Incorporate feedback

bin/epaa.py

@@ -708,12 +708,12 @@ def create_affinity_values(allele, length, j, method, max_scores, allele_strings
         return np.nan
 
 
-def create_binder_values(pred_score, method, thresholds):
-    if not pd.isnull(pred_score):
+def create_binder_values(pred_value, method, thresholds):
+    if not pd.isnull(pred_value):
         if 'syf' in method:
-            return True if pred_score > thresholds[method] else False
+            return True if pred_value > thresholds[method] else False
         else:
-            return True if pred_score <= thresholds[method.lower()] else False
+            return True if pred_value <= thresholds[method.lower()] else False
     else:
         return np.nan
 
@@ -962,7 +962,7 @@ def __main__():
     parser.add_argument('-ml', "--min_length", help="Minimum peptide length")
     parser.add_argument('-t', "--tools", help="Tools used for peptide predictions", required=True, type=str)
     parser.add_argument('-tt', "--tool_thresholds", help="Customize thresholds of given tools using a json file", required=False, type=str)
-    parser.add_argument('-at', "--affinity_thresholds", help="Use affinity instead of rank for thresholding", required=False, action='store_true')
+    parser.add_argument('-at', "--use_affinity_thresholds", help="Use affinity instead of rank for thresholding", required=False, action='store_true')
     parser.add_argument('-sv', "--versions", help="File containing parsed software version numbers.", required=True)
     parser.add_argument('-a', "--alleles", help="<Required> MHC Alleles", required=True, type=str)
     parser.add_argument('-r', "--reference", help="Reference, retrieved information will be based on this ensembl version", required=False, default='GRCh37', choices=['GRCh37', 'GRCh38'])
@@ -1034,9 +1034,9 @@ def __main__():
         if version not in EpitopePredictorFactory.available_methods()[method]:
             raise ValueError("The specified version " + version + " for " + method + " is not supported by epytope.")
 
-    thresholds = {"syfpeithi":60, "mhcflurry":500, "mhcnuggets-class-1":500, "mhcnuggets-class-2":500, "netmhc":500, "netmhcpan":500, "netmhcii":500, "netmhciipan":500}
+    thresholds = {"syfpeithi":50, "mhcflurry":500, "mhcnuggets-class-1":500, "mhcnuggets-class-2":500, "netmhc":500, "netmhcpan":500, "netmhcii":500, "netmhciipan":500}
     # Define binders based on the rank metric for netmhc family tools
-    # NOTE these recommendet thresholds might change in the future with new versions of the tools
+    # NOTE these recommended thresholds might change in the future with new versions of the tools
     if "netmhc" in ''.join(methods.keys()) and not args.affinity_thresholds:
         thresholds.update({"netmhc":2, "netmhcpan":2, "netmhcii":10, "netmhciipan":5})
 

modules/local/epytope_peptide_prediction.nf

@@ -37,8 +37,8 @@ process EPYTOPE_PEPTIDE_PREDICTION {
         argument = "--tool_thresholds ${params.tool_thresholds} " + argument
     }
 
-    if (params.affinity_thresholds) {
-        argument = "--affinity_thresholds " + argument
+    if (params.use_affinity_thresholds) {
+        argument = "--use_affinity_thresholds " + argument
     }
 
     def netmhc_paths_string = netmhc_paths.join(",")

nextflow.config

@@ -23,7 +23,7 @@ params {
     mhc_class = 1
     tools = 'syfpeithi'
     tool_thresholds = null
-    affinity_thresholds = false
+    use_affinity_thresholds = false
 
     // Options: Filtering
     filter_self = false

nextflow_schema.json

@@ -116,13 +116,13 @@
                 "tool_thresholds": {
                     "type": "string",
                     "description": "Specifies tool-specific binder thresholds in a JSON file. This can be used to override the given default binder threshold values.",
-                    "help_text": "Default thresholds to determine whether a peptide is considered as a binder are the following: `syfpeithi` > 60, `mhcflurry` <=500, `mhcnuggets-class-1` <= 500, `mhcnuggets-class-2` <= 500, `netmhc` <= 2, `netmhcpan` <= 2, `netmhcii` <= 5, `netmhciipan` <= 5. Note that the default threshold for NetMHC tools is based on the rank metric. The remaining predictors thresholds are based on affinities. Thresholds can be customized in a JSON file: `tool-name:value`"
+                    "help_text": "Default thresholds to determine whether a peptide is considered as a binder are the following: `syfpeithi` > 50, `mhcflurry` <=500, `mhcnuggets-class-1` <= 500, `mhcnuggets-class-2` <= 500, `netmhc` <= 2, `netmhcpan` <= 2, `netmhcii` <= 5, `netmhciipan` <= 5. Note that the default threshold for NetMHC tools is based on the rank metric. The remaining predictors thresholds are based on affinities. Thresholds can be customized in a JSON file: `tool-name:value`"
                 },
-                "affinity_thresholds": {
+                "use_affinity_thresholds": {
                     "type": "boolean",
                     "default": false,
                     "description": "Specifies the affinity metric instead of the rank metric used for determining whether a peptide is considered as a binder.",
-                    "help_text": "Default affinity thresholds to determine whether a peptide is considered as a binder are the following:: `syfpeithi` > 60, `mhcflurry` <=500, `mhcnuggets-class-1` <= 500, `mhcnuggets-class-2` <= 500, `netmhc` <= 500, `netmhcpan` <= 500, `netmhcii` <= 500, `netmhciipan` <= 500."
+                    "help_text": "Switches the prediction metric of netMHC tools from rank to affinity. Default: `netmhc` <= 500, `netmhcpan` <= 500, `netmhcii` <= 500, `netmhciipan` <= 500."
                 },
                 "wild_type": {
                     "type": "boolean",