def test_meta_parsing(self):
vi = VcfIterator(get_vcf_file_obj(None))
meta = vi.getMeta()
self.assertEquals(
meta['FORMAT'],
[
{
'Description': 'Genotype',
'Type': 'String',
'ID': 'GT',
'Number': '1'
},
{
'Description': 'Genotype Quality',
'Type': 'Integer',
'ID': 'GQ',
'Number': '1'
},
{
'Description': 'Read Depth',
'Type': 'Integer',
'ID': 'DP',
'Number': '1'
},
{
'Description': 'Haplotype Quality',
'Type': 'Integer',
'ID': 'HQ',
'Number': '2'
}
]
)
import json
import sys
import argparse
from vcfiterator import VcfIterator
parser = argparse.ArgumentParser(
"Iterates over a .vcf file, outputting one JSON structure per line")
parser.add_argument("vcf_file", help="Path to .vcf file")
parser.add_argument("--pretty", action="store_true", help="Pretty print JSON")
args = parser.parse_args()
path = args.vcf_file
v = VcfIterator(path)
for value in v.iter():
kw = {}
if args.pretty:
kw['indent'] = 4
print(json.dumps(value, **kw))
def get_data(self):
v = '20\t14370\trs6054257\tG\tA\t29\tPASS\tNS=3;DP=14;AF=0.5;DB;H2\tGT:GQ:DP:HQ\t0|0:48:1:51,51\t1|0:48:8:51,51\t1/1:43:5:.,.'
vi = VcfIterator(get_vcf_file_obj(v))
return list(vi.iter())[0]
def test_get_samples(self):
vi = VcfIterator(get_vcf_file_obj(None))
self.assertEquals(
vi.getSamples(),
['TESTSAMPLE1', 'TESTSAMPLE2', 'TESTSAMPLE3']
)