amalgkit metadata for specific SRA-IDs

kfuku52 / amalgkit

RNA-seq data amalgamation for a large-scale evolutionary transcriptomics

BSD 3-Clause "New" or "Revised" License

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amalgkit metadata for specific SRA-IDs #89

Closed Hego-CCTB closed 2 years ago

Hego-CCTB commented 2 years ago

I started working on recreating your vertebrae dataset for the amalgkit paper and it got me thinking. There will be cases of people trying to recreate datasets or trying to work on sequencing data from specific studies. So they will already know which SRA-IDs they want to run through amalgkit. It could be really useful to have an alternative mode or just .config file, which takes a list of SRA-IDs as input and gets the metadata from just these entries.

@kfuku52 What do you think?

kfuku52 commented 2 years ago

It should already be doable by putting the ids in search_term_keyword.config.

Hego-CCTB commented 2 years ago

Huh, yeah, that seems to work. Never really occured to me, that search_term_keyword.configcan be used with IDs as well.

Nevermind, then. :D

kfuku52 commented 2 years ago

It would be nice to clarify it in the Wiki. Please include it in the metadata's instruction page.

Hego-CCTB commented 2 years ago

yes! Wiki needs an overhaul anyway. I'll take care of it!