Update PEP8

Changes in sequence_model_processor

README.md

@@ -1,14 +1,50 @@
 # Phylo_flow pipeline 
 
 ## Description
-This tool, developed within the scope of xxxxx, aims toxxxxxxx.
+This tool, developed within the scope of ASB, aims to create a pipeline.
 ![Pipeline](./extras/pictures/pipeline.png)
 
 
 ## Requisites
-* Docker;
-* Docker Desktop (Opcional)
-* Acess to internet (Only when installing the app)
+* Python;
+* Mafft;
+* modeltest-ng;
+* raxml-ng;
+* Toytree.
+
+## Installation
+```bash
+# Download the project from GitLab
+wget https://github.com/Rendrick27/Assignment_01/archive/refs/heads/main.zip
+
+# Unzip the folder
+unzip Assignment_01-main.zip
+```
+
+## Usage
+```bash
+# Navigate to the Snakemake directory
+cd Assignment_01-main.zip
+```
+Then, run the following command:
+```bash
+snakemake --use-conda all --cores 1
+```
+
+## Docker
+### Build it
+```bash
+docker build -t {image_name} .
+
+docker run -it --name {container_name} {image_name} /bin/bash
+```
+### Pull docker image
+```bash
+docker pull rendrick27/phylo_flow:latest
+```
+
+## Settings
+You may adjust settings in the Snakemake file, such as threads and bootstraps in params, but remember that using more threads may cause more issues.
 
 ## Credits
 <p> <a href= "https://github.com/Rendrick27"> Rendrick Carreira - 201901365 </a> </p>

python/sequence_model_processor.py

@@ -1,6 +1,7 @@
-import sys
-import os
 import glob
+import os
+import sys
+
 
 def get_sequence_length(fasta_file):
     """
@@ -10,7 +11,8 @@ def get_sequence_length(fasta_file):
         fasta_file (str): Path to the FASTA file.
 
     Returns:
-        int: The total length of the sequence in the file, excluding header lines and whitespace.
+        int: The total length of the sequence in the file,
+            excluding header lines and whitespace.
     """
     seq_length = 0
     with open(fasta_file, 'r') as file:
@@ -22,13 +24,15 @@ def get_sequence_length(fasta_file):
             seq_length += len(line.strip())
     return seq_length
 
+
 def process_sequences(directory, output_file):
     """
-    Processes each FASTA file in the directory to calculate sequence lengths and generate output
-    based on corresponding model data.
+    Processes each FASTA file in the directory to calculate sequence
+    lengths and generate output based on corresponding model data.
 
     Args:
-        directory (str): Directory containing FASTA files and corresponding model files.
+        directory (str): Directory containing FASTA files
+                        and corresponding model files.
         output_file (str): File to which the formatted output will be written.
     """
     fasta_files = sorted(glob.glob(os.path.join(directory, '*.fasta')))
@@ -56,6 +60,7 @@ def process_sequences(directory, output_file):
         for output in outputs:
             file.write(output + "\n")
 
+
 if __name__ == "__main__":
     if len(sys.argv) < 3:
         print("Usage: python script.py <directory> <output_file>")