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arpcard / rgi

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
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Heatmap command error RGI 7.0.0 #211

Closed namnh7 closed 1 year ago

namnh7 commented 1 year ago

I tried the command rgi heatmap -h but it is an error:

rgi: error: argument command: invalid choice: 'heatmap' (choose from 'main', 'tab', 'parser', 'load', 'auto_load', 'clean', 'galaxy', 'database', 'bwt', 'tm', 'card_annotation', 'wildcard_annotation', 'baits_annotation', 'remove_duplicates', 'kmer_build', 'kmer_query')

Is heatmap command removed?

fmaguire commented 1 year ago

heatmap and other visualisation tools for RGI/CARD data are scheduled to be moved to a new tool (https://github.com/arpcard/rgi-viz) that hasn't been released yet. This is part of a simplification of the RGI codebase that should result in more visualisation capacity and a faster/easier to install RGI.

We only really recommend using RGI's stable releases (i.e., from https://github.com/arpcard/rgi/releases/ instead of using the pre-release development code) but to prevent anyone else having the same issue I've reverted the master branch to the last release and moved pre-release code to a dev branch.

If you re-install from the repo/conda or the release page https://github.com/arpcard/rgi/releases/ you will be able to use rgi heatmap as normal.