update to put all files in one place

Author: evelyn-schmidt

scripts/color_peptides51mer.py

@@ -30,8 +30,10 @@ def parse_arguments():
                         help='The path to the classI all_epitopes.aggregated.tsv used in pVACseq', required=True)
     parser.add_argument('-classII',
                         help='The path to the classII all_epitopes.aggregated.tsv used in pVACseq', required=True)
+    parser.add_argument('-WB',
+                        help='the path to the gcp_immuno folder of the trial you wish to tun script on, defined as WORKING_BASE in envs.txt')
+    parser.add_argument('-samp', help='Name of the sample')
 
-    parser.add_argument('-o', help="Output location", required=True)
 
     return(parser.parse_args())
 
@@ -344,10 +346,14 @@ def main():
             print("ClassI: ", classI_peptide)
             print("ClassII: ", classII_peptide, "\n")
 
-    with open(args.o, "w", encoding = 'utf-8') as file:
-        file.write(modified_html)
+    if args.WB:
+        html_file_name = args.WB +  '/../manual_review/' + args.samp + ".Colored_Peptides.html" 
+    else:
+        html_file_name  =  args.samp + ".Colored_Peptides.html"
 
+    with open(html_file_name, "w", encoding = 'utf-8') as file:
+        file.write(modified_html)
 
 
 if __name__ == "__main__":
-    main()
+    main()  main()

scripts/generate_reviews_files.py

@@ -1,4 +1,4 @@
-mport argparse
+import argparse
 import csv
 import pandas as pd
 import sys

scripts/get_FDA_thresholds.py

@@ -349,8 +349,12 @@ def main():
 
 
 
-
-    fda_quality_thresholds = pd.read_csv("/opt/scripts/fda_quality_thresholds.csv")
+    try:
+        fda_quality_thresholds = pd.read_csv("/opt/scripts/fda_quality_thresholds.csv")
+    except:
+        print("Running Locally, not in Docker")
+        fda_quality_thresholds = pd.read_csv("scripts/fda_quality_thresholds.csv")
+        print()
 
     qc = reshape_quality_thresholds(fda_quality_thresholds)
 
@@ -362,7 +366,7 @@ def main():
 
 
     if args.WB:
-        qc.to_csv(args.WB + final_result + '/fda_quality_thresholds_report.tsv', sep="\t", index=False)
+        qc.to_csv(args.WB +  '/../manual_review/fda_quality_thresholds_report.tsv', sep="\t", index=False)
     else:
         qc.to_csv('fda_quality_thresholds_report.tsv', sep="\t", index=False)
 
@@ -374,3 +378,4 @@ def main():
 if __name__ == "__main__":
     main()
 
+

scripts/get_neoantigen_qc.py

@@ -270,7 +270,7 @@ def main():
 
     # create a text file to store results
     if args.WB:
-        qc_file = open(args.WB + final_result + '/qc_file.txt', 'w')
+        qc_file = open(args.WB + '/../manual_review/qc_file.txt', 'w')
     else:
         qc_file = open('qc_file.txt', 'w')
 
@@ -291,4 +291,4 @@ def main():
 
 
 if __name__ == "__main__":
-    main()
+    main()

scripts/setup_review.py

@@ -4,35 +4,41 @@
 # Define the command-line arguments
 parser = argparse.ArgumentParser(description='Sets up manuel review files')
 
+parser.add_argument('-WB',
+                    help='the path to the gcp_immuno folder of the trial you wish to tun script on, defined as WORKING_BASE in envs.txt')
+
 parser.add_argument('-samp', help='Name of the sample')
 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('-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.")
+if not args.classI or not args.classII or not args.WB:
+    parser.error("Missing required arguments. Please provide -p, -classI, -classII, and -WB.")
 
 
 
-command1 = f"python /opt/scripts/generate_reviews_files.py -a {args.a} -c {args.c} -samp {args.samp}"
-command2 = f"python /opt/scripts/color_peptides51mer.py -p {args.samp}_Peptides_51-mer.xlsx -classI {args.classI} -classII {args.classII} -o {args.o}"
+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
 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.")
+