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phac-nml / staramr

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
Apache License 2.0
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Update database #22

Closed apetkau closed 6 years ago

apetkau commented 6 years ago

This makes a few minor changes to staramr:

  1. I updated the default ResFinder/PointFinder databases to fix issues with some phenotypes showing as unknown.
    1. Part of this update also includes updating some entries in the mapping from gene to phenotype.
  2. I fixed a regex expression for extracting gene/variant/accession, which was causing issues with accessions with underscores _ in them (e.g., NC_003197). This includes an integration test for this case.
  3. I made it so that STDERR of makeblastdb will get shown on an error. Specifically, errors get shown in cases where you have a fasta input file with duplicate sequence IDs (e.g., with two sequences with id >sequence).
  4. I updated the tutorial to reflect new database changes.
apetkau commented 6 years ago

Thanks @peterk87, changed header in 9c7d47e