def test_reads_meta(self):
from idiva.io.vcf import proxy as vcf_proxy
with open(vcf_file, mode='r') as fd:
proxy = vcf_proxy(fd)
reference = [
"fileformat=VCFv4.0",
'FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">'
]
candidate = [proxy.meta[0], proxy.meta[-1]]
self.assertListEqual(reference, candidate)
def test_reads_datalines(self):
from idiva.io.vcf import proxy as vcf_proxy
with open(vcf_file, mode='r') as fd:
proxy = vcf_proxy(fd)
reference = [
"20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.",
"20 17330 None T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3",
"20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4",
]
candidate = list(
map(str, at_most_n(proxy.datalines, len(reference))))
self.assertListEqual(reference, candidate)
def test_reads_dataline_number(self):
from idiva.io.vcf import proxy as vcf_proxy
with open(vcf_file, mode='r') as fd:
proxy = vcf_proxy(fd)
self.assertEqual(5, len(list(proxy.datalines)))
def test_needs_open_file(self):
from idiva.io.vcf import proxy as vcf_proxy
with open(vcf_file, mode='r') as fd:
proxy = vcf_proxy(fd)
with self.assertRaises(ValueError):
list(next(iter(proxy.datalines)))
def test_reads_header(self):
from idiva.io.vcf import proxy as vcf_proxy
with open(vcf_file, mode='r') as fd:
proxy = vcf_proxy(fd)
header = "CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003"
self.assertEqual(header, proxy.header)
def test_call(self):
from idiva.io.vcf import proxy as vcf_proxy
with open(vcf_file, mode='r') as fd:
vcf_proxy(fd)