I'm trying to implement the topological ordering with Kahn's algorithm:
from collections import defaultdict
def ordering(graph:dict):
in_counts = defaultdict(int)
for k, v in graph.items():
if not k in in_counts:
in_counts[k] = 0
for in_node in v:
in_counts[in_node] += 1
queue = []
for in_node in in_counts.keys():
if in_counts[in_node] == 0:
queue.append(in_node)
topological_order = []
while queue:
print("in_counts:", in_counts)
print("queue:", queue)
current_node = queue.pop(0)
topological_order.append(current_node)
print("result:", topological_order)
if not current_node in graph:
continue
for in_node in graph[current_node]:
in_counts[in_node] -= 1
if in_counts[in_node] == 0:
queue.append(in_node)
return topological_order
print(ordering({'GTTGA': ['CTGAG'], 'TTCAC': ['GTTGA'], 'AAGGC': ['GTTGA', 'TAACA', 'TTCAC'], 'CGGGC': ['GTTGA', 'TAACA'], 'CCCTC': ['GTTGA', 'TAACA', 'TTCAC', 'AAGGC', 'CGGGC', 'CTGAG'], 'AGCTT': ['GTTGA']}))
The debug output:
in_counts: defaultdict(<class 'int'>, {'GTTGA': 5, 'CTGAG': 2, 'TTCAC': 2, 'AAGGC': 1, 'TAACA': 3, 'CGGGC': 1, 'CCCTC': 0, 'AGCTT': 0})
queue: ['CCCTC', 'AGCTT']
result: ['CCCTC']
in_counts: defaultdict(<class 'int'>, {'GTTGA': 4, 'CTGAG': 1, 'TTCAC': 1, 'AAGGC': 0, 'TAACA': 2, 'CGGGC': 0, 'CCCTC': 0, 'AGCTT': 0})
queue: ['AGCTT', 'AAGGC', 'CGGGC']
result: ['CCCTC', 'AGCTT']
in_counts: defaultdict(<class 'int'>, {'GTTGA': 3, 'CTGAG': 1, 'TTCAC': 1, 'AAGGC': 0, 'TAACA': 2, 'CGGGC': 0, 'CCCTC': 0, 'AGCTT': 0})
queue: ['AAGGC', 'CGGGC']
result: ['CCCTC', 'AGCTT', 'AAGGC']
in_counts: defaultdict(<class 'int'>, {'GTTGA': 2, 'CTGAG': 1, 'TTCAC': 0, 'AAGGC': 0, 'TAACA': 1, 'CGGGC': 0, 'CCCTC': 0, 'AGCTT': 0})
queue: ['CGGGC', 'TTCAC']
result: ['CCCTC', 'AGCTT', 'AAGGC', 'CGGGC']
in_counts: defaultdict(<class 'int'>, {'GTTGA': 1, 'CTGAG': 1, 'TTCAC': 0, 'AAGGC': 0, 'TAACA': 0, 'CGGGC': 0, 'CCCTC': 0, 'AGCTT': 0})
queue: ['TTCAC', 'TAACA']
result: ['CCCTC', 'AGCTT', 'AAGGC', 'CGGGC', 'TTCAC']
in_counts: defaultdict(<class 'int'>, {'GTTGA': 0, 'CTGAG': 1, 'TTCAC': 0, 'AAGGC': 0, 'TAACA': 0, 'CGGGC': 0, 'CCCTC': 0, 'AGCTT': 0})
queue: ['TAACA', 'GTTGA']
result: ['CCCTC', 'AGCTT', 'AAGGC', 'CGGGC', 'TTCAC', 'TAACA']
in_counts: defaultdict(<class 'int'>, {'GTTGA': 0, 'CTGAG': 1, 'TTCAC': 0, 'AAGGC': 0, 'TAACA': 0, 'CGGGC': 0, 'CCCTC': 0, 'AGCTT': 0})
queue: ['GTTGA']
result: ['CCCTC', 'AGCTT', 'AAGGC', 'CGGGC', 'TTCAC', 'TAACA', 'GTTGA']
in_counts: defaultdict(<class 'int'>, {'GTTGA': 0, 'CTGAG': 0, 'TTCAC': 0, 'AAGGC': 0, 'TAACA': 0, 'CGGGC': 0, 'CCCTC': 0, 'AGCTT': 0})
queue: ['CTGAG']
result: ['CCCTC', 'AGCTT', 'AAGGC', 'CGGGC', 'TTCAC', 'TAACA', 'GTTGA', 'CTGAG']
The expected result is:
['CCCTC', 'CGGGC', 'AGCTT', 'AAGGC', 'TAACA', 'TTCAC', 'GTTGA', 'CTGAG']
which is different from my result(see above).
I understand that CGGGC should be placed right after CCCTC, however I don't understand how this would be not conflicting with the algorithm: at the start both CCCTC and AGCTT have the in-degree of 0, and CGGGC gets on the queue after AGCTT.
What am I missing?