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bmdavid2 / OligoRL

A Reinforcement Learning Framework for Pooled Oligonucleotide Design
MIT License
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`LongDNASeq` -> `LongDNA` #2

Open cariaso opened 1 year ago

cariaso commented 1 year ago

https://github.com/bmdavid2/OligoRL/pull/1 seems to be the canary in the coalmine for a larger issue. BioSequences seems to have changed LongDNASeq -> LongDNA as per https://github.com/BioJulia/BioSequences.jl/blob/master/CHANGELOG.md https://github.com/BioJulia/BioSequences.jl/issues/216

however my simple attempt at string substitution did not get a completed run, and instead complains about

-    sequence=LongDNASeq.(sequence)
+    sequence=LongDNA.(sequence)

on CutFreeRL/CutFreeRL.jl:306

bmdavid2 commented 1 year ago

I see, that is a frustrating change. I'll take a more comprehensive view at the tools and implement a solution. Which tool are you interested in? I can start there.

cariaso commented 1 year ago

CutFreeRL

On Thu, Sep 29, 2022 at 1:34 PM Ben David @.***> wrote:

I see, that is a frustrating change. I'll take a more comprehensive view at the tools and implement a solution. Which tool are you interested in? I can start there.

— Reply to this email directly, view it on GitHub https://github.com/bmdavid2/OligoRL/issues/2#issuecomment-1262593765, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAA6TEWEHP5LIVUGOZFLRQ3WAXHJXANCNFSM6AAAAAAQY7MZEM . You are receiving this because you authored the thread.Message ID: @.***>

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bmdavid2 commented 1 year ago

I pushed an update to the CutFreeRL tool that should fix the issue. Only CtuFreeRL has been fixed, so I will leave the issue open until everything has been fixed.

cariaso commented 1 year ago

Confirming that this has worked for me.