debruijn-tp/debruijn/debruijn.py

"""
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