def save(self, filename):
from sourmash_lib import signature
# this is here only for triggering the property load
# before we reopen the file (and overwrite the previous
# content...)
self.data
with open(filename, 'w') as fp:
signature.save_signatures([self.data], fp)
def main():
p = argparse.ArgumentParser()
p.add_argument('sigfile')
p.add_argument('--scaled', default=10000, type=int)
args = p.parse_args()
sigs = list(signature.load_signatures(args.sigfile))
print('loaded {} signatures'.format(len(sigs)), file=sys.stderr)
dsout = []
for sig in sigs:
sig.minhash = sig.minhash.downsample_scaled(args.scaled)
dsout.append(sig)
signature.save_signatures(dsout, sys.stdout)
def test_load_one_succeed(track_abundance):
e1 = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance)
sig1 = SourmashSignature(e1)
x = save_signatures([sig1])
y = load_one_signature(x)
assert sig1 == y
def test_load_minified(track_abundance):
sigfile = utils.get_test_data('genome-s10+s11.sig')
sigs = load_signatures(sigfile)
minified = save_signatures(sigs)
with open(sigfile, 'r') as f:
orig_file = f.read()
assert len(minified) < len(orig_file)
assert '\n' not in minified
def main():
parser = argparse.ArgumentParser()
parser.add_argument('sigfiles', nargs='+')
parser.add_argument('--name', type=str, default='')
args = parser.parse_args()
assert args.name
for sigfile in args.sigfiles:
print('setting name on "%s" to "%s"' % (sigfile, args.name))
with open(sigfile, 'rt') as fp:
sigs = sig.load_signatures(fp)
for s in sigs:
s.d['name'] = args.name
outputname = os.path.basename(sigfile)
with open(outputname, 'wt') as fp:
sig.save_signatures(sigs, fp)
def test_roundtrip(track_abundance):
e = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance)
e.add("AT" * 10)
sig = SourmashSignature(e)
s = save_signatures([sig])
siglist = list(load_signatures(s))
sig2 = siglist[0]
e2 = sig2.minhash
assert sig.similarity(sig2) == 1.0
assert sig2.similarity(sig) == 1.0
def test_load_one_fail_multisig(track_abundance):
e1 = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance)
sig1 = SourmashSignature(e1)
e2 = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance)
sig2 = SourmashSignature(e2)
x = save_signatures([sig1, sig2])
with pytest.raises(ValueError):
y = load_one_signature(x)
def test_roundtrip_empty(track_abundance):
# edge case, but: empty minhash? :)
e = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance)
sig = SourmashSignature(e)
s = save_signatures([sig])
siglist = list(load_signatures(s))
sig2 = siglist[0]
e2 = sig2.minhash
assert sig.similarity(sig2) == 0
assert sig2.similarity(sig) == 0
def test_save_minified(track_abundance):
e1 = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance)
sig1 = SourmashSignature(e1, name="foo")
e2 = sourmash_lib.MinHash(n=1, ksize=25, track_abundance=track_abundance)
sig2 = SourmashSignature(e2, name="bar baz")
x = save_signatures([sig1, sig2])
assert '\n' not in x
assert len(x.split('\n')) == 1
y = list(load_signatures(x))
assert len(y) == 2
assert any(sig.name() == 'foo' for sig in y)
assert any(sig.name() == 'bar baz' for sig in y)
def test_save_load_multisig(track_abundance):
e1 = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance)
sig1 = SourmashSignature(e1)
e2 = sourmash_lib.MinHash(n=1, ksize=25, track_abundance=track_abundance)
sig2 = SourmashSignature(e2)
x = save_signatures([sig1, sig2])
y = list(load_signatures(x))
print(x)
assert len(y) == 2
assert sig1 in y # order not guaranteed, note.
assert sig2 in y
assert sig1 != sig2
def test_roundtrip_max_hash(track_abundance):
e = sourmash_lib.MinHash(n=0,
ksize=20,
track_abundance=track_abundance,
max_hash=10)
e.add_hash(5)
sig = SourmashSignature(e)
s = save_signatures([sig])
siglist = list(load_signatures(s))
sig2 = siglist[0]
e2 = sig2.minhash
assert e.max_hash == e2.max_hash
assert sig.similarity(sig2) == 1.0
assert sig2.similarity(sig) == 1.0
def save(self, filename):
with open(filename, 'w') as fp:
signature.save_signatures([self.data], fp)
def test_load_one_fail_nosig(track_abundance):
x = save_signatures([])
print((x, ))
with pytest.raises(ValueError):
y = load_one_signature(x)
