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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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Feature/update drugtable other fixes #16

Closed apetkau closed 6 years ago

apetkau commented 6 years ago

This merge updates the gene/drug mapping table to the latest version, updates command-line options, fixes a few other small issues, and updates the README.md for release. Some of the fixes include:

  1. Auto-fitting column widths in Excel (issue #7), done in Search.py. Also only print 2 decimal places in Excel output.
  2. Inverts command-line options so you have to pass --exclude-negatives and --exclude-resistance-phenotypes to exclude those results (issue #2). Done in Search.py.
  3. Groups together common command-line options. Done in Search.py.
  4. Adds in many command-line options for defining specific output files (for Galaxy tool). Done in Search.py.
apetkau commented 6 years ago

Thanks for the general comments. For version, I guess it's not so important, but there still is a few additions that need to be added. Mainly, I want to add support for the other organisms beyond salmonella for the PointFinder database. That will be for a later release, and I'd like to name that one 1.0.0 and keep this one pre-1.0.

What do you think?

peterk87 commented 6 years ago

@apetkau I think that's a good idea if there's still a major feature you want to add. This software is looking pretty much production ready though!

apetkau commented 6 years ago

@peterk87 thanks for the comment. I think I will keep this release as 0.2.0 and use 1.0.0 for the next release.

apetkau commented 6 years ago

Awesome. Yep, I'm happy with it.