#186 is completed

Author: Hamid Gasmi

09-problems/graph-algorithms-in-genome-sequencing/de_bruijn_string.py

@@ -2,18 +2,59 @@
 
 class De_Bruijn_Graph:
     def __init__(self, k, text):
-        pass
+        
+        assert(k > 1)
+        assert(len(text) >= k)
 
-    def _build_adjacency_list(self):
-        pass
+        self._build_gragh(k, text)
+
+    def _build_gragh(self, k, text):
+        
+        self.nodes = []
+        self.adjacency_list = []
+        node_kmer_no_dict = dict()
+        for i in range(len(text) - k + 1):
+
+            prefix_node_no = self.get_node_no(text[0:k-1], node_kmer_no_dict) if i == 0 else suffix_node_no
+            suffix_node_no = self.get_node_no(text[i+1:i+k], node_kmer_no_dict)
+
+            self.adjacency_list[prefix_node_no].append(suffix_node_no)
+            
+    def get_node_no(self, kmer, node_kmer_no_dict):
+        
+        if kmer in node_kmer_no_dict:
+            node_no = node_kmer_no_dict[kmer]
+
+        else:
+            node_no = len(self.nodes)
+            self.nodes.append(kmer)
+            self.adjacency_list.append([])
+            node_kmer_no_dict[kmer] = node_no
+
+        return node_no
 
     def str_adjacency_list(self):
-        pass
+
+        result_list = []
+        for node in range(len(self.nodes)):
+            if len(self.adjacency_list[node]) == 0:
+                continue
+            
+            node_adjacents = [ self.nodes[node] ]
+            node_adjacents.append(' -> ')
+            for a in range(len(self.adjacency_list[node])):
+                adjacent_node_id = self.adjacency_list[node][a]
+                node_adjacents.append(self.nodes[adjacent_node_id])
+                if a < len(self.adjacency_list[node]) - 1:
+                    node_adjacents.append(',')
+            result_list.append(''.join(node_adjacents))
+
+        return '\n'.join(result_list)
 
 if __name__ == "__main__":
     k = int(sys.stdin.readline().strip())
     text = sys.stdin.readline().strip()
 
     de_bruijn_graph = De_Bruijn_Graph(k, text)
-    
+
     print(de_bruijn_graph.str_adjacency_list())