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Add emmtyper, update shigapass and fix quast #92

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merged 9 commits into from
Oct 10, 2024
Merged

Add emmtyper, update shigapass and fix quast #92

merged 9 commits into from
Oct 10, 2024

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ryanjameskennedy
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@ryanjameskennedy ryanjameskennedy commented Oct 7, 2024 •
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Added

  • Added emmtyper and parser

Fixed

Changed

  • Changed Shigapass models to be consistent with other typing models
  • Changed Shigapass parsers to be consistent with other typing parsers
  • Changed ref genome related variables to be optional in quast

mhkc
mhkc requested changes Oct 8, 2024
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Also the tests are failing.

prp/parse/typing.py Outdated Show resolved Hide resolved
prp/parse/typing.py Outdated Show resolved Hide resolved
prp/parse/phenotype/emmtyper.py Outdated Show resolved Hide resolved
prp/models/phenotype.py Outdated Show resolved Hide resolved
prp/models/phenotype.py Outdated Show resolved Hide resolved
prp/models/phenotype.py Outdated Show resolved Hide resolved
ryanjameskennedy
ryanjameskennedy commented Oct 8, 2024
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mhkc
mhkc approved these changes Oct 10, 2024
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Looks good. Great that you added some tests as well!

@ryanjameskennedy ryanjameskennedy merged commit ba8c9b3 into master Oct 10, 2024
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@ryanjameskennedy ryanjameskennedy deleted the 91-add-emmtyper branch October 10, 2024 13:06
@ryanjameskennedy ryanjameskennedy linked an issue Nov 11, 2024 that may be closed by this pull request
Add emmtyper to output #91
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Add emmtyper to output
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@ryanjameskennedy @mhkc