class TestAbiFake(unittest.TestCase):
def test_file_type(self):
"""Test if error is raised if filetype is not ABIF."""
open_files(test_data_fake)
for trace in test_data_fake:
self.assertRaises(IOError, SeqIO.read, test_data_fake[trace]['handle'], 'abi')
close_files(test_data_fake)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity = 2)
unittest.main(testRunner=runner)