added new wrappers

cami_src/algorithms/CustomWrapper.py

+from algorithms.AlgorithmWrapper import AlgorithmWrapper
+import subprocess
+
+from configparser import ConfigParser
+
+class CustomWrapper(AlgorithmWrapper):
+    def __init__(self,config):
+        """Wrapper that allows to use results from any algorithm that is not included in the CAMI suite yet
+           has a class variable 'external_prediction_path' that points to the path of the external prediction file
+        """
+        super().__init__(config)
+        self.name = 'custom_algorithm'
+        self.code = -1
+        self.external_prediction_path = 'path/to/external/prediction/file'
+        ppi_vertex2gene = self.ppi_graph.vertex_properties["name"]
+        self.ppi_gene2vertex = {ppi_vertex2gene[vertex]: vertex for vertex in self.ppi_graph.vertices()}
+
+    def run_algorithm(self, inputparams):
+        """extract the output from the external prediction file, that contains the name of the external tool in the first line
+           set the name for the algorithm to the name of the external tool
+        Args:
+            inputparams (list): A list of parameters for the algorithm that is defined via
+                                prepare_input()
+
+        Returns:
+            list: A list of resulting genes extracted from the generated output file
+        """
+        external_prediction_file = inputparams[0]
+        result_list = []
+        with open(external_prediction_file) as rfile:
+            for idx, line in enumerate(rfile):
+                if idx == 0:
+                    self.name = line.strip()
+                else:
+                    node = line.strip()
+                    if node in self.ppi_gene2vertex:
+                        result_list.append(self.ppi_gene2vertex[node])
+        return result_list
+
+    def prepare_input(self):
+        """this function returns the path to the external prediction file
+        """
+        return self.external_prediction_path
+
+    def extract_output(self, algo_output):
+        """this function does not do anything in the case of an external algorithm
+        """
+        pass
+    
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