Add entry point json_2_interaction_graph to the command_line module

command_line/cadbiom_cmd/cadbiom_cmd.py

@@ -93,6 +93,26 @@ def solutions_2_json(args):
         conditions=not params['no_conditions'], # Reverse the param...
     )
 
+
+def json_2_interaction_graph(args):
+    """Make an interaction weighted graph based on the searched molecule of interest.
+
+    Read decompiled solutions files (*.json* files produced by the
+    directive 'solutions_2_json') and make a graph of the relationships
+    between one or more molecules of interest, the genes and other
+    frontier places/boundaries found among all the solutions.
+    """
+
+    # Module import
+    import interaction_graph
+    params = args_to_param(args)
+    interaction_graph.json_2_interaction_graph(
+        params['output'],
+        params['molecules_of_interest'],
+        params['path'],
+    )
+
+
 def model_comparison(args):
     """Isomorphism test.
 
@@ -308,6 +328,27 @@ def main():
     parser_solutions_2_json.set_defaults(func=solutions_2_json)
 
 
+    # subparser: Make an interaction weighted graph based on the searched
+    # molecule of interest
+    # Require JSON decompilated solutions files
+    parser_json_2_interaction_graph = subparsers.add_parser(
+        'json_2_interaction_graph',
+        help=json_2_interaction_graph.__doc__,
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser_json_2_interaction_graph.add_argument('molecules_of_interest',
+        nargs='+',
+        help="One or multiple molecule of interest to search in the trajectories"
+             " of every solutions")
+    parser_json_2_interaction_graph.add_argument('--path',
+        nargs='?', default='decompiled_solutions/',
+        help="JSON formated file containing all data from complete MAC files"
+             "(*cam_complete files) generated with the 'solutions_2_json' command.")
+    parser_json_2_interaction_graph.add_argument('--output', action=ReadableDir,
+        nargs='?', default='graphs/',
+        help="Directory for the newly created file.")
+    parser_json_2_interaction_graph.set_defaults(func=json_2_interaction_graph)
+
+
     # subparser: Merge solutions to a csv file
     # Solution file (cam)
     # Output (csv)

command_line/cadbiom_cmd/interaction_graph.py

@@ -31,6 +31,7 @@ from __future__ import unicode_literals
 from __future__ import print_function
 
 # Standard imports
+import time
 import json
 import os
 import glob
@@ -103,12 +104,7 @@ def get_solutions_and_related_places_from_file(file_path):
 
 
 def get_solutions_and_related_places(path):
-    """Entry point for
-
-    Read decompiled solutions files (\*.json\* files produced by the
-    directive ``solutions_2_json``) and make a graph of the relationships
-    between one or more molecules of interest, the genes and other
-    frontier places/boundaries found among all the solutions.
+    """Read decompiled solutions files (\*.json\* files)
 
     This functions tests if the given path is a directory or a file.
 
@@ -435,5 +431,32 @@ def build_graph(all_genes, all_stimuli, unique_genes_interactions,
     nx.write_graphml(G, "test.graphml")
 
 
+def json_2_interaction_graph(output_dir, molecules_of_interest, path):
+    """Entry point for json_2_interaction_graph
+
+    Read decompiled solutions files (\*.json\* files produced by the
+    directive ``solutions_2_json``) and make a graph of the relationships
+    between one or more molecules of interest, the genes and other
+    frontier places/boundaries found among all the solutions.
+
+    More information about the graph and its legend:
+    :meth:`~cadbiom_cmd.interaction_graph.build_graph`.
+    """
+
+    chrono_start = time.time()
+
+    # get_solutions_and_related_places: trajectories
+    # filter_trajectories: filtered_macs, binary_interactions
+    # build_interactions: data to unpack for build_graph
+    build_graph(
+        *build_interactions(
+            *filter_trajectories(
+                get_solutions_and_related_places(path),
+                molecules_of_interest
+            )
+        )
+    )
+
+    LOGGER.info("Graph generated in %s", time.time() - chrono_start)
+
 
-    nx.write_graphml(G, "test.graphml")