#187 is completed

Author: Hamid Gasmi

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

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+import sys
+
+class De_Bruijn_Graph:
+    def __init__(self, patterns):
+        
+        assert(len(patterns) > 0)
+        self._pattern_size = len(patterns[0])
+        assert(self._pattern_size > 0)
+
+        self._build_gragh(patterns)
+
+    def _build_gragh(self, patterns):
+        
+        self.nodes = []
+        self.adjacency_list = []
+        node_kmer_no_dict = dict()
+        for pattern in patterns:
+            assert(len(pattern) == self._pattern_size)
+
+            prefix_node_no = self.get_node_no(pattern[0:self._pattern_size-1], node_kmer_no_dict)
+            suffix_node_no = self.get_node_no(pattern[1:self._pattern_size], 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):
+
+        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__":
+    patterns = sys.stdin.read().strip().splitlines()
+
+    de_bruijn_graph = De_Bruijn_Graph(patterns)
+
+    print(de_bruijn_graph.str_adjacency_list())

09-problems/graph-algorithms-in-genome-sequencing/de_bruijn_kmers_tests/01.exp

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+GAG -> AGG
+CAG -> AGG,AGG
+GGG -> GGG,GGA
+AGG -> GGG
+GGA -> GAG

09-problems/graph-algorithms-in-genome-sequencing/de_bruijn_kmers_tests/01.in

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+GAGG
+CAGG
+GGGG
+GGGA
+CAGG
+AGGG
+GGAG

09-problems/graph-algorithms-in-genome-sequencing/de_bruijn_kmers_tests/02.exp

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+GCAA -> CAAG
+CAGC -> AGCT
+TGAC -> GACG

09-problems/graph-algorithms-in-genome-sequencing/de_bruijn_kmers_tests/02.in

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+GCAAG
+CAGCT
+TGACG

09-problems/graph-algorithms-in-genome-sequencing/de_bruijn_kmers_tests/03.exp

@@ -0,0 +1,2 @@
+AGG -> GGT,GGC
+GGC -> GCT

09-problems/graph-algorithms-in-genome-sequencing/de_bruijn_kmers_tests/03.in

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+AGGT
+GGCT
+AGGC

09-problems/graph-algorithms-in-genome-sequencing/de_bruijn_kmers_tests/04.exp

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+TTC -> TCT,TCT
+GGC -> GCT,GCT
+AAG -> AGT

09-problems/graph-algorithms-in-genome-sequencing/de_bruijn_kmers_tests/04.in

@@ -0,0 +1,5 @@
+TTCT
+GGCT
+AAGT
+GGCT
+TTCT

09-problems/graph-algorithms-in-genome-sequencing/de_bruijn_kmers_tests/05.exp

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+C -> A,A,A,A,C,A

09-problems/graph-algorithms-in-genome-sequencing/de_bruijn_kmers_tests/05.in

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+CA
+CA
+CA
+CA
+CC
+CA