Merge branch 'main' into nishant-code-review

Author: RJain12

README.md

@@ -68,8 +68,6 @@ Assets including images and branding for the ICOR tool, hosted on the [biotools
 ### Tool
 The ICOR tool has been divided into four directories: models, optimizers, resources, and scripts. In the `/tool/optimizers` directory sits the `icor_optimizer.py` file: an interactive script to optimize a sequence utilizing the trained ICOR model.
 
-> Note as of 8/24/2021, this ICOR optimizer Python script has a bug, although it works, it does not output the correct sequence. The other script "run_icor_from_mat" does work and outputs the correct sequence given an input of a .mat file. However, a user would be inputting either a FASTA file or pasting in a sequence. This script currently accepts the pasted sequence, but the optimizer portion is not working as expected. It outputs a sequence but it is not correct. Since the same model was being inferenced in the run_icor_from_mat script, I have isolated that this issue is not because of the model file. It is because of the encoding done in this script. I have 1-2 things that I still need to try which I believe will solve this issue.
-
 Supporting files were used to train, evaluate, and test the ICOR model. Descriptions for these can be found below:
 
 #### Models
@@ -83,7 +81,7 @@ The ICOR model was trained in the MATLAB environment. For more details on model
 
 #### Optimizers
 `brute_force_optimizer.py`
-> Naive optimizer creates a directory containing amino acid sequences in the FASTA format and saves these "optimized" / "generated" DNA sequences in a directory. It generates 10,000 sequences and chooses the one with the highest CAI.
+> Brute force optimizer creates a directory containing amino acid sequences in the FASTA format and saves these "optimized" / "generated" DNA sequences in a directory. It generates 10,000 sequences and chooses the one with the highest CAI.
 
 `icor_optimizer.py`
 > ICOR optimizer outputs a text file given a sequence input of amino acids or DNA. It is an interactive Python command-line script. It runs an inference through the ICOR model.
@@ -114,10 +112,6 @@ The following is a description of the purpose for each script in the repository.
 - Negative CIS elements
 - Negative repeat elements
 
-`run_icor_from_mat.ipynb`
-> A notebook that accepts a `.mat` file that contains one variable called "XTrain" of the cell array type. Cell array used in experiments was of value/shape 42266x1.
-> Note: as of 8/24/2021 this script successfully outputs the ICOR optimized sequence and it does indeed match the correct ICOR optimization.
-
 #### Resources
 The following is a description of the purpose for each resource in the resources folder.
 

tool/optimizers/icor_optimizer.py

@@ -87,7 +87,7 @@ def aa2int(seq: str) -> List[int]:
 i = 0
 # style nit: more pythonic to write for i in range(0, len(aa_placement)):
 while i < len(aa_placement):
-    oh_array[aa_placement[i]-1, i] = 1
+    oh_array[aa_placement[i], i] = 1
     i += 1
 
 oh_array = [oh_array]