Remove for check for valid alleles - this is now done later to includ…

…e also user-provided ones

workflow/scripts/combine_optitype_results.py

@@ -7,11 +7,6 @@
 def main():
     alleles = []
 
-    # load alleles
-    allele_list = load_alleles('workflow/scripts/valid_alleles/netmhcpan.txt')
-
-    #print(allele_list)
-
     for alfile in sys.argv[1].split(' '):
         with open(alfile, 'r') as f:
             next(f)
@@ -21,25 +16,21 @@ def main():
                 for i in range(1,7):
                     # modify header
                     modname = 'HLA-' + line_list[i]
-                    if modname in allele_list:
-                        if modname not in alleles:
-                            alleles.append(modname)
+                    if modname not in alleles:
+                        alleles.append(modname)
     # remove duplicates
     alleles = list(set(alleles))
 
-
     output = open(sys.argv[2], 'w')
     for i in alleles:
         output.write(i + '\n')
     output.close()
 
-
 def load_alleles(alleles_file):
     alleles = []
     with open(alleles_file, 'r') as f:
         for line in f:
             alleles.append(line.rstrip())
     return alleles
 
-
 main()