forked from biopython/biopython
/
test_EmbossPrimer.py
240 lines (209 loc) · 9.67 KB
/
test_EmbossPrimer.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
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
#!/usr/bin/env python
"""Tests for Primer-based programs in the Emboss suite.
"""
# standard library
import sys
import os
import unittest
# local stuff
from Bio.Emboss import PrimerSearch, Primer3
class Primer3ParseTest(unittest.TestCase):
def setUp(self):
self.test_files = \
[os.path.join("Emboss", "bac_find.primer3"),
os.path.join("Emboss", "cds_forward.primer3"),
os.path.join("Emboss", "cds_reverse.primer3"),
os.path.join("Emboss", "short.primer3"),
os.path.join("Emboss", "internal_oligo.primer3"),
]
def test_simple_parse(self):
"""Make sure that we can use all single target primer3 files.
"""
for file in self.test_files:
# First using read...
h = open(file, "r")
Primer3.read(h)
h.close()
# Now using parse...
h = open(file, "r")
self.assertEqual(1, len(list(Primer3.parse(h))))
h.close()
def test_indepth_regular_parse(self):
"""Make sure we get the data from normal primer3 files okay.
"""
regular_file = self.test_files[0]
h = open(regular_file, "r")
primer_info = Primer3.read(h)
h.close()
self.assertEqual(len(primer_info.primers), 5)
self.assertEqual(primer_info.comments,
"# PRIMER3 RESULTS FOR AC074298\n")
self.assertEqual(primer_info.primers[1].forward_seq,
"CCGGTTTCTCTGGTTGAAAA")
self.assertEqual(primer_info.primers[2].reverse_seq,
"TCACATTCCCAAATGTAGATCG")
self.assertEqual(primer_info.primers[0].size, 218)
self.assertEqual(len(primer_info.primers[0]), 218)
self.assertEqual(primer_info.primers[3].forward_start, 112)
self.assertEqual(primer_info.primers[3].forward_length, 20)
self.assertEqual(primer_info.primers[3].forward_tm, 59.57)
self.assertEqual(primer_info.primers[3].forward_gc, 45.00)
self.assertEqual(primer_info.primers[4].reverse_start, 304)
self.assertEqual(primer_info.primers[4].reverse_length, 22)
self.assertEqual(primer_info.primers[4].reverse_tm, 59.61)
self.assertEqual(primer_info.primers[4].reverse_gc, 40.91)
def test_in_depth_single_parse(self):
"""Make sure we get info right from a single primer find.
"""
file = self.test_files[1]
h = open(file, "r")
primer_info = Primer3.read(h)
h.close()
self.assertEqual(len(primer_info.primers), 5)
self.assertEqual(primer_info.comments,
"# PRIMER3 RESULTS FOR 26964-28647#\n")
self.assertEqual(primer_info.primers[1].reverse_seq, "")
self.assertEqual(primer_info.primers[1].internal_seq, "")
self.assertEqual(primer_info.primers[3].forward_seq, "TGTGATTGCTTGAGCTGGAC")
self.assertEqual(primer_info.primers[3].internal_seq, "")
self.assertEqual(primer_info.primers[3].forward_start, 253)
def test_internal_oligo_single_parse(self):
''' Make sure we can parse an internal oligo file correctly '''
# these files are generated when designing hybridization probes.
file = self.test_files[4]
h = open(file, "r")
primer_info = Primer3.read(h)
h.close()
self.assertEqual(len(primer_info.primers), 5)
self.assertEqual(primer_info.comments,
"# EPRIMER3 RESULTS FOR YNL138W-A\n")
self.assertEqual(primer_info.primers[0].internal_length, 22)
self.assertEqual(primer_info.primers[1].internal_seq,
'TTGCGCTTTAGTTTGAATTGAA')
self.assertEqual(primer_info.primers[2].internal_tm, 58.62)
self.assertEqual(primer_info.primers[3].internal_start, 16)
self.assertEqual(primer_info.primers[4].internal_gc, 35.00)
def test_mutli_record_fwd(self):
"""Test parsing multiple primer sets (NirK forward)"""
h = open(os.path.join("Emboss", "NirK.primer3"))
targets = list(Primer3.parse(h))
h.close()
self.assertEqual(len(targets), 16)
for target in targets:
self.assertEqual(len(target.primers), 5)
self.assertEqual(targets[0].primers[0].forward_seq,
"GCAAACTGAAAAGCGGACTC")
self.assertEqual(targets[0].primers[1].forward_seq,
"GGGACGTACTTTCGCACAAT")
self.assertEqual(targets[0].primers[2].forward_seq,
"GTCTTATGCGTGGTGGAGGT")
self.assertEqual(targets[0].primers[3].forward_seq,
"GTACATCAACATCCGCAACG")
self.assertEqual(targets[0].primers[4].forward_seq,
"CGTACATCAACATCCGCAAC")
self.assertEqual(targets[1].primers[0].forward_seq,
"GGAAGTGCTTCTCGTTTTCG")
self.assertEqual(targets[1].primers[1].forward_seq,
"TACAGAGCGTCACGGATGAG")
self.assertEqual(targets[1].primers[2].forward_seq,
"TTGTCATCGTGCTCTTCGTC")
self.assertEqual(targets[1].primers[3].forward_seq,
"GACTCCAACCTCAGCTTTCG")
self.assertEqual(targets[1].primers[4].forward_seq,
"GGCACGAAGAAGGACAGAAG")
self.assertEqual(targets[15].primers[0].forward_seq,
"TGCTTGAAAATGACGCACTC")
self.assertEqual(targets[15].primers[1].forward_seq,
"CTCGCTGGCTAGGTCATAGG")
self.assertEqual(targets[15].primers[2].forward_seq,
"TATCGCACCAAACACGGTAA")
self.assertEqual(targets[15].primers[3].forward_seq,
"CGATTACCCTCACCGTCACT")
self.assertEqual(targets[15].primers[4].forward_seq,
"TATCGCAACCACTGAGCAAG")
def test_mutli_record_full(self):
"""Test parsing multiple primer sets (NirK full)"""
h = open(os.path.join("Emboss", "NirK_full.primer3"))
targets = list(Primer3.parse(h))
h.close()
self.assertEqual(len(targets), 16)
for target in targets:
self.assertEqual(len(target.primers), 5)
self.assertEqual(targets[15].primers[0].forward_seq,
"ACTCACTTCGGCTGAATGCT")
self.assertEqual(targets[15].primers[1].forward_seq,
"GGCGATTAGCGCTGTCTATC")
self.assertEqual(targets[15].primers[2].forward_seq,
"ACTCACTTCGGCTGAATGCT")
self.assertEqual(targets[15].primers[3].forward_seq,
"TAGGCGTATAGACCGGGTTG")
self.assertEqual(targets[15].primers[4].forward_seq,
"AGCAAGCTGACCACTGGTTT")
self.assertEqual(targets[15].primers[0].reverse_seq,
"CATTTAATCCGGATGCCAAC")
self.assertEqual(targets[15].primers[1].reverse_seq,
"TGGCCTTTCTCTCCTCTTCA")
self.assertEqual(targets[15].primers[2].reverse_seq,
"ATTTAATCCGGATGCCAACA")
self.assertEqual(targets[15].primers[3].reverse_seq,
"CACACATTATTGGCGGTCAC")
self.assertEqual(targets[15].primers[4].reverse_seq,
"TCTGAAACCACCAAGGAAGC")
self.assertEqual(targets[15].primers[0].internal_seq,
"CCCACCAATATTTGGCTAGC")
self.assertEqual(targets[15].primers[1].internal_seq,
"AATCTTCTGTGCACCTTGCC")
self.assertEqual(targets[15].primers[2].internal_seq,
"CCCACCAATATTTGGCTAGC")
self.assertEqual(targets[15].primers[3].internal_seq,
"TGAGCCTGTGTTCCACACAT")
self.assertEqual(targets[15].primers[4].internal_seq,
"CTATGCCCTTCTGCCACAAT")
class PrimersearchParseTest(unittest.TestCase):
def setUp(self):
self.test_files = \
[os.path.join("Emboss", "bac_find.psearch")]
def test_simple_parse(self):
"""Make sure that we can parse all primersearch files.
"""
for file in self.test_files:
h = open(file, "r")
PrimerSearch.read(h)
h.close()
def test_in_depth_normal_parse(self):
"""Make sure the output from a simple primersearch file is correct.
"""
file = self.test_files[0]
h = open(file, "r")
amp_info = PrimerSearch.read(h)
h.close()
self.assertEqual(len(amp_info.amplifiers), 1)
self.assertTrue("Test" in amp_info.amplifiers)
self.assertEqual(len(amp_info.amplifiers["Test"]), 1)
self.assertEqual(amp_info.amplifiers["Test"][0].length, 218)
self.assertEqual(amp_info.amplifiers["Test"][0].hit_info,
"AC074298 AC074298 \n"
"\tTelomere associated sequence for Arabidopsis thaliana "
"TEL1N from chromosome I, complete sequence.\n"
"\tCCGGTTTCTCTGGTTGAAAA hits forward strand at 114 with "
"0 mismatches\n"
"\tTCACATTCCCAAATGTAGATCG hits reverse strand at [114] with "
"0 mismatches")
class PrimerSearchInputTest(unittest.TestCase):
"""Test creating input files for primersearch.
"""
def setUp(self):
pass
def test_primer_representation(self):
"""Make sure we can output primer information correctly.
"""
p_info = PrimerSearch.InputRecord()
p_info.add_primer_set("Test", "GATC", "CATG")
p_info.add_primer_set("Test2", "AATA", "TTAT")
output = str(p_info)
self.assertEqual(output,
"Test GATC CATG\n"
"Test2 AATA TTAT\n")
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity = 2)
unittest.main(testRunner=runner)