Compatibility with CAFA assessment added

Author: mariasche

file_utils.py

@@ -51,17 +51,18 @@ def read_embeddings(embeddings_in):
     return embeddings
 
 
-def write_predictions_cafa(predictions, out_file, model_num):
+def write_predictions_cafa(predictions, out_file, model_num, team_name):
     """
     Write prediictions in CAFA format
     :param predictions: predictions to write
     :param out_file: output file
     :param model_num: number of model that is used
+    :param team_name: Team name to use in output file
     :return:
     """
     with open(out_file, 'w') as out:
-        out.write('AUTHOR\tRostlab2\nMODEL\t{}\nKEYWORDS\thomolog, machine learning, natural language processing.'
-                  '\n'.format(model_num))
+        out.write('AUTHOR\t{}\nMODEL\t{}\nKEYWORDS\thomolog, machine learning, natural language processing.'
+                  '\n'.format(team_name, model_num))
         for p in predictions.keys():
             prediction = predictions[p]
             for pred in prediction.keys():

function_prediction.py

@@ -218,3 +218,24 @@ def write_predictions(predictions, out_file):
                     ri = prediction[pred]
                     out.write('{}\t{}\t'.format(p, pred))
                     out.write('{:0.2f}\n'.format(float(ri)))
+                    
+    @staticmethod
+    def write_predictions_cafa(predictions, out_file, model_num, team_name):
+        """
+        Write prediictions in CAFA format
+        :param predictions: predictions to write
+        :param out_file: output file
+        :param model_num: number of model that is used
+        :param team_name: Team name to use in output file
+        :return:
+        """
+    with open(out_file, 'w') as out:
+        out.write('AUTHOR\t{}\nMODEL\t{}\nKEYWORDS\thomolog, machine learning, natural language processing.'
+                  '\n'.format(team_name, model_num))
+        for p in predictions.keys():
+            prediction = predictions[p]
+            for pred in prediction.keys():
+                ri = prediction[pred]
+                out.write('{}\t{}\t'.format(p, pred))
+                out.write('{:0.2f}\n'.format(float(ri)))
+        out.write('END')

predict_go_embedding_inference.py

@@ -40,5 +40,10 @@ def main():
             predictions_out = '{}_{}_{}.txt'.format(config_data['output'], dist, o)
             FunctionPrediction.write_predictions(predictions, predictions_out)
 
+            # for compatibility with CAFA assessment tool use the following lines
+            # team_name = RandomTeam
+            # predictions_out = '{}_{}_all_go_{}.txt'.format(team_name, dist, o.upper())
+            # FunctionPrediction.write_predictions_cafa(predictions, predictions_out, dist, team_name)
+
 
 main()