Merge pull request #1139 from griffithlab/combine_class_ii_alleles

Fix issue where class ii alleles were filtered out as invalid before combining alpha and beta chains
griffithlab · Sep 6, 2024 · ff35eb5 · ff35eb5
2 parents d70277a + 8dc7a6a
commit ff35eb5
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Showing 4 changed files with 8 additions and 8 deletions.
diff --git a/pvactools/tools/pvacbind/run.py b/pvactools/tools/pvacbind/run.py
@@ -58,8 +58,8 @@ def main(args_input = sys.argv[1:]):
     base_output_dir = os.path.abspath(args.output_dir)
 
     (class_i_prediction_algorithms, class_ii_prediction_algorithms) = pvactools.lib.run_utils.split_algorithms(args.prediction_algorithms)
-    (class_i_alleles, class_ii_alleles, species) = pvactools.lib.run_utils.split_alleles(args.allele)
-    class_ii_alleles = pvactools.lib.run_utils.combine_class_ii_alleles(class_ii_alleles)
+    alleles = pvactools.lib.run_utils.combine_class_ii_alleles(args.allele)
+    (class_i_alleles, class_ii_alleles, species) = pvactools.lib.run_utils.split_alleles(alleles)
 
     shared_arguments = {
         'input_file'                : args.input_file,

diff --git a/pvactools/tools/pvacfuse/run.py b/pvactools/tools/pvacfuse/run.py
@@ -131,8 +131,8 @@ def main(args_input = sys.argv[1:]):
     base_output_dir = os.path.abspath(args.output_dir)
 
     (class_i_prediction_algorithms, class_ii_prediction_algorithms) = pvactools.lib.run_utils.split_algorithms(args.prediction_algorithms)
-    (class_i_alleles, class_ii_alleles, species) = pvactools.lib.run_utils.split_alleles(args.allele)
-    class_ii_alleles = pvactools.lib.run_utils.combine_class_ii_alleles(class_ii_alleles)
+    alleles = pvactools.lib.run_utils.combine_class_ii_alleles(args.allele)
+    (class_i_alleles, class_ii_alleles, species) = pvactools.lib.run_utils.split_alleles(alleles)
 
     shared_arguments = {
         'input_file_type'           : 'fasta',

diff --git a/pvactools/tools/pvacseq/run.py b/pvactools/tools/pvacseq/run.py
@@ -74,8 +74,8 @@ def main(args_input = sys.argv[1:]):
     base_output_dir = os.path.abspath(args.output_dir)
 
     (class_i_prediction_algorithms, class_ii_prediction_algorithms) = pvactools.lib.run_utils.split_algorithms(args.prediction_algorithms)
-    (class_i_alleles, class_ii_alleles, species) = pvactools.lib.run_utils.split_alleles(args.allele)
-    class_ii_alleles = pvactools.lib.run_utils.combine_class_ii_alleles(class_ii_alleles)
+    alleles = pvactools.lib.run_utils.combine_class_ii_alleles(args.allele)
+    (class_i_alleles, class_ii_alleles, species) = pvactools.lib.run_utils.split_alleles(alleles)
 
     shared_arguments = {
         'input_file'                : args.input_file,

diff --git a/pvactools/tools/pvacvector/run.py b/pvactools/tools/pvacvector/run.py
@@ -442,8 +442,8 @@ def main(args_input=sys.argv[1:]):
     elif len(class_ii_prediction_algorithms) == 0:
         print("No MHC class II prediction algorithms chosen. Skipping MHC class II predictions.")
 
-    (class_i_alleles, class_ii_alleles, species) = pvactools.lib.run_utils.split_alleles(args.allele)
-    class_ii_alleles = pvactools.lib.run_utils.combine_class_ii_alleles(class_ii_alleles)
+    alleles = pvactools.lib.run_utils.combine_class_ii_alleles(args.allele)
+    (class_i_alleles, class_ii_alleles, species) = pvactools.lib.run_utils.split_alleles(alleles)
     if len(class_i_alleles) == 0:
         print("No MHC class I alleles chosen. Skipping MHC class I predictions.")
     elif len(class_ii_alleles) == 0: