lattice-automation / icor-codon-optimization Goto Github PK

cannot see it in the training folder

I am answering the following questions asked by @SandhiyaRa

1. File named ‘optimum.csv’ / 'optimum_genes.csv'

As explained in the comments of the code, this is a CSV file that is generated by GenScript's Tool that contains the sequences. If you want to generate this file, you can input sequences into their website manually. The sequences that we used in our study have already been converted into FASTA sequence files.

2. How is the benchmark results computed for ICOR tool?

All of the benchmark results including those of the ICOR tool were generated by our benchmarking script.

3. Training and testing dataset availability?

As mentioned in the manuscript, our datasets were retrieved from the NCBI. This data was partitioned and processed as per the methodology outlined in the manuscript: "24. National Center for Biotechnology Information. Genome Escherichia coli. Bethesda [Internet]. 2021. Available from: ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Escherichia_coli"

Hope this is helpful!

For example, let's say you had a bunch of genes from organism X and also transcriptomics for that organism. Could you build a custom model to optimize codons for this organism? If so, are there any tutorials for this?

Hi, I followed the "quickstart" instructions and ran icor_optimizer.py and input a sequence, but I'm getting the ONNXRuntimeError NO_SUCHFILE for icor.onnx. I'm running on OSX, so I changed model_path (with backslashes in it) to point to where my copy of icor.onnx resides, but this didn't solve it. What can I do to run it?

sess = C.InferenceSession(session_options, self._model_path, True, self._read_config_from_model) onnxruntime.capi.onnxruntime_pybind11_state.NoSuchFile: [ONNXRuntimeError] : 3 : NO_SUCHFILE : Load model from ~/repos/icor-codon-optimization/tool/models/icor.onnx failed:Load model ~/repos/icor-codon-optimization/tool/models/icor.onnx failed. File doesn't exist

despite:

$ ls -1 ~/repos/icor-codon-optimization/tool/models/icor.onnx >/dev/null ; echo $?
0

Dear github author:
Recently I have read your project and am interested in it, and I also have a question that, where could I open icor.onnx this model or could I find the original matlab code of this model icor？ I am looking forward to your letter.

Best regards.