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[MRG] added --name to merge #1480

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merged 6 commits into from
Apr 30, 2021
Merged

[MRG] added --name to merge #1480

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90a77d7
added --name to merge
hehouts Apr 22, 2021
fff6ae4
Merge branch 'latest' into add/merge_name
bluegenes Apr 23, 2021
470593d
added test for --name when merging
hehouts Apr 29, 2021
b058970
Merge branch 'add/merge_name' of https://github.com/dib-lab/sourmash …
hehouts Apr 29, 2021
fd1e6f9
fixed --name when merging test
hehouts Apr 29, 2021
fcdfce2
Merge branch 'latest' of https://github.com/dib-lab/sourmash into add…
hehouts Apr 29, 2021
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4 changes: 4 additions & 0 deletions src/sourmash/cli/sig/merge.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,10 @@ def subparser(subparsers):
'--flatten', action='store_true',
help='remove abundances from all signatures'
)
subparser.add_argument(
'--name',
help='rename merged signature'
)
add_ksize_arg(subparser, 31)
add_moltype_args(subparser)

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2 changes: 1 addition & 1 deletion src/sourmash/sig/__main__.py
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Expand Up @@ -382,7 +382,7 @@ def merge(args):
error("no signatures to merge!?")
sys.exit(-1)

merged_sigobj = sourmash.SourmashSignature(mh)
merged_sigobj = sourmash.SourmashSignature(mh, name=args.name)

with FileOutput(args.output, 'wt') as fp:
sourmash.save_signatures([merged_sigobj], fp=fp)
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19 changes: 19 additions & 0 deletions tests/test_cmd_signature.py
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Expand Up @@ -90,6 +90,25 @@ def test_sig_merge_1_multisig(c):
assert actual_merge_sig.minhash == test_merge_sig.minhash


@utils.in_tempdir
def test_sig_merge_1_name(c):
# check name arg
sig2 = utils.get_test_data('2.fa.sig')
sig63 = utils.get_test_data('63.fa.sig')

assignedSigName = 'SIG_NAME'
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for future reference, we typically use non-CamelCase variables for things that aren't class names. So it's MinHash and SourmashSignature but load_signature. In this case, I would suggest assigned_sig_name. As this is a test, however, there's no need to change it, this is just an FYI!

outsig = c.output('merged2and63.sig')

c.run_sourmash('sig', 'merge', sig2, sig63, '--dna', '-k', '31', '-o', "merged2and63.sig", '--name', assignedSigName )

test_merge_sig = sourmash.load_one_signature(outsig)

print("outsig", outsig)
print("xx_test_merge_sig.name", test_merge_sig.name)

assert assignedSigName == test_merge_sig.name


@utils.in_tempdir
def test_sig_merge_1_ksize_moltype(c):
# check ksize, moltype args
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