added debruijn.py with read functions and build_graph

debruijn/debruijn.py

@@ -0,0 +1,67 @@
+"""
+Small assembly module based on de bruijn graphs
+"""
+import networkx as nx
+
+def read_fastq(fichier):
+    """
+    Arguments:
+        fichier, str: path to fastq file
+
+    Returns:
+        a str generator, generator of sequences
+    """
+    with open(fichier, 'r') as filin:
+        for line in filin:
+            yield filin.readline().strip()
+            filin.readline()
+            filin.readline()
+
+def cut_kmer(seq, k):
+    """
+    Arguments:
+        seq, str: a sequence
+        k, int: k-mer size, must be shorter than len(seq)
+
+    Returns:
+        an iterator returning str
+    """
+    for i in range(len(seq)-(k-1)):
+        yield seq[i:i+k]
+
+def build_kmer_dict(fichier, k):
+    """
+    Arguments:
+        fichier, str: path to fastq file
+        k, int: k-mer size, must be shorter than len(seq)
+
+    Return:
+        hash_table, dict: dictionnary with key = k-mer as str
+                          and value count of k-mer occurence
+    """
+    hash_table = {}
+    it_fastq = read_fastq(fichier)
+    for seq in it_fastq:
+        it_kmer = cut_kmer(seq, k)
+        for kmer in it_kmer:
+            try:
+                hash_table[kmer]
+            except KeyError:
+                hash_table[kmer] = 1
+            else:
+                hash_table[kmer] += 1
+
+    return hash_table
+
+def build_graph(hash_table):
+    """
+    Arguments:
+        hash_table, dict: dictionnary obtained with build_kmer_dict() function
+    Return:
+        graph, nx.Graph: the de Bruijn tree corresponding to hash_table
+    """
+    graph = nx.DiGraph()
+    for key in hash_table:
+        graph.add_edge(key[:-1], key[1:], weight=hash_table[key])
+
+    return graph