From aa71ae31269a186d27f6a96d9d5262bbed2c3f58 Mon Sep 17 00:00:00 2001
From: Sabrina Krakau <sabrina.krakau.qbic@gmail.com>
Date: Wed, 22 Apr 2020 20:15:54 +0200
Subject: [PATCH] Use allele.organism instead of str for allele conversion

---
 Fred2/EpitopePrediction/ANN.py | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/Fred2/EpitopePrediction/ANN.py b/Fred2/EpitopePrediction/ANN.py
index 3278b970..26c98bfa 100644
--- a/Fred2/EpitopePrediction/ANN.py
+++ b/Fred2/EpitopePrediction/ANN.py
@@ -149,9 +149,9 @@ def _represent(self, allele):
             :return: str
             """
             if isinstance(allele, MouseAllele):
-                return "H-2-%s%s%s" % (allele.locus, allele.supertype.upper(), allele.subtype)
+                return "%s-%s%s%s" % (allele.organism, allele.locus, allele.supertype.upper(), allele.subtype)
             else:
-                return "HLA-%s%s%s" % (allele.locus, allele.supertype, allele.subtype)
+                return "%s-%s%s%s" % (allele.organism, allele.locus, allele.supertype, allele.subtype)
 
         # Converts FRED2s internal allele representation into the format required by mhcnuggets
         def convert_alleles(self, alleles):
@@ -308,9 +308,9 @@ def _represent(self, allele):
             :return: str
             """
             if isinstance(allele, MouseAllele):
-                return "H-2-%s%s%s" % (allele.locus, allele.supertype, allele.subtype)
+                return "%s-%s%s%s" % (allele.organism, allele.locus, allele.supertype, allele.subtype)
             else:
-                return "HLA-%s%s:%s" % (allele.locus, allele.supertype, allele.subtype)
+                return "%s-%s%s:%s" % (allele.organism, allele.locus, allele.supertype, allele.subtype)
 
         # Converts the internal mhcnuggets-class-1 HLA representation back into a FRED2 representation
         def revert_allele_repr(self, name):
@@ -408,12 +408,12 @@ def _represent(self, allele):
             """
             if isinstance(allele, MouseAllele):
                 # expects H-2-XXx
-                return "H-2-%s%s%s" % (allele.locus, allele.supertype.upper(), allele.subtype)
+                return "%s-%s%s%s" % (allele.organism, allele.locus, allele.supertype.upper(), allele.subtype)
             elif isinstance(allele, CombinedAllele):
-                return "HLA-%s%s%s-%s%s%s" % (allele.alpha_locus, allele.alpha_supertype, allele.alpha_subtype,
+                return "%s-%s%s%s-%s%s%s" % (allele.organism, allele.alpha_locus, allele.alpha_supertype, allele.alpha_subtype,
                                         allele.beta_locus, allele.beta_supertype, allele.beta_subtype)
             else:
-                return "HLA-%s%s%s" % (allele.locus, allele.supertype, allele.subtype)
+                return "%s-%s%s%s" % (allele.organism, allele.locus, allele.supertype, allele.subtype)
 
         # Converts FRED2s internal allele representation into the format required by mhcnuggets
         def convert_alleles(self, alleles):
@@ -599,12 +599,12 @@ def _represent(self, allele):
             """
             if isinstance(allele, MouseAllele):
                 # expects H-2-XXx
-                return "H-2-%s%s%s" % (allele.locus, allele.supertype.upper(), allele.subtype)
+                return "%s-%s%s%s" % (allele.organism, allele.locus, allele.supertype.upper(), allele.subtype)
             elif isinstance(allele, CombinedAllele):
-                return "HLA-%s%s:%s-%s%s:%s" % (allele.alpha_locus, allele.alpha_supertype, allele.alpha_subtype,
+                return "%s-%s%s:%s-%s%s:%s" % (allele.organism, allele.alpha_locus, allele.alpha_supertype, allele.alpha_subtype,
                                         allele.beta_locus, allele.beta_supertype, allele.beta_subtype)
             else:
-                return "HLA-%s%s:%s" % (allele.locus, allele.supertype, allele.subtype)
+                return "%s-%s%s:%s" % (allele.organism, allele.locus, allele.supertype, allele.subtype)
 
         # Converts the internal mhcnuggets-class-2 representation back into a FRED2 representation
         def revert_allele_repr(self, name):
@@ -684,9 +684,9 @@ def _represent(self, allele):
             :return: str
             """
             if isinstance(allele, MouseAllele):
-                return "H-2-%s%s%s" % (allele.locus, allele.supertype, allele.subtype)
+                return "%s-%s%s%s" % (allele.organism, allele.locus, allele.supertype, allele.subtype)
             else:
-                return "HLA-%s%s%s" % (allele.locus, allele.supertype, allele.subtype)
+                return "%s-%s%s%s" % (allele.organism, allele.locus, allele.supertype, allele.subtype)
 
         # Converts FRED2s internal allele representation into the format required by MHCFlurry
         def convert_alleles(self, alleles):
@@ -825,9 +825,9 @@ def _represent(self, allele):
             :return: str
             """
             if isinstance(allele, MouseAllele):
-                return "H-2-%s%s%s" % (allele.locus, allele.supertype, allele.subtype)
+                return "%s-%s%s%s" % (allele.organism, allele.locus, allele.supertype, allele.subtype)
             else:
-                return "HLA-%s*%s:%s" % (allele.locus, allele.supertype, allele.subtype)
+                return "%s-%s*%s:%s" % (allele.organism, allele.locus, allele.supertype, allele.subtype)
 
         # Converts the internal MHCFlurry representation back into a FRED2 representation
         def revert_allele_repr(self, name):