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legumeinfo / LIS-autocontent

Scrapes the LIS datastore and populates various configs and databases for deployment
Apache License 2.0
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populate-jbrowse2: add refNameAliases when available #30

Open nathanweeks opened 9 months ago

nathanweeks commented 9 months ago

Could the populate-jbrowse2 subcommand support per-assembly refNameAliases file (like the jbrowse add-assembly --refNameAliases option: https://jbrowse.org/jb2/docs/cli/#jbrowse-add-assembly-sequence)?

I'm not entirely sure what the CLI would look like. One suggestion is perhaps populate-jbrowse2 --refNameAliases_dir=<path>, where <path> is a path to a directory of refNameAliases TSV files named, e.g., <name>.txt; for each reference assembly name that is encountered in the yml config files, if <path>/<name>.txt exists, then a refNameAliases property is added to the output config.json. Could be other ways to implement this too.

adf-ncgr commented 9 months ago

Thanks @nathanweeks and sorry for the delayed response. It's a good idea, my initial reaction is that we ought to have a standardized (but optional) file resident in the datastore that iff present autocontent would just pass along as a URL for the --refNameAliases option value. I think that's pretty similar to what you suggested, except that there would be no option on the populate-jbrowse2 subcommand, it would just make it happen depending on the state of the datastore content. Would that work for your intended uses?

adf-ncgr commented 9 months ago

PS. IIRC, you can have a single tab-delimited file with multiple aliases per record, but if that isn't the case having a directory for these files as you suggested might be needed