Issues Identified in AAV Sequence Design Repository

[khanburged]

I hope this message finds you well. I have been reviewing the code in the AAV sequence design repository and would like to bring a few issues to your attention that are currently affecting usability and reproducibility:

1. Missing Method in MutantGenerator Class
   The method generate_mutations_n_distance_away is referenced in the codebase but is not defined within the sequence_design_utils.MutantGenerator class. Please confirm whether this method was intended to be implemented. If it is deprecated, consider removing or replacing the reference.

2. Undefined Method in oligo.py
   The oligo.py script attempts to invoke a set_homopolymer method on the Synthesis pipeline, which is currently undefined. This results in a runtime error. Kindly implement the method or update the code to reflect the correct functionality.

3. TensorFlow Version Discrepancy
   There is a discrepancy between the TensorFlow versions mentioned. The associated publication references TensorFlow 1.3, while the README specifies version 1.2 with tf.Estimator. The current implementation does not appear to work reliably with either version. For improved reproducibility, we recommend specifying the exact dependencies via a requirements.txt or environment.yml file.

4. Missing TFRecord Validation Data
   The training script (train.py) expects TFRecord validation data, which is not included in the repository. Providing a sample TFRecord file or clear instructions for generating the necessary data would be highly beneficial.

Relevant Resources for Debugging:

GitHub Repository: https://github.com/google-research/google-research/tree/master/aav
Additional Files: https://www.dropbox.com/scl/fo/7h3sd1xl3hx7h4l4dvfuh/AAADsly3Y15lCBty7rAEfkY?rlkey=kddwn8x01u8gkjvyoypcyladh&e=1&dl=0

We appreciate your contributions to the research community and thank you in advance for your time and attention to these matters.

Best regards,
Khan Lodoi
Data Research Analyst
Email: Lodoi.Khanburged@jichi.ac.jp
Jichi Medical University