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Ignore Underscores within Brackets of Plasmid FASTA Record ID #159

Merged
merged 7 commits into from
Oct 26, 2022
Merged

Ignore Underscores within Brackets of Plasmid FASTA Record ID #159

merged 7 commits into from
Oct 26, 2022

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emarinier
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Fixes #158

Solution is provided by this StackOverflow post: https://stackoverflow.com/a/26634150

@emarinier emarinier changed the title Ignoring underscores within brackets. Ignore Underscores within Brackets of Plasmid FASTA Record ID Oct 25, 2022
@emarinier emarinier self-assigned this Oct 25, 2022
@emarinier emarinier added the bug Something isn't working label Oct 25, 2022
@emarinier emarinier requested a review from apetkau October 25, 2022 17:32
apetkau
apetkau requested changes Oct 25, 2022
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Thanks @emarinier for the quick fix 😄

Could you add a test case in https://github.com/phac-nml/staramr/blob/development/staramr/tests/integration/detection/test_AMRDetectionPlasmid.py ? You can use the same file from this github issue.

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apetkau commented Oct 25, 2022

Also, could you add a message to CHANGELOG.md about this (make a new section for version 0.9.1).

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Okay, it should be good to go now.

@apetkau apetkau self-requested a review October 26, 2022 19:27
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Okay, thanks so much Eric. This is perfect.

I also checked what PlasmidFinder does in this case, and here is the results:

image

So, it's the same as what we're doing. So it all looks good.

@apetkau apetkau merged commit 6e8ded8 into development Oct 26, 2022
@apetkau apetkau deleted the fix/parsing branch October 26, 2022 19:29
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Some plasmidfinder blast results causing staramr to crash
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@emarinier @apetkau