starting an avaluation/debug script

evaluate.py

+#!/usr/bin/env python3
+
+
+import sys
+import argparse
+from termcolor import colored
+
+import networkx as nx
+
+
+def parse_args():
+    parser = argparse.ArgumentParser(description='Process some integers.')
+    parser.add_argument('filename', type=str,
+                        help='The output file to evalute')
+
+    args = parser.parse_args()
+
+    return args
+
+
+def load_graph(filename):
+    if filename.endswith('.graphml'):
+        return nx.read_graphml(filename)
+    elif filename.endswith('.gexf'):
+        return nx.read_gexf(filename)
+    else:
+        print("Wrong file format. Require graphml or gefx format", file=sys.stderr)
+        exit()
+
+
+""" Compute appearance frequencies from node names.
+    All the node names must be under the format :
+    {idx}:{mol1_id}_{mol2_id}_...{molx_id}.other_things_here
+    @param graph The networkx graph representinf the deconvolved graph
+    @param only_wong If True, don't print correct nodes
+    @param file_pointer Where to print the output. If set to stdout, then pretty print. If set to None, don't print anything.
+    @return A tuple containing two dictionaries. The first one with theoritical frequences of each node, the second one with observed frequencies.
+"""
+def parse_graph_frequencies(graph, only_wrong=False, file_pointer=sys.stdout):
+    # Compute origin nodes formated as `{idx}:{mol1_id}_{mol2_id}_...`
+    observed_frequences = {}
+    origin_node_names = []
+    for node in graph.nodes():
+        first_dot = node.find(".")
+        origin_name = node[:first_dot]
+
+        # Count frequency
+        if not origin_name in observed_frequences:
+            observed_frequences[origin_name] = 0
+            origin_node_names.append(origin_name)
+        observed_frequences[origin_name] += 1
+    
+    # Compute wanted frequencies
+    theoritical_frequencies = {}
+    for node_name in origin_node_names:
+        _, composition = node_name.split(':')
+
+        mol_ids = composition.split('_')
+        # The node should be splited into the number of molecules inside itself
+        theoritical_frequencies[node_name] = len(mol_ids)
+
+    # Print results
+    if file_pointer != None:
+        print("--- Frequency analysis ---", file=file_pointer)
+        for key in theoritical_frequencies:
+            obs, the = observed_frequences[key], theoritical_frequencies[key]
+            result = f"{key}: {obs}/{the}"
+
+            if file_pointer == sys.stdout:
+                result = colored(result, 'green' if obs==the else 'red')
+
+            if only_wrong and obs==the:
+                continue
+
+            print(result, file=file_pointer)
+
+    return theoritical_frequencies, observed_frequences
+
+
+def print_summary(frequencies, file_pointer=sys.stdout):
+    print("--- Global summary ---", file=file_pointer)
+
+
+
+def main():
+    args = parse_args()
+    graph = load_graph(args.filename)
+    frequencies = parse_graph_frequencies(graph)
+
+    print_summary(frequencies)
+
+
+if __name__ == "__main__":
+    main()

requirements.txt

-networkx>=2.2
\ No newline at end of file
+networkx>=2.2
+termcolor>=1.1
\ No newline at end of file