modified code to work when using standalone iedb

griffithlab · Jan 23, 2025 · 3aeb360 · 3aeb360
1 parent 355d67f
commit 3aeb360
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Showing 5 changed files with 14 additions and 8 deletions.
diff --git a/pvactools/lib/netmhc_pan_version.py b/pvactools/lib/netmhc_pan_version.py
@@ -2,7 +2,7 @@
 
 
 class NetMHCPanVersion:
-    valid_versions = ["4.3", "4.2", "4.1", "4.0"]
+    valid_versions = ["4.3", "4.2", "4.1", "4.0 (Not supported by standalone IEDB)"]
 
     def __init__(self, list):
         self.list = list

diff --git a/pvactools/lib/output_parser.py b/pvactools/lib/output_parser.py
@@ -173,7 +173,10 @@ def get_scores(self, line, method):
         elif method.lower() == 'netmhcpan_el':
             return {'score': float(line['score'])}
         elif 'netmhciipan_el' in method.lower():
-            return {'score': float(line['score'])}
+            try:
+                return {'score': float(line['score'])}
+            except:
+                return {'ic50': float(line['ic50'])}
         else:
             return {'ic50': float(line['ic50'])}
 

diff --git a/pvactools/lib/prediction_class.py b/pvactools/lib/prediction_class.py
@@ -654,7 +654,7 @@ def parse_iedb_allele_file(self):
         #Ultimately we probably want this method to call out to IEDB but their command is currently broken
         #curl --data "method=ann&species=human" http://tools-api.iedb.org/tools_api/mhci/
         file_name = next(
-            (name for name in ["NetMHCIIpan", "netmhciipan_el"] if name in self.iedb_prediction_method),
+            (name for name in ["netmhciipan", "netmhciipan_el"] if name in self.iedb_prediction_method),
             self.iedb_prediction_method
         )
         base_dir               = os.path.abspath(os.path.join(os.path.dirname(os.path.realpath(__file__)), '..'))
@@ -685,14 +685,14 @@ class NetMHCIIVersion:
 class NetMHCIIpan(IEDBMHCII):
     @property
     def iedb_prediction_method(self):
-        if NetMHCIIVersion.netmhcii_pan_version:
-            return 'NetMHCIIpan-' + NetMHCIIVersion.netmhcii_pan_version
-        return 'NetMHCIIpan'
+        if NetMHCIIVersion.netmhcii_pan_version in ['4.0', '4.2', '4.3']:
+            return 'netmhciipan_ba-' + NetMHCIIVersion.netmhcii_pan_version
+        return 'netmhciipan_ba'
 
 class NetMHCIIpanEL(IEDBMHCII):
     @property
     def iedb_prediction_method(self):
-        if NetMHCIIVersion.netmhcii_pan_version:
+        if NetMHCIIVersion.netmhcii_pan_version in ['4.0', '4.2', '4.3']:
             return 'netmhciipan_el-' + NetMHCIIVersion.netmhcii_pan_version
         return 'netmhciipan_el'
 

diff --git a/...seq/iedb_alleles/class_ii/NetMHCIIpan.tsv → ...seq/iedb_alleles/class_ii/netmhciipan.tsv b/...seq/iedb_alleles/class_ii/NetMHCIIpan.tsv → ...seq/iedb_alleles/class_ii/netmhciipan.tsv
diff --git a/pvactools/tools/pvacseq/run.py b/pvactools/tools/pvacseq/run.py
@@ -74,10 +74,13 @@ def main(args_input = sys.argv[1:]):
     input_file_type = 'vcf'
     base_output_dir = os.path.abspath(args.output_dir)
 
+    if (args.netmhc_pan_version == '4.0' and args.iedb_install_directory is not None):
+        raise Exception("Standalone IEDB does not support version 4.0")
+
     if (args.netmhc_pan_version and ("NetMHCIIpan" in args.prediction_algorithms or "NetMHCIIpanEL" in args.prediction_algorithms)):
         NetMHCIIVersion.netmhcii_pan_version = args.netmhc_pan_version
     elif (args.netmhc_pan_version and not ("NetMHCIIpan" in args.prediction_algorithms or "NetMHCIIpanEL" in args.prediction_algorithms or "all_class_ii" in args.prediction_algorithms)):
-        raise Exception("NetMHCIIpan and NetMHCIIpanEL version was specified but neither algorithm was selected.")
+        raise Exception("NetMHCIIpan and NetMHCIIpanEL version was specified but neither algorithm was selected")
 
     (class_i_prediction_algorithms, class_ii_prediction_algorithms) = split_algorithms(args.prediction_algorithms)
     alleles = combine_class_ii_alleles(args.allele)