Update pep8

Fasta cleaner

README.md

@@ -1,4 +1,4 @@
-# Phylo_flow pipeline 
+# Phylo Flow 
 
 ## Description
 This tool, developed within the scope of ASB, aims to create a pipeline.

python/fasta_cleaner.py

@@ -1,15 +1,20 @@
 import sys
 
+
 def clean_fasta(input_file, output_file):
     """
-    Processes a FASTA file to remove all occurrences of the letter 'n' (lowercase) from the DNA sequences.
-    
+    Processes a FASTA file to remove all occurrences of the letter 'n'
+        (lowercase) from the DNA sequences.
+
     Args:
     input_file (str): The path to the input FASTA file.
-    output_file (str): The path to the output FASTA file where the cleaned sequences will be saved.
-    
-    Each sequence in the file is expected to start with a header line that begins with '>'.
-    This script retains the header lines and writes the cleaned sequences to the output file.
+    output_file (str): The path to the output FASTA file
+        where the cleaned sequences will be saved.
+
+    Each sequence in the file is expected to start
+        with a header line that begins with '>'.
+    This script retains the header lines and writes the cleaned sequences
+        to the output file.
     """
     with open(input_file, 'r') as f, open(output_file, 'w') as fout:
         for line in f:
@@ -19,11 +24,12 @@ def clean_fasta(input_file, output_file):
                 cleaned_sequence = line.strip().replace('N', '')
                 fout.write(cleaned_sequence + '\n')
 
+
 if __name__ == "__main__":
     if len(sys.argv) != 3:
         print("Usage: python3 script_name.py <input_fasta> <output_fasta>")
         sys.exit(1)
-    
+
     input_file = sys.argv[1]
     output_file = sys.argv[2]
     clean_fasta(input_file, output_file)

python/newick_tree_visualizer.py

@@ -62,7 +62,7 @@ def tree_generator(infile, outfile):
     labels = [f"{round(float(s), 2)}" if s else "" for s in support_values]
 
     # Create and save the phylogenetic tree plot
-    canvas, axes, mark = tree.draw(node_labels=labels, node_sizes=30, 
+    canvas, axes, mark = tree.draw(node_labels=labels, node_sizes=30,
                                    width=width, height=height, tree_style="n")
     toyplot.svg.render(canvas, outfile)