fixing missing AA and adding set_up script

Author: evelyn-schmidt

scripts/color_peptides51mer.py

@@ -116,6 +116,7 @@ def set_underline(peptide_sequence, mutant_peptide_pos):
     classI_position = 0
 
     if '-' in mutant_peptide_pos:
+
         positions = mutant_peptide_pos.split("-")
 
         start_position = int(positions[0])
@@ -197,6 +198,7 @@ def create_stylized_sequence(peptide_sequence):
         if nucleotide.open_tag or nucleotide.close_tag:
             if nucleotide.close_tag:
                 new_string += '</span>'
+                
 
             if nucleotide.open_tag:
 
@@ -225,9 +227,11 @@ def create_stylized_sequence(peptide_sequence):
                 elif nucleotide.bold and not nucleotide.color and nucleotide.underline:
                     new_string += '<span style="font-weight:bold;text-decoration:underline;">'
                     new_string += nucleotide.nucleotide
+
+            if not nucleotide.large and not nucleotide.bold and not nucleotide.color and not nucleotide.underline:
+                new_string += nucleotide.nucleotide
         else:
             new_string += nucleotide.nucleotide
-
     return(new_string)   
 
 def main():
@@ -330,7 +334,7 @@ def main():
             modified_html = peptides_51mer_soup.prettify(formatter=None)
 
         else:
-            print("Search string not found.")
+            print("\nSearch string: ", search_string, " not found.\n")
 
     with open(args.o, "w", encoding = 'utf-8') as file:
         file.write(modified_html)

scripts/setup_review.py

@@ -0,0 +1,39 @@
+import argparse
+import subprocess
+
+# Define the command-line arguments
+parser = argparse.ArgumentParser(description='Sets up manuel review files')
+
+parser.add_argument('-a', help='Path to ITB Reviewed Candidates')
+parser.add_argument('-c', help='Path to annotated_filtered.vcf-pass-51mer.fa.manufacturability.tsv')
+parser.add_argument('-samp', help='Name of the sample')
+parser.add_argument('-f', "--fin_results", help='Name of the final results folder')
+
+parser.add_argument('-classI', help='Path to classI all_epitopes.aggregated.tsv', required=True)
+parser.add_argument('-classII', help='Path to classII all_epitopes.aggregated.tsv', required=True)
+parser.add_argument('-o', help='The name of the html in which the coloring will be printed', required=True)
+
+
+
+# Parse the command-line arguments
+args = parser.parse_args()
+
+# Check if the required arguments are provided
+if not args.classI or not args.classII or not args.o:
+    parser.error("Missing required arguments. Please provide -p, -classI, -classII, and -o.")
+
+
+
+command1 = f"python scripts/generate_reviews_files.py -a {args.a} -c {args.c} -samp {args.samp}"
+command2 = f"python scripts/color_peptides51mer.py -p {args.samp}_Peptides_51-mer.xlsx -classI {args.classI} -classII {args.classII} -o {args.o}"
+
+
+# Execute the first script
+print("Generating Review Files...")
+subprocess.run(command1, shell=True)
+
+# Execute the second script
+print("Coloring Peptide Sequeces...")
+subprocess.run(command2, shell=True)
+
+print("Scripts have been executed successfully.")