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[MRG] Add append option to sbt_index #120

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merged 5 commits into from
May 18, 2017
Merged

[MRG] Add append option to sbt_index #120

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f82b0e1
Add append option to sbt_index
luizirber Jan 20, 2017
02673a2
Remove do_load
luizirber Jan 20, 2017
2007c4b
Fix tests
luizirber May 17, 2017
780b69a
Add help message
luizirber May 17, 2017
5f27b3c
Merge branch 'master' into feature/sbt_append
luizirber May 18, 2017
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9 changes: 7 additions & 2 deletions sourmash_lib/commands.py
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Original file line number Diff line number Diff line change
Expand Up @@ -542,15 +542,20 @@ def sbt_index(args):
help='signatures to load into SBT')
parser.add_argument('-k', '--ksize', type=int, default=None)
parser.add_argument('--traverse-directory', action='store_true')
parser.add_argument('--append', action='store_true', default=False,
help='add signatures to an existing SBT')
parser.add_argument('-x', '--bf-size', type=float, default=1e5)

sourmash_args.add_moltype_args(parser)

args = parser.parse_args(args)
moltype = sourmash_args.calculate_moltype(args)

factory = GraphFactory(1, args.bf_size, 4)
tree = SBT(factory)
if args.append:
tree = SBT.load(args.sbt_name, leaf_loader=SigLeaf.load)
else:
factory = GraphFactory(1, args.bf_size, 4)
tree = SBT(factory)

if args.traverse_directory:
inp_files = list(sourmash_args.traverse_find_sigs(args.signatures))
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46 changes: 46 additions & 0 deletions tests/test_sourmash.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1103,6 +1103,52 @@ def test_do_sourmash_sbt_combine():
assert err.count(filename) == 3


def test_do_sourmash_sbt_index_append():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
testdata2 = utils.get_test_data('short2.fa')
testdata3 = utils.get_test_data('short3.fa')
status, out, err = utils.runscript('sourmash',
['compute', testdata1, testdata2, testdata3],
in_directory=location)

status, out, err = utils.runscript('sourmash',
['sbt_index', 'zzz',
'short.fa.sig', 'short2.fa.sig'],
in_directory=location)

assert os.path.exists(os.path.join(location, 'zzz.sbt.json'))

sbt_name = os.path.join(location, 'zzz',)
sig_loc = os.path.join(location, 'short3.fa.sig')
status, out, err = utils.runscript('sourmash',
['sbt_search', sbt_name, sig_loc])
print(out)

assert testdata1 in err
assert testdata2 in err
assert testdata3 not in err

status, out, err = utils.runscript('sourmash',
['sbt_index', '--append',
'zzz',
'short3.fa.sig'],
in_directory=location)

assert os.path.exists(os.path.join(location, 'zzz.sbt.json'))

sbt_name = os.path.join(location, 'zzz',)
sig_loc = os.path.join(location, 'short3.fa.sig')
status, out, err = utils.runscript('sourmash',
['sbt_search', '--threshold', '0.95',
sbt_name, sig_loc])
print(out)

assert testdata1 not in err
assert testdata2 in err
assert testdata3 in err


def test_do_sourmash_sbt_search_otherdir():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('short.fa')
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