Speichern des Links und der HTML von nVenn hinzugefügt

cami/AlgorithmWrapper.py

@@ -15,6 +15,9 @@ class AlgorithmWrapper(object):
         self.ppi_network = Graph()
         self.seeds = list()
         self.home_path = ''
+    def set_weight(self, weight):
+        self.weight = weight
+        
     def set_ppi_network(self, graph):
         self.ppi_network = graph
 

cami/cami.py

@@ -4,6 +4,7 @@ import shutil
 from DiamondWrapper import DiamondWrapper
 from DominoWrapper import DominoWrapper
 from RobustWrapper import RobustWrapper
+from HHotNetWrapper import HHotNetWrapper
 import preprocess
 import uuid
 import cami_suite
@@ -13,14 +14,21 @@ import webbrowser
 def main(ppi_network, seeds, tools, tool_weights, consensus, evaluate,
          output_dir, identifier, save_temps, visualize, save_image, force):
     print('CAMI started')
-    ppi_graph = preprocess.csv2graph(ppi_network)
+    nof_tools = len(tools)
+    ppi_graph = preprocess.csv2graph(ppi_network, nof_tools=nof_tools)
     seed_lst = preprocess.txt2lst(seeds)
+    if tool_weights == None:
+        tool_weights = nof_tools * [1]
+    initial_seedlst = seed_lst.copy()
     # rename seeds with their corresponding indices in the ppi_graph
     name2index = preprocess.name2index_dict(ppi_graph)
     checked_seed_lst = [name2index[v] for v in seed_lst if v in name2index]
     print('Created the PPI-network Graph and seed list.')
-    
-    if len(checked_seed_lst) != len(seed_lst) and not force:
+    n = len(checked_seed_lst)
+    m = len(seed_lst)
+    if n != m  and not force:
+        name = ppi_graph.vertex_properties["name"]
+        print(f'There are {abs(m-n)} seeds missing in the PPI network: ({set([name[cseed] for cseed in checked_seed_lst]).symmetric_difference(set(initial_seedlst))})')
         choice = input('Continue? [y/n]')
         if choice == 'y':
             pass
@@ -71,16 +79,21 @@ def main(ppi_network, seeds, tools, tool_weights, consensus, evaluate,
 
     wrappers = {'diamond': DiamondWrapper(),
                 'domino': DominoWrapper(),
-                'robust': RobustWrapper() #,
-#                'hotnet': HotnetWrapper()
+                'robust': RobustWrapper(),
+                'hotnet': HHotNetWrapper()
                 }
 
     tool_wrappers = [wrappers[tool] for tool in tools]     
 
+    for idx, tool in enumerate(tool_wrappers):
+        tool.set_weight(tool_weights[idx])
+
     cami = cami_suite.cami(ppi_graph, seed_lst, tool_wrappers, output_dir, identifier, tmp_dir, home_path)
     for tool in tool_wrappers:
         cami.initialize_tool(tool)
 
+    cami.set_initial_seed_lst(initial_seedlst)
+        
     if consensus or (not consensus and not evaluate):
         result_sets = cami.make_predictions()
         cami.create_consensus(result_sets)
@@ -124,15 +137,15 @@ if __name__ == "__main__":
     parser.add_argument('-t', '--tools', nargs='+', action='store', default=["diamond", "domino", "robust"],
             help="List of tools that the user wants to use for prediction.\n Available tools are:\n" + \
                 "domino\ndiamond\nrobust\hotnet\nThe default tools are: diamond, domino and robust.")
-    parser.add_argument('-w', '--tool_weights', nargs='+', action='store', default=[1,1,1],
+    parser.add_argument('-w', '--tool_weights', nargs='+', action='store', default=None,
             help="List of weights for the tools. If you have [domino, diamond, robust] as list of tools and diamonds weight should be twice as high as the other tools type: 1 2 1")
     parser.add_argument('-c', '--consensus', action='store_true', help="run only the consensus prediction part of cami")
     parser.add_argument('-e', '--evaluate', action='store_true', help="run only the evaluation part of cami")
     parser.add_argument('-o', '--output_dir', action='store', help="path to output directory")
     parser.add_argument('-id', '--identifier', action='store', help="ID for the current excecution of cami. Defaults to a randomly generated ID")
     parser.add_argument('-tmp', '--save_temps', action='store_true', help="keep all temporary files")
-    parser.add_argument('-v', '--visualize', action='store_true', help="Visualize results using Degradome, an external webtool")
-    parser.add_argument('-img', '--save_image', action='store_true', help="Save the venn diagram from the visualization as png.")
+    parser.add_argument('-v', '--visualize', action='store_true', help="Visualize results using Degradome, an external webtool. Please note that degradome can only be used for visualization with up to 5 tools.")
+    parser.add_argument('-img', '--save_image', action='store_true', help="Save the venn diagram from the visualization as png. (Only possible for up to 5 tools)")
     parser.add_argument('-f', '--force', action='store_true', help="Ignore warnings and overwrite everything when excecuting CAMI.")
     #TODO List with additional arguments if needed by certain tools
 
@@ -146,8 +159,8 @@ if __name__ == "__main__":
 # add name for implemented tools here:
     implemented_tools = ["domino",
                          "diamond",
-                         "robust" #,
-                         #"hotnet"
+                         "robust",
+                         "hotnet"
                          ]
     if args['tools']:
         for tool in args['tools']:

cami/cami_suite.py

@@ -59,6 +59,7 @@ class cami():
         self.ppi_graph = ppi_graph
         self.ppi_vertex2gene = self.ppi_graph.vertex_properties["name"]
         self.ppi_gene2vertex = {self.ppi_vertex2gene[vertex]:vertex for vertex in self.ppi_graph.vertices()}
+        self.initial_seed_lst = None
         self.seed_lst = seed_lst
         self.tool_wrappers = tool_wrappers
         self.output_dir = output_dir
@@ -70,6 +71,9 @@ class cami():
         self.code2toolname[0] = 'CAMI'
         self.home_path = home_path
 
+    def set_initial_seed_lst(self, seedlst):
+        self.initial_seed_lst = seedlst
+
     def initialize_tool(self, tool):
         tool.set_ppi_network(self.ppi_graph)
         tool.set_seeds(self.seed_lst)
@@ -191,7 +195,7 @@ class cami():
         # translate tool code to string
         codes2tools = {vertex:[self.code2toolname[idx] for idx,code in enumerate(predicted_by[vertex]) if code == 1] for vertex in self.ppi_graph.vertices()}
         
-        for vertex in cami_vertices:
+        for vertex in cami_vlist:
             print(f'{name[vertex]}\t{cami_scores[vertex]}\t{codes2tools[vertex]}')
 
         # save the results in outputfiles
@@ -200,7 +204,8 @@ class cami():
         
         # save all predictions by all tools
         with open(f'{self.output_dir}/all_predictions_{self.uid}.tsv', 'w') as outputfile:
-            outputfile.write(f'CAMI predictions with {len(self.seed_lst)} seeds ({seed_genes}):\n')
+            outputfile.write(f'CAMI predictions with {len(self.seed_lst)} of initially {len(self.initial_seed_lst)} seeds: {seed_genes}\n,'+
+                             f'initially: {self.initial_seed_lst}\n')
             outputfile.write(f'gene\tpredicted_by\tcami_score\tindex_in_graph\tdegree_in_graph\n')
             all_vertices = cami_vertices.union(putative_vertices)
             for vertex in all_vertices:
@@ -208,18 +213,18 @@ class cami():
         print(f'saved all predictions by the used tools in: {self.output_dir}/all_predictions_{self.uid}.tsv')
 
         # save the predictions made by cami
-        with open(f'{self.output_dir}/CAMI_{self.uid}_output.tsv', 'w') as outputfile:
+        with open(f'{self.output_dir}/CAMI_output_{self.uid}.tsv', 'w') as outputfile:
             outputfile.write('gene\tindex_in_graph\tcami_score\n')
             for vertex in cami_vlist:
-                outputfile.write(f'{name[vertex]}\t{str(vertex)}\t{cami_scores[vertex]}\n')
-        print(f'saved cami output in: {self.output_dir}/CAMI_{self.uid}_output.tsv')
+                outputfile.write(f'{name[vertex]}\t{str(vertex)}\t{cami_scores[vertex]}\t{vertex.out_degree()}\n')
+        print(f'saved cami output in: {self.output_dir}/CAMI_output_{self.uid}.tsv')
         
         # for visualization
         # transform all vertex indices to their corresponding gene names in a result set
-        self.result_gene_sets['CAMI'] = cami_genes
+        
         for tool in result_sets:
             self.result_gene_sets[tool.name] = set([name[vertex] for vertex in result_sets[tool]])
-
+        self.result_gene_sets['CAMI'] = cami_genes
     def visualize(self):
         """Create Venn Diagrams via a external tool named degradome.
            Sends a request via requests to the degradome server.
@@ -232,6 +237,8 @@ class cami():
                               for tool in self.result_gene_sets 
                                 if len(self.result_gene_sets[tool])>0}
             url = degradome.send_request(degradome_sets)
+            with open(f'{self.output_dir}/venn_link_{self.uid}.txt', 'w') as f:
+                f.write(url)
             return url
            # TODO: save the venn diagram images in an outputfolder
            # TODO: Include seeds?
@@ -245,5 +252,7 @@ class cami():
             print('Cannot use degradome to create venn diagrams of 6 or more tools')
 
     def download_diagram(self, url):
-        imagefile = f'{self.output_dir}/{self.uid}_vdiagram.png'
-        degradome.download_image(url, imagefile)
\ No newline at end of file
+        venn_name = f'{self.output_dir}/vdiagram_{self.uid}'
+        response = degradome.download_image(url, venn_name + '.png')
+        with open(f'{venn_name}.html', 'w') as r:
+            r.write(response.html.html)
\ No newline at end of file

cami/degradome.py

@@ -18,7 +18,7 @@ def send_request(sets=dict()):
               'header': 'rawData'
              }
     print(f'Sending result sets to {url} to create Venn diagrams...')
-    r = requests.post(url, data=values, timeout=30)
+    r = requests.post(url, data=values)
     if r.ok:
         match = re.search(r'(<a href=\\")(http:\/\/degradome.*)(\\">)', r.text)
         if match:
@@ -37,13 +37,12 @@ def download_image(degradome_url, file):
     from requests_html import HTMLSession
     session = HTMLSession()
     response = session.get(degradome_url)
-    response.html.render(timeout=20, sleep=5)
+    response.html.render(timeout=20, sleep=3)
     link_list = response.html.absolute_links
     session.close()
     for link in link_list:
         if 'data:image/png;' in link:
             urllib.request.urlretrieve(link, file)
             print(f'Venn diagram image saved under: {file}')
-            return
+            return response
     print(f'Something went wrong. Could not automatically download the venn diagram. Please try it manually under: {degradome_url}')
-    session.close()

cami/preprocess.py

 import graph_tool
 from idna import InvalidCodepointContext
 
-def csv2graph(inputfile, delimiter="\t"):
+def csv2graph(inputfile, delimiter="\t", nof_tools = 4):
     """transforms a csv-file to a Graph() object
 
     :param inputfile: inputfile in csv-format
@@ -14,7 +14,8 @@ def csv2graph(inputfile, delimiter="\t"):
     g = graph_tool.load_graph_from_csv(inputfile, skip_first=True,
         csv_options={'delimiter': '\t', 'quotechar': '"'})
     g.vertex_properties["cami_score"] = g.new_vertex_property("float", val=0.0)
-    g.vertex_properties["predicted_by"] = g.new_vertex_property("vector<int16_t>", val=[-1,-1,-1,-1,-1])
+    values = (nof_tools + 6) * [-1]
+    g.vertex_properties["predicted_by"] = g.new_vertex_property("vector<int16_t>", val=values)
     return g
 
 def txt2lst(seed_file):

DIAMOnD @ 24379748

-Subproject commit 24379748c5ee34f477a968ba3f1c0b325ff0614f