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kfuku52 / amalgkit

RNA-seq data amalgamation for a large-scale evolutionary transcriptomics
BSD 3-Clause "New" or "Revised" License
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free keyword config #39

Closed kfuku52 closed 3 years ago

kfuku52 commented 3 years ago

Currently the config files lack the one for free keywords (i.e., keywords that are not associated with a particular Entrez search field), but search_term_tissue.config can be used as is, so why don't we rename it as search_term_keyword.config?

Hego-CCTB commented 3 years ago

makes sense, esp. since a user might look for whole organs, conditions mutants etc. rather than tissue.

Renaming everything, the entrez search command now looks like this: Entrez search term: "Aquilegia coerulea"[Organism] AND (root OR flower OR leaf OR drought stress) AND [...]

I also renamed all relevant instances for "tissue" to "keyword".

kfuku52 commented 3 years ago

Thank you. Sounds good!

kfuku52 commented 3 years ago

It would be nice if you could tag the commit when it's done. https://github.com/kfuku52/amalgkit/commit/73ce56fd3aa28536774b86e6453122c1564e56de

kfuku52 commented 3 years ago

search_term_keyword.config is missing. https://github.com/kfuku52/amalgkit/tree/master/config/test

https://github.com/kfuku52/amalgkit/tree/master/config/viridiplantae_test

Hego-CCTB commented 3 years ago

Ah, they slipped past the commit as unversioned files. Updated in: https://github.com/kfuku52/amalgkit/commit/a5783a4f4e9824be6f2e16bb8268d0d979d0bcc1