-
Notifications
You must be signed in to change notification settings - Fork 8
/
test_vcfnp.py
284 lines (223 loc) · 8.99 KB
/
test_vcfnp.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
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
"""
Some simple unit tests for the vcfnp extension.
"""
import os
from vcfnp import variants, calldata, EFF_DEFAULT_DTYPE, eff_default_transformer, calldata_2d
import vcfnp
from nose.tools import eq_, assert_almost_equal
import re
import numpy as np
def test_variants():
a = variants('fixture/sample.vcf', arities={'ALT': 2, 'AC': 2})
print repr(a)
eq_(9, len(a))
eq_('19', a[0]['CHROM'])
eq_(111, a[0]['POS'])
eq_('rs6054257', a[2]['ID'])
eq_('A', a[0]['REF'])
eq_('ATG', a[8]['ALT'][1])
eq_(10.0, a[1]['QUAL'])
eq_(True, a[2]['FILTER']['PASS'])
eq_(False, a[3]['FILTER']['PASS'])
eq_(True, a[3]['FILTER']['q10'])
eq_(2, a[0]['num_alleles'])
eq_(False, a[5]['is_snp'])
# INFO fields
eq_(3, a[2]['NS'])
eq_(.5, a[2]['AF'])
eq_(True, a[2]['DB'])
eq_((3, 1), tuple(a[6]['AC']))
def test_variants_flatten_filter():
a = variants('fixture/sample.vcf', flatten_filter=True)
eq_(True, a[2]['FILTER_PASS'])
eq_(False, a[3]['FILTER_PASS'])
eq_(True, a[3]['FILTER_q10'])
def test_variants_region():
a = variants('fixture/sample.vcf.gz', region='20')
eq_(6, len(a))
def test_variants_region_empty():
a = variants('fixture/sample.vcf.gz', region='18')
eq_(0, len(a))
a = variants('fixture/sample.vcf.gz', region='19:113-200')
eq_(0, len(a))
def test_variants_count():
a = variants('fixture/sample.vcf', count=3)
eq_(3, len(a))
def test_variants_exclude_fields():
a = variants('fixture/sample.vcf', exclude_fields=['ID', 'FILTER'])
assert 'CHROM' in a.dtype.names
assert 'ID' not in a.dtype.names
assert 'FILTER' not in a.dtype.names
def test_variants_slice():
a = variants('fixture/sample.vcf.gz')
eq_('rs6054257', a['ID'][2])
a = variants('fixture/sample.vcf.gz', slice=(0, None, 2))
eq_('rs6054257', a['ID'][1])
def test_calldata():
a = calldata('fixture/sample.vcf')
print repr(a)
eq_('0|0', a[0]['NA00001']['GT'])
eq_(True, a[0]['NA00001']['is_called'])
eq_(True, a[0]['NA00001']['is_phased'])
eq_((0, 0), tuple(a[0]['NA00001']['genotype']))
eq_((-1, -1), tuple(a[6]['NA00003']['genotype']))
eq_((-1, -1), tuple(a[7]['NA00003']['genotype']))
eq_((10, 10), tuple(a[0]['NA00001']['HQ']))
#>>> a['NA00001']
#array([(True, True, [0, 0], '0|0', 0, 0, [10, 10]),
# (True, True, [0, 0], '0|0', 0, 0, [10, 10]),
# (True, True, [0, 0], '0|0', 48, 1, [51, 51]),
# (True, True, [0, 0], '0|0', 49, 3, [58, 50]),
# (True, True, [1, 2], '1|2', 21, 6, [23, 27]),
# (True, True, [0, 0], '0|0', 54, 0, [56, 60]),
# (True, False, [0, 1], '0/1', 0, 4, [0, 0]),
# (True, False, [0, 0], '0/0', 0, 0, [0, 0]),
# (True, False, [0, -1], '0', 0, 0, [0, 0])],
# dtype=[('is_called', '|b1'), ('is_phased', '|b1'), ('genotype', '|i1', (2,)), ('GT', '|S3'), ('GQ', '|u1'), ('DP', '<u2'), ('HQ', '<i4', (2,))])
def test_calldata_region():
a = calldata('fixture/sample.vcf.gz', region='20')
eq_(6, len(a))
def test_calldata_region_empty():
a = calldata('fixture/sample.vcf.gz', region='18')
eq_(0, len(a))
a = calldata('fixture/sample.vcf.gz', region='19:113-200')
eq_(0, len(a))
def test_condition():
V = variants('fixture/sample.vcf')
eq_(9, len(V))
C = calldata('fixture/sample.vcf', condition=V['FILTER']['PASS'])
eq_(5, len(C))
Vf = variants('fixture/sample.vcf', condition=V['FILTER']['PASS'])
eq_(5, len(Vf))
def test_variable_calldata():
C = calldata('fixture/test1.vcf')
eq_((1, 0), tuple(C['test2']['AD'][0]))
eq_((1, 0), tuple(C['test2']['AD'][1]))
eq_((1, 0), tuple(C['test2']['AD'][2]))
eq_('.', C['test2']['GT'][0])
eq_('0', C['test2']['GT'][1])
eq_('1', C['test2']['GT'][2])
def test_missing_calldata():
C = calldata('fixture/test1.vcf')
eq_('.', C['test3']['GT'][2])
eq_((-1, -1), tuple(C['test3']['genotype'][2]))
eq_('./.', C['test4']['GT'][2])
eq_((-1, -1), tuple(C['test4']['genotype'][2]))
def test_override_vcf_types():
V = variants('fixture/test4.vcf')
eq_(0, V['MQ0FractionTest'][2])
V = variants('fixture/test4.vcf', vcf_types={'MQ0FractionTest': 'Float'})
assert_almost_equal(0.03, V['MQ0FractionTest'][2], )
def test_variants_transformers():
V = variants('fixture/test12.vcf',
dtypes={'EFF': EFF_DEFAULT_DTYPE},
arities={'EFF': 1},
transformers={'EFF': eff_default_transformer()})
eq_('STOP_GAINED', V['EFF']['Effect'][0])
eq_('HIGH', V['EFF']['Effect_Impact'][0])
eq_('NONSENSE', V['EFF']['Functional_Class'][0])
eq_('Cag/Tag', V['EFF']['Codon_Change'][0])
eq_('Q236*', V['EFF']['Amino_Acid_Change'][0])
eq_(749, V['EFF']['Amino_Acid_Length'][0])
eq_('NOC2L', V['EFF']['Gene_Name'][0])
eq_('.', V['EFF']['Transcript_BioType'][0])
eq_(1, V['EFF']['Gene_Coding'][0])
eq_('NM_015658', V['EFF']['Transcript_ID'][0])
eq_(-1, V['EFF']['Exon'][0])
eq_('NON_SYNONYMOUS_CODING', V['EFF']['Effect'][1])
eq_('MODERATE', V['EFF']['Effect_Impact'][1])
eq_('MISSENSE', V['EFF']['Functional_Class'][1])
eq_('gTt/gGt', V['EFF']['Codon_Change'][1])
eq_('V155G', V['EFF']['Amino_Acid_Change'][1])
eq_(-1, V['EFF']['Amino_Acid_Length'][1])
eq_('PF3D7_0108900', V['EFF']['Gene_Name'][1])
eq_('.', V['EFF']['Transcript_BioType'][1])
eq_(-1, V['EFF']['Gene_Coding'][1])
eq_('rna_PF3D7_0108900-1', V['EFF']['Transcript_ID'][1])
eq_(1, V['EFF']['Exon'][1])
eq_('.', V['EFF']['Effect'][2])
eq_('.', V['EFF']['Effect_Impact'][2])
eq_('.', V['EFF']['Functional_Class'][2])
eq_('.', V['EFF']['Codon_Change'][2])
eq_('.', V['EFF']['Amino_Acid_Change'][2])
eq_(-1, V['EFF']['Amino_Acid_Length'][2])
eq_('.', V['EFF']['Gene_Name'][2])
eq_('.', V['EFF']['Transcript_BioType'][2])
eq_(-1, V['EFF']['Gene_Coding'][2])
eq_('.', V['EFF']['Transcript_ID'][2])
eq_(-1, V['EFF']['Exon'][2])
def test_svlen():
# V = variants('fixture/test13.vcf').view(np.recarray)
# assert hasattr(V, 'svlen')
# eq_(0, V.svlen[0])
# eq_(1, V.svlen[1])
# eq_(-1, V.svlen[2])
# eq_(3, V.svlen[3])
# eq_(3, V.svlen[4])
V = variants('fixture/test13.vcf', arities={'svlen': 2}).view(np.recarray)
# assert hasattr(V, 'svlen')
# eq_((3, 0), tuple(V.svlen[3]))
# eq_((3, -2), tuple(V.svlen[4]))
def test_duplicate_field_definitions():
V = variants('fixture/test10.vcf')
# should not raise, but print useful message to stderr
C = calldata('fixture/test10.vcf')
# should not raise, but print useful message to stderr
def test_missing_info_definition():
# INFO field DP not declared in VCF header
V = variants('fixture/test14.vcf', fields=['DP'])
eq_('14', V[2]['DP']) # default is string
V = variants('fixture/test14.vcf', fields=['DP'], vcf_types={'DP':'Integer'})
eq_(14, V[2]['DP'])
# what about a field which isn't present at all?
V = variants('fixture/test14.vcf', fields=['FOO'])
eq_('', V[2]['FOO']) # default missing value for string field
def test_missing_format_definition():
# FORMAT field DP not declared in VCF header
C = calldata('fixture/test14.vcf', fields=['DP'], vcf_types={'DP':'Integer'})
eq_(1, C[2]['NA00001']['DP'])
def test_explicit_pass_definition():
# explicit PASS FILTER definition
V = variants('fixture/test16.vcf')
# should not raise
def test_caching():
vcf_fn = 'fixture/sample.vcf.gz'
cache_fn = vcfnp._mk_cache_fn(vcf_fn, type='variants')
if os.path.exists(cache_fn):
os.remove(cache_fn)
A = variants(vcf_fn, cache=True, verbose=True)
A2 = np.load(cache_fn)
assert np.all(A == A2)
cache_fn = vcfnp._mk_cache_fn(vcf_fn, type='calldata')
if os.path.exists(cache_fn):
os.remove(cache_fn)
A = calldata(vcf_fn, cache=True, verbose=True)
A2 = np.load(cache_fn)
assert np.all(A == A2)
cache_fn = vcfnp._mk_cache_fn(vcf_fn, type='calldata_2d')
if os.path.exists(cache_fn):
os.remove(cache_fn)
A = calldata_2d(vcf_fn, cache=True, verbose=True)
A2 = np.load(cache_fn)
assert np.all(A == A2)
def test_caching_cachedir():
vcf_fn = 'fixture/sample.vcf.gz'
cachedir = 'fixture/custom.vcfnp_cache/foo'
cache_fn = vcfnp._mk_cache_fn(vcf_fn, type='variants', cachedir=cachedir)
if os.path.exists(cache_fn):
os.remove(cache_fn)
A = variants(vcf_fn, cache=True, verbose=True, cachedir=cachedir)
A2 = np.load(cache_fn)
assert np.all(A == A2)
cache_fn = vcfnp._mk_cache_fn(vcf_fn, type='calldata', cachedir=cachedir)
if os.path.exists(cache_fn):
os.remove(cache_fn)
A = calldata(vcf_fn, cache=True, verbose=True, cachedir=cachedir)
A2 = np.load(cache_fn)
assert np.all(A == A2)
cache_fn = vcfnp._mk_cache_fn(vcf_fn, type='calldata_2d', cachedir=cachedir)
if os.path.exists(cache_fn):
os.remove(cache_fn)
A = calldata_2d(vcf_fn, cache=True, verbose=True, cachedir=cachedir)
A2 = np.load(cache_fn)
assert np.all(A == A2)