Add antimicrobial resistance annotations #23
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We add a new argument --amr argument to the run script and use amrfinder to search for antibiotics resistances when the argument is set. For now, amrfinder can only be run as a container.
This is a temporary hack that allows to add zDB specific methods to the DB class. In future refactoring we will move at least part of the db_utils to the zDB repo so will see then what refactoring is necessary.
These URLs were broken by auto PEP8 formatting.
This is necessary to be able to import the zdb.database module.
It seems pycodestyle has a bug in handling f-strings with format specifiers, introducing white space after the colon
tpillone
approved these changes
Dec 19, 2023
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Nice work! |
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Ok I've added the gene with a link to the HMM profile, but I left the "scope" column, as this is pretty important (if unclear). I've added a tooltip to the table to send users to the AMRFinderPlus documentation for more information on the fields. |
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With this PR we add a pipeline to extract AMR annotations using the AMRFinderPlus software and add them to the database. I also added the annotations to the locus and orthogroup views.
Also note that:
Screenshot of the annotations on a locus tag view
