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
|
import os
import pytest
from pyfaidx import FastaVariant, Fasta
path = os.path.dirname(__file__)
os.chdir(path)
@pytest.fixture
def remove_index():
yield
try:
os.remove('data/chr22.fasta.fai')
except EnvironmentError:
pass # some tests may delete this file
def test_fetch_variant(remove_index):
try:
import pysam
fasta = FastaVariant('data/chr22.fasta', 'data/chr22.vcf.gz', hom=True, het=True, as_raw=True)
assert fasta['22'][32330458:32330462] == 'CAGG' # het
assert fasta['22'][32352282:32352286] == 'CAGC' # hom
except (ImportError, IOError):
pytest.skip("pysam not installed.")
def test_fetch_hom_variant(remove_index):
try:
import pysam
fasta = FastaVariant('data/chr22.fasta', 'data/chr22.vcf.gz', hom=True, het=False, as_raw=True)
assert fasta['22'][32330458:32330462] == 'CGGG' # het
assert fasta['22'][32352282:32352286] == 'CAGC' # hom
except (ImportError, IOError):
pytest.skip("pysam not installed.")
def test_fetch_het_variant(remove_index):
try:
import pysam
fasta = FastaVariant('data/chr22.fasta', 'data/chr22.vcf.gz', hom=False, het=True, as_raw=True)
assert fasta['22'][32330458:32330462] == 'CAGG' # het
assert fasta['22'][32352282:32352286] == 'CGGC' # hom
except (ImportError, IOError):
pytest.skip("pysam not installed.")
def test_fetch_chr_not_in_vcf(remove_index):
try:
import pysam
fasta = FastaVariant('data/chr22andfake.fasta', 'data/chr22.vcf.gz', hom=True, het=True, as_raw=True)
assert fasta['fake'][:10] == 'ATCG' # fake is not in vcf
except (ImportError, IOError):
pytest.skip("pysam not installed.")
def test_all_pos(remove_index):
try:
import pysam
fasta = FastaVariant('data/chr22.fasta', 'data/chr22.vcf.gz', hom=True, het=True, as_raw=True)
assert fasta['22'].variant_sites == (16042793, 21833121, 29153196, 29187373, 29187448, 29194610, 29821295, 29821332, 29993842, 32330460, 32352284)
except (ImportError, IOError):
pytest.skip("pysam not installed.")
def test_all_diff(remove_index):
try:
import pysam
fasta = FastaVariant('data/chr22.fasta', 'data/chr22.vcf.gz', hom=True, het=True, as_raw=True)
ref = Fasta('data/chr22.fasta', as_raw=True)
print([(ref['22'][pos-1], fasta['22'][pos-1]) for pos in fasta['22'].variant_sites])
assert all(ref['22'][pos-1] != fasta['22'][pos-1] for pos in fasta['22'].variant_sites)
except (ImportError, IOError):
pytest.skip("pysam not installed.")
|
