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pnnl-predictive-phenomics / concerto

Apache License 2.0
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Incorporate protein structure prediction #25

Open djinnome opened 1 month ago

kimdn commented 1 month ago

@djinnome Done as

https://github.com/pnnl-predictive-phenomics/concerto/commit/faedc7dcd7e4948544783f0a6aef258eab97fbd2

Please read my README.txt file

kimdn commented 1 month ago

install chai-1 w: newest git commit.pptx

winatony commented 1 month ago

@kimdn @djinnome

I worked through 3/4 steps of the chai-1 structure prediction pipeline. Ran into a bug where the individual fasta files and the individual sbatch files generated for each protein are including escape characters at newlines "\". My guess this is likely due to the split_fasta_from_file function in 1_prepare_multi_inputs.py. You use .replace('\n', ''), maybe you need to escape the backslash? Once the backslash is removed chai1 runs. If you can get to a fix on the repo thats great, otherwise I will try and get something done myself.

kimdn commented 1 month ago

@winatony

At one point, I added .replace('\n', '') to avoid error on my end/machine. However, I think that we need to have working version on your end.

I don't know your working version. Can you simply replace .replace('\n', '') into #.replace('\n', '') # used to work for DooNam's case/file, but not for Winston and add your working line? and request a review as a pull request to me please?

djinnome commented 1 month ago

I think .replace(r'\n', '') will escape the backslash.

winatony commented 1 month ago

That worked, I will submit a pull request when I have gone through one working iteration of the pipeline.