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johnchase / cual-id

A package for creating and managing sample identifiers in comparative -omics datasets.
BSD 3-Clause "New" or "Revised" License
23 stars 7 forks source link

Couple ideas for cual-id after using it for 2 large projects #44

Open jcocking opened 6 years ago

jcocking commented 6 years ago

My lab has been using the cual-id system for our barcodes for 2 large projects. It has worked great for us. Having made over 800 barcodes and working with them on a daily basis, we have noticed 2 things that we think could be improved, as a suggestion.

  1. When there's an "e" as the second to last character in the barcode, excel recognizes it as an exponential number and you have to manually change the format of the cell so that it displays correctly.
  2. With many students working on this project, and people having different handwriting styles, we've noticed some mix ups between a "6" and a "b". Just thought I would tell you about these after working with so many of your barcodes. :-) Hope it helps a bit.
ebolyen commented 6 years ago

I think cual-id itself addresses 2 by nature (did you have any issues correcting after the typo/misidentification was made?)

As for 1, what if cual-id just had a prefix (like z or maybe U for UUID?) This might address #42 as well. I don't remember if we'd already ruled out that option, but it seems easy to work around/with.

jcocking commented 6 years ago

Thanks for getting back to me so quickly. Yes, we have always been able to track down any mix ups between "b" and "6" and have tried to be more careful now that we know it's an issue. As for 1, it's not a huge deal just to modify the cell but I thought I would point out it's something we've noticed. Thanks again.

johnchase commented 6 years ago

@jcocking Thank you for feedback! @shiffer1 has run into similar issues and posted an issue about it here #42. You can see some of the thoughts regarding the issue, my conclusion in the past is that I would like to make cual-id more spreadsheet friendly though I don't know how to do this in a way that won't cause other issues.

@ebolyen , I like the idea of being able to add a prefix to an ID, we could allow an arbitrary prefix so that the user would be responsible for that, i.e. the prefix you would want to add for excel may be different than the prefix for R (R also modifies IDs by placing an 'x' in front of the ID).

Like you mentioned I feel like we explored this idea in the past, but I am not able to think of a reason why this would not work of the top of my head

gregcaporaso commented 2 years ago

Another similar issue that I've been running into is cual-ids that are composed of all integers - this can cause some annoying formatting, and I have seen .0 appended to them in spreadsheets (i.e., it gets treated as a floating point number).

I like the prefix idea as it would address all of these. A default that could be overridden on the command line should let us handle different cases.

I also remember talking about prefixes at some point, and also don't remember if we ruled it out for any reason. Given that, I think we can just try it out and see if it comes up again, whenever we get around to working on cual-id again. (For what it's worth, I still use cual-id regularly, and the NMDC is now recommending universally unique sample identifiers.)

gregcaporaso commented 1 month ago

These ideas came up again in a conversation. It might reduce some of the transcription errors if we outputted the UUIDs/cual-ids in uppercase rather than lowercase.