added required package for MW and removed extra ID column

Author: evelyn-schmidt

scripts/color_peptides51mer.py

@@ -273,7 +273,6 @@ def main():
     for index, row in peptides_51mer.iterrows():
 
         search_string = row['51mer ID']
-        print(search_string)
 
         #classII_sequence 
         classII_peptide = merged_peptide_51mer.loc[merged_peptide_51mer['51mer ID'] == search_string, 'Best Peptide Class II'].values[0]
@@ -310,6 +309,9 @@ def main():
 
             next_td_tags[2].string = new_string
 
+            # Remove the tag_with_search_string from the BeautifulSoup tree
+            tag_with_search_string.decompose()
+
             modified_html = peptides_51mer_soup.prettify(formatter=None)
 
         else:

scripts/requirements.txt

@@ -2,4 +2,5 @@ argparse
 pandas
 et-xmlfile == 1.1.0 
 openpyxl == 3.1.2
-bs4 == 0.0.1
+bs4 == 0.0.1
+biopython

scripts/setup_review.py

@@ -25,8 +25,8 @@
 
 
 
-command1 = f"python /Volumes/mgriffit/Active/griffithlab/gc2596/e.schmidt/neoag_vaccine_scripts/scripts/generate_reviews_files.py -WB {args.WB} -a {args.a} -c {args.c} -samp {args.samp}"
-command2 = f"python /Volumes/mgriffit/Active/griffithlab/gc2596/e.schmidt/neoag_vaccine_scripts/scripts/color_peptides51mer.py -WB {args.WB} -p {args.WB}/../manual_review/{args.samp}_Peptides_51-mer.xlsx -classI {args.classI} -classII {args.classII} -samp {args.samp}"
+command1 = f"python /opt/scripts/generate_reviews_files.py -WB {args.WB} -a {args.a} -c {args.c} -samp {args.samp}"
+command2 = f"python /opt/scripts/color_peptides51mer.py -WB {args.WB} -p {args.WB}/../manual_review/{args.samp}_Peptides_51-mer.xlsx -classI {args.classI} -classII {args.classII} -samp {args.samp}"
 
 
 # Execute the first script