def main(args):
with rsidx.open(args.vcf, 'r') as vcffh:
with sqlite3.connect(args.dbfile) as dbconn:
index(dbconn,
vcffh,
cache_size=args.cache_size,
mmap_size=args.mmap_size)
def test_index_multi(capsys):
vcffile = data_file('chr9-multi.vcf.gz')
with TempFileName(suffix='.rsidx') as idxfile, rsidx.open(vcffile,
'r') as vcffh:
with sqlite3.connect(idxfile) as dbconn:
rsidx.index.index(dbconn, vcffh)
arglist = ['search', vcffile, idxfile, 'rs60995877']
args = rsidx.cli.get_parser().parse_args(arglist)
rsidx.search.main(args)
terminal = capsys.readouterr()
assert terminal.out.count('\trs60995877\t') == 7
def test_index_bogus_rsids():
with NamedTemporaryFile(suffix='.sqlite3') as db:
with sqlite3.connect(db.name) as dbconn:
vcffile = data_file('chr4-sample-corrupted-ids.vcf.gz')
with rsidx.open(vcffile, 'r') as vcffh:
rsidx.index.index(dbconn, vcffh)
c = dbconn.cursor()
query = ('SELECT * FROM rsid_to_coord WHERE rsid IN '
'(538736078, 547329663, 1440788236, 1234497371)')
results = list(c.execute(query))
assert results == [(1234497371, '4', 218446)]
def test_index_multi_rsids():
with NamedTemporaryFile(suffix='.sqlite3') as db:
with sqlite3.connect(db.name) as dbconn:
vcffile = data_file('multiple_id.vcf.gz')
with rsidx.open(vcffile, 'r') as vcffh:
rsidx.index.index(dbconn, vcffh)
c = dbconn.cursor()
query = ('SELECT * FROM rsid_to_coord WHERE rsid IN '
'(72634902, 145742571)')
results = list(c.execute(query))
assert sorted(results) == sorted([(72634902, '1', 1900106),
(145742571, '1', 1900106)])
def test_index(cachesize, mmapsize):
with NamedTemporaryFile(suffix='.sqlite3') as db:
with sqlite3.connect(db.name) as dbconn:
with rsidx.open(data_file('chr17-sample.vcf.gz'), 'r') as vcffh:
rsidx.index.index(dbconn,
vcffh,
cache_size=cachesize,
mmap_size=mmapsize,
logint=10)
c = dbconn.cursor()
query = ('SELECT * FROM rsid_to_coord WHERE rsid IN '
'(1238461543, 1472751972)')
results = list(c.execute(query))
assert sorted(results) == sorted([(1238461543, '17', 624973),
(1472751972, '17', 132359)])
def test_search_cli(doheader, numlines, suffix):
with NamedTemporaryFile(suffix=suffix) as outfile:
arglist = [
'search',
data_file('chr17-sample.vcf.gz'),
data_file('chr17-sample.rsidx'), '--out', outfile.name,
'rs1472751972', 'rs1287502205', 'rs897983471', 'rs1172219431',
'rs189123651'
]
args = rsidx.cli.get_parser().parse_args(arglist)
args.header = doheader
rsidx.search.main(args)
with rsidx.open(outfile.name, 'r') as fh:
outlines = fh.read().strip().split('\n')
assert len(outlines) == numlines
def main(args):
if os.path.exists(args.idx):
message = 'WARNING: index file "{:s}" exists'.format(args.idx)
if args.force:
message += ', overwriting'
try:
os.unlink(args.idx)
except FileNotFoundError: # prevent exploits # pragma: no cover
pass
else:
message += ', stubbornly refusing to proceed'
print('[rsidx]', message, file=sys.stderr)
if not args.force:
raise SystemExit
with rsidx.open(args.vcf, 'r') as vcffh:
with sqlite3.connect(args.idx) as dbconn:
index(dbconn, vcffh, cache_size=args.cache_size,
mmap_size=args.mmap_size)
def main(args):
conn = sqlite3.connect(args.dbfile)
with rsidx.open(args.out, 'w') as out:
for line in search(args.rsid, conn, args.vcf, header=args.header):
print(line, end='', file=out)
conn.close()
def test_open():
with NamedTemporaryFile() as tf:
with pytest.raises(ValueError, match=r'invalid mode "rwx"'):
with rsidx.open(tf.name, 'rwx') as fh:
pass
