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from __future__ import print_function
import os.path
import tempfile
import unittest
from textwrap import dedent
from pbcore.io import Vcf4Record
from pbcore.io.VcfIO import merge_vcfs_sorted
def rm_out(fname):
if os.path.exists(fname):
os.remove(fname)
class TestVcfSorting(unittest.TestCase):
vcf_meta = dedent("""\
##fileformat=VCFv4.3
##fileDate=20170328
##source=GenomicConsensusV2.2.0
##reference=ecoliK12_pbi_March2013.fasta
##contig=<ID=ecoliK12_pbi_March2013,length=4642522>
#CHROM POS ID REF ALT QUAL FILTER INFO""")
vcf_recs = [
Vcf4Record.fromString("ecoliK12_pbi_March2013\t84\t.\tTG\tT\t48\tPASS\tDP=53"),
Vcf4Record.fromString("ecoliK12_pbi_March2013\t218\t.\tGA\tG\t47\tPASS\tDP=58"),
Vcf4Record.fromString("ecoliK12_pbi_March2013\t1536\t.\tG\tGC\t47\tPASS\tDP=91")]
@classmethod
def setUpClass(cls):
cls.files = []
for i in range(2):
file_name = "tmp_pbcore_%d.vcf" % i
with open(file_name, "w") as f:
print(cls.vcf_meta, file=f)
recs = cls.vcf_recs[2:] if i == 0 else cls.vcf_recs[:2]
for r in recs:
print(str(r), file=f)
cls.files.append(file_name)
@classmethod
def tearDownClass(cls):
for file_name in cls.files:
if os.path.exists(file_name):
os.remove(file_name)
def test_merge_vcfs_sorted(self):
vcf_out = "tmp_pbcore_merged_sorted.vcf"
merge_vcfs_sorted(self.files, vcf_out)
meta = []
recs = []
with open(vcf_out) as f:
for l in f:
l = l.strip()
if not l:
continue
elif l[0] == "#":
meta.append(l)
else:
recs.append(Vcf4Record.fromString(l))
self.assertEqual(self.vcf_meta.strip().split('\n'), meta)
self.assertEqual(self.vcf_recs, recs)
rm_out(vcf_out)
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