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MRG: add support for -E/--extension to sig split #2712

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Aug 12, 2023
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MRG: add support for -E/--extension to sig split #2712

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4 changes: 4 additions & 0 deletions src/sourmash/cli/sig/split.py
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Original file line number Diff line number Diff line change
Expand Up @@ -59,6 +59,10 @@
'--from-file',
help='a text file containing a list of files to load signatures from'
)
subparser.add_argument(

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'-E', '--extension', type=str, default='.sig',
help="write files with this extension ('.sig' by default)"
)
add_ksize_arg(subparser)
add_moltype_args(subparser)
add_picklist_args(subparser)
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4 changes: 2 additions & 2 deletions src/sourmash/sig/__main__.py
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Expand Up @@ -139,8 +139,8 @@
_extend_signatures_with_from_file(args)

output_names = set()
output_scaled_template = '{md5sum}.k={ksize}.scaled={scaled}.{moltype}.dup={dup}.{basename}.sig'
output_num_template = '{md5sum}.k={ksize}.num={num}.{moltype}.dup={dup}.{basename}.sig'
output_scaled_template = '{md5sum}.k={ksize}.scaled={scaled}.{moltype}.dup={dup}.{basename}' + args.extension
output_num_template = '{md5sum}.k={ksize}.num={num}.{moltype}.dup={dup}.{basename}' + args.extension

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if args.output_dir:
if not os.path.exists(args.output_dir):
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36 changes: 36 additions & 0 deletions tests/test_cmd_signature.py
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Expand Up @@ -1456,6 +1456,42 @@ def test_sig_split_3_multisig(c):
assert os.path.exists(c.output(filename))


def test_sig_split_3_multisig_sig_gz(runtmp):
# split 47 and 47+63-multisig.sig with a .sig.gz extension
c = runtmp

sig47 = utils.get_test_data('47.fa.sig')
multisig = utils.get_test_data('47+63-multisig.sig')
c.run_sourmash('sig', 'split', sig47, multisig, '-E', '.sig.gz')

outlist = ['57e2b22f.k=31.scaled=1000.DNA.dup=0.none.sig.gz',
'bde81a41.k=31.scaled=1000.DNA.dup=0.none.sig.gz',
'f033bbd8.k=31.scaled=1000.DNA.dup=0.none.sig.gz',
'87a9aec4.k=31.scaled=1000.DNA.dup=0.none.sig.gz',
'837bf2a7.k=31.scaled=1000.DNA.dup=0.none.sig.gz',
'485c3377.k=31.scaled=1000.DNA.dup=0.none.sig.gz']
for filename in outlist:
assert os.path.exists(c.output(filename))


def test_sig_split_3_multisig_zip(runtmp):
# split 47 and 47+63-multisig.sig with a .zip extension
c = runtmp

sig47 = utils.get_test_data('47.fa.sig')
multisig = utils.get_test_data('47+63-multisig.sig')
c.run_sourmash('sig', 'split', sig47, multisig, '-E', '.zip')

outlist = ['57e2b22f.k=31.scaled=1000.DNA.dup=0.none.zip',
'bde81a41.k=31.scaled=1000.DNA.dup=0.none.zip',
'f033bbd8.k=31.scaled=1000.DNA.dup=0.none.zip',
'87a9aec4.k=31.scaled=1000.DNA.dup=0.none.zip',
'837bf2a7.k=31.scaled=1000.DNA.dup=0.none.zip',
'485c3377.k=31.scaled=1000.DNA.dup=0.none.zip']
for filename in outlist:
assert os.path.exists(c.output(filename))


@utils.in_tempdir
def test_sig_split_4_sbt_prot(c):
# split sbt
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