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Use sourmash_args.get_moltype in "sig describe" #907

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Use sourmash_args.get_moltype in "sig describe" #907

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14ab8e1
Use sourmash_args to get moltype for `sourmash sig describe`
olgabot Feb 17, 2020
a4f69ce
Adding a test, can't get sourmash to install with cargo on my new mac…
olgabot Feb 19, 2020
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53 changes: 53 additions & 0 deletions tests/test_cmd_signature.py
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Original file line number Diff line number Diff line change
Expand Up @@ -882,6 +882,59 @@ def test_sig_describe_1_hp(c):
assert cleaned_line in expected_output


def test_describe_bug_905():
# Explicitly test https://github.com/dib-lab/sourmash/issues/905
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data('protein_905.sig')

status, out, err = utils.runscript('sourmash',
['signature', 'describe',
testdata1],
in_directory=location)
expected_output == """== This is sourmash version 3.2.2. ==
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Suggested change
expected_output == """== This is sourmash version 3.2.2. ==
expected_output = """

there is an extra = here, and since versions change all the time we don't want that in the test

== Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==

loaded 3 signatures total.
---
signature filename: test.sig
signature: test.prot
source file: test.prot
md5: 57ae47c24a08a24b630dae80f0c6e256
k=11 molecule=protein num=0 scaled=20 seed=42 track_abundance=1
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I think we can check for this line (and the equivalent on the other two sigs) instead of all the lines in the expected output.

This test as is will always require very stringent formatting of the sig describe output, which we might change in the future.

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Ah that makes sense. I can update the test!

size: 34
signature license: CC0

---
signature filename: test.sig
signature: test.prot
source file: test.prot
md5: 407a774f7a2e13c650ff67255d2056f8
k=11 molecule=dayhoff num=0 scaled=20 seed=42 track_abundance=1
size: 4
signature license: CC0

---
signature filename: test.sig
signature: test.prot
source file: test.prot
md5: 72560192a7f4c23f0b4d71b3eaaa44db
k=11 molecule=hp num=0 scaled=20 seed=42 track_abundance=1
size: 2
signature license: CC0"""
print(out)
print(err)
assert status == 0

# Add final trailing slash for this OS
testdata_dirname = os.path.dirname(testdata1) + os.sep
location = c.location + os.sep

for line in out.splitlines():
cleaned_line = line.strip().replace(
testdata_dirname, '').replace(location, '')
assert cleaned_line in expected_output


@utils.in_tempdir
def test_sig_describe_1_multisig(c):
# get basic info on multiple signatures in a single file
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