def test_liftover_chain_file():
'''
This is just a smoke test. (NB: it loads actual hg17-to-hg18.over.chain, attempting to download it to cache).
'''
# Simple example
data = example_1 + example_2
chains = LiftOverChainFile._load_chains(StringIO(data))
assert len(chains) == 2
index = LiftOverChainFile._index_chains(chains)
assert len(index) == 1
assert len(index['chrY']) == 9+4
assert len(index['chrY'].query(25985406)) == 2
assert len(index['chrY'].query(25985403)) == 1
assert len(index['chrY'].query(25985402)) == 0
assert len(index['chrY'].query(25985405)) == 1
assert index['chrY'].query(25985405)[0][2][2] == chains[0]
cf = LiftOverChainFile(StringIO(data))
assert len(cf.query('chrY', 25985406)) == 2
assert len(cf.query('chrY', 25985403)) == 1
assert len(cf.query('chrY', 25985402)) == 0
assert len(cf.query('chrY', 25985405)) == 1
assert cf.query('chrY', 25985405)[0][2][2] == cf.chains[0]
assert cf.query('chrZ', 25985405) is None
# hg17-to-hg18 example
f = open_liftover_chain_file('hg17', 'hg18')
chains = LiftOverChainFile._load_chains(f)
assert len(chains) > 1000
f.close()
index = LiftOverChainFile._index_chains(chains)
assert len(index) >= 22
def test_liftover_chain_file():
'''
This is just a smoke test. (NB: it loads actual hg17-to-hg18.over.chain, attempting to download it to cache).
'''
# Simple example
data = example_1 + example_2
chains = LiftOverChainFile._load_chains(StringIO(data))
assert len(chains) == 2
index = LiftOverChainFile._index_chains(chains)
assert len(index) == 1
assert len(index['chrY']) == 9 + 4
assert len(index['chrY'].query(25985406)) == 2
assert len(index['chrY'].query(25985403)) == 1
assert len(index['chrY'].query(25985402)) == 0
assert len(index['chrY'].query(25985405)) == 1
assert index['chrY'].query(25985405)[0][2][2] == chains[0]
cf = LiftOverChainFile(StringIO(data))
assert len(cf.query('chrY', 25985406)) == 2
assert len(cf.query('chrY', 25985403)) == 1
assert len(cf.query('chrY', 25985402)) == 0
assert len(cf.query('chrY', 25985405)) == 1
assert cf.query('chrY', 25985405)[0][2][2] == cf.chains[0]
assert cf.query('chrZ', 25985405) is None
# hg17-to-hg18 example
f = open_liftover_chain_file('hg17', 'hg18')
chains = LiftOverChainFile._load_chains(f)
assert len(chains) > 1000
f.close()
index = LiftOverChainFile._index_chains(chains)
assert len(index) >= 22
def test_open_liftover_chain_file():
if SKIP_TEST:
return
# No-web, no-cache, must return none
f = open_liftover_chain_file(from_db, to_db, search_dir=None, cache_dir=None, use_web=False, write_cache=False)
assert f is None
assert not os.path.exists(cache_dir)
# No-web, cache, nonexistent search dir, must return none
f = open_liftover_chain_file(from_db, to_db, search_dir=search_dir, cache_dir=cache_dir, use_web=False, write_cache=True)
assert f is None
assert not os.path.exists(cache_dir)
# Web, no write cache, nonexistent search dir, must open temp file
f = open_liftover_chain_file(from_db, to_db, search_dir=search_dir, cache_dir=cache_dir, use_web=True, write_cache=False)
assert f is not None
assert not os.path.exists(cache_dir)
ln = f.readline()
assert ln.startswith(b'##matrix')
f.close()
os.unlink(f.name)
# Web, nonexistent db. Must not modify cache.
f = open_liftover_chain_file(from_db, 'blablabla', search_dir=search_dir, cache_dir=cache_dir, use_web=True, write_cache=True)
assert f is None
assert not os.path.exists(cache_dir)
# Web, write cache, nonexistent search dir, must save to cache, creating cache dir
f = open_liftover_chain_file(from_db, to_db, search_dir=search_dir, cache_dir=cache_dir, use_web=True, write_cache=True)
assert f is not None
assert os.path.exists(cache_dir)
ln = f.readline()
assert ln.startswith(b'##matrix')
f.close()
# No web, file in cache, nonexistent search dir, must exist
f = open_liftover_chain_file(from_db, to_db, search_dir=search_dir, cache_dir=cache_dir, use_web=False, write_cache=True)
assert f is not None
ln = f.readline()
assert ln.startswith(b'##matrix')
f.close()
# No web, no file in cache, nonexistent db
f = open_liftover_chain_file(from_db, 'blablabla', search_dir=search_dir, cache_dir=cache_dir, use_web=False, write_cache=True)
assert f is None
os.mkdir(search_dir)
# File both in cache and search_dir. Assert search_dir is used and uncompressed file is preferred
filename = '%sTo%s.over.chain' % (from_db, to_db[0].upper() + to_db[1:])
filename = os.path.join(search_dir, filename)
fout = open(filename, 'wb')
fout.write(b'test-test')
fout.close()
f = open_liftover_chain_file(from_db, to_db, search_dir=search_dir, cache_dir=cache_dir, use_web=True, write_cache=True)
assert f is not None
assert f.readline() == b'test-test'
f.close()
# gzipped file is preferred
fout = gzip.open(filename + '.gz', 'w')
fout.write(b'test-test-gzip')
fout.close()
f = open_liftover_chain_file(from_db, to_db, search_dir=search_dir, cache_dir=cache_dir, use_web=True, write_cache=True)
assert f is not None
assert f.readline() == b'test-test-gzip'
f.close()
os.unlink(filename)
os.unlink(filename + '.gz')
def test_open_liftover_chain_file():
if SKIP_TEST:
return
# No-web, no-cache, must return none
f = open_liftover_chain_file(from_db,
to_db,
search_dir=None,
cache_dir=None,
use_web=False,
write_cache=False)
assert f is None
assert not os.path.exists(cache_dir)
# No-web, cache, nonexistent search dir, must return none
f = open_liftover_chain_file(from_db,
to_db,
search_dir=search_dir,
cache_dir=cache_dir,
use_web=False,
write_cache=True)
assert f is None
assert not os.path.exists(cache_dir)
# Web, no write cache, nonexistent search dir, must open temp file
f = open_liftover_chain_file(from_db,
to_db,
search_dir=search_dir,
cache_dir=cache_dir,
use_web=True,
write_cache=False)
assert f is not None
assert not os.path.exists(cache_dir)
ln = f.readline()
assert ln.startswith(b'##matrix')
f.close()
os.unlink(f.name)
# Web, nonexistent db. Must not modify cache.
f = open_liftover_chain_file(from_db,
'blablabla',
search_dir=search_dir,
cache_dir=cache_dir,
use_web=True,
write_cache=True)
assert f is None
assert not os.path.exists(cache_dir)
# Web, write cache, nonexistent search dir, must save to cache, creating cache dir
f = open_liftover_chain_file(from_db,
to_db,
search_dir=search_dir,
cache_dir=cache_dir,
use_web=True,
write_cache=True)
assert f is not None
assert os.path.exists(cache_dir)
ln = f.readline()
assert ln.startswith(b'##matrix')
f.close()
# No web, file in cache, nonexistent search dir, must exist
f = open_liftover_chain_file(from_db,
to_db,
search_dir=search_dir,
cache_dir=cache_dir,
use_web=False,
write_cache=True)
assert f is not None
ln = f.readline()
assert ln.startswith(b'##matrix')
f.close()
# No web, no file in cache, nonexistent db
f = open_liftover_chain_file(from_db,
'blablabla',
search_dir=search_dir,
cache_dir=cache_dir,
use_web=False,
write_cache=True)
assert f is None
os.mkdir(search_dir)
# File both in cache and search_dir. Assert search_dir is used and uncompressed file is preferred
filename = '%sTo%s.over.chain' % (from_db, to_db[0].upper() + to_db[1:])
filename = os.path.join(search_dir, filename)
fout = open(filename, 'wb')
fout.write(b'test-test')
fout.close()
f = open_liftover_chain_file(from_db,
to_db,
search_dir=search_dir,
cache_dir=cache_dir,
use_web=True,
write_cache=True)
assert f is not None
assert f.readline() == b'test-test'
f.close()
# gzipped file is preferred
fout = gzip.open(filename + '.gz', 'w')
fout.write(b'test-test-gzip')
fout.close()
f = open_liftover_chain_file(from_db,
to_db,
search_dir=search_dir,
cache_dir=cache_dir,
use_web=True,
write_cache=True)
assert f is not None
assert f.readline() == b'test-test-gzip'
f.close()
os.unlink(filename)
os.unlink(filename + '.gz')