Update README.md

README.md

@@ -179,50 +179,59 @@ pip3 install torch torchvision torchaudio
 
   
 
+We provided code to test CLASPP (see section below) 
 
+  
+:tada: you are know ready to run the code :tada: 
+  
 
-## Uses
-
-<!-- Address questions around how the model is intended to be used, including the foreseeable users of the model and those affected by the model. -->
-
-### Direct Use
-
-<!-- This section is for the model use without fine-tuning or plugging into a larger ecosystem/app. -->
-
-[More Information Needed]
-
-
-### Recommendations
-
-<!-- This section is meant to convey recommendations with respect to the bias, risk, and technical limitations. -->
-
-Users (both direct and downstream) should be made aware of the risks, biases and limitations of the model. More information needed for further recommendations.
-
-
+Use the code below to get started with the model.
 
 
 
+## Uses
 
+<!-- Address questions around how the model is intended to be used, including the foreseeable users of the model and those affected by the model. -->
 
+### Direct Use
+```
+Usage: python3 claspp_forward.py [OPTION]... --input INPUT [FASTA_FILE or TXT_FILE]...
+predict PTM events on peptides or full sequences
 
-## Citation [optional]
+Example 1: python3 claspp_forward.py -B 100 -S 0 -i random.txt
+Example 2: python3 claspp_forward.py -B 50 -S 1 -i random.fasta
 
-<!-- If there is a paper or blog post introducing the model, the APA and Bibtex information for that should go in this section. -->
+FASTA_FILE contain protein sequences in proper fasta or a2m format
+TXT_FILE cointain protien peptides 21 in length with the center
+residue being the PTM modification site
 
-**BibTeX:**
 
-[More Information Needed]
+Pattern selection and interpretation:
+  -B, --batch_size          (int) that describes how many predictions
+                            can be predicted at a time on the GPU
+                            (reduce if you get run out of GPU space)
 
-**APA:**
+  -S  --scrape_fasta        (int) should be a 1 or a 0 
+                            1 = read a fasta and scrape posible 21 peptides
+                            that can be modified by a PTM 
+                            0 = read a txt file that has the 21mer already 
+                            sperated and all peptides should be sperated by 
+                            a '\\n' (can be faster) than fasta option
+  
+  -h  --help                your reading it right now
 
-[More Information Needed]
+  -i  --input               location of the input fasta or txt
 
+  -o  --output              location of the output csv
 
+```
 
 
 
 
-- **Developed by:** [Nathan Gravel]
+- **Developed by:** Major author for most code Nathan Gravel. Finetuning code inspried by Zhongliang Zhou,
+- Contrastive learing code inspried by Ruili Fang, Codebase testing and verstion controle by Austin Downes,
+- Webtool dev Saber Soleymani
 - **Funded by [optional]:** [NIH]
 - **Shared by [optional]:** [More Information Neede]
 - **Model type:** [Text classication]
@@ -230,4 +239,4 @@ Users (both direct and downstream) should be made aware of the risks, biases and
 - **License:** [MIT]
 - **Finetuned from model [optional]:** [ESM-2 150M]
 
-[More Information Needed]
+[More Information Needed]