AmyloTool: Console Application For Detection Of Amyloid Signalling Motifs

This tool is intended for binary classification of potentionally amyloidogenic protein sequences from FASTA files.

Features

Read protein sequences from a .fa file.
Predict protein sequences with an optional prediction threshold.
Generate CSV output with sequence ID, start index, end index, and prediction values.

Build the Docker image:
```
docker build -t image-name .
```
Run the application: You need to mount your local directory to access data from inside the Docker container. The following command mounts the path/to/local/dir directory and processes a file named proteins.fa located inside of it:
```
docker run --name container-name -v path/to/local/dir:/data image-name /data/proteins.fa
```
Example (Windows):
```
docker run --name amylotool-console -v C:/Users/chris:/data amylotool-console /data/proteins.fa --threshold 0.5 --output_csv results.csv
```

sequence_file (mandatory): This is the path to the .fa file containing protein sequences you wish to predict.

--threshold (optional, default: 0.0): A float value ranging between 0 to 1. Values below it will not be saved in the final output.

--output_csv (optional, default: output.csv): Specify the name of the output CSV file where predictions will be written.