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  • 12 Overlap Graphs

    Problem

    A graph whose nodes have all been labeled can be represented by an adjacency list, in which each row of the list contains the two node labels corresponding to a unique edge.

    directed graph (or digraph) is a graph containing directed edges, each of which has an orientation. That is, a directed edge is represented by an arrow instead of a line segment; the starting and ending nodes of an edge form its tail and head, respectively. The directed edge with tail vv and head ww is represented by (v,w)(v,w) (but not by (w,v)(w,v)). A directed loop is a directed edge of the form (v,v)(v,v).

    For a collection of strings and a positive integer kk, the overlap graph for the strings is a directed graph OkOk in which each string is represented by a node, and string ss is connected to string ttwith a directed edge when there is a length kk suffix of ss that matches a length kk prefix of tt, as long as sts≠t; we demand sts≠t to prevent directed loops in the overlap graph (although directed cycles may be present).

    Given: A collection of DNA strings in FASTA format having total length at most 10 kbp.

    Return: The adjacency list corresponding to O3O3. You may return edges in any order.

    Sample Dataset

    >Rosalind_0498
    AAATAAA
    >Rosalind_2391
    AAATTTT
    >Rosalind_2323
    TTTTCCC
    >Rosalind_0442
    AAATCCC
    >Rosalind_5013
    GGGTGGG
    

    Sample Output

    Rosalind_0498 Rosalind_2391
    Rosalind_0498 Rosalind_0442
    Rosalind_2391 Rosalind_2323


    方法一
    # coding=utf-8
    
    # method1
    data ={'Rosalind_0442': 'AAATCCC',
     'Rosalind_0498': 'AAATAAA',
     'Rosalind_2323': 'TTTTCCC',
     'Rosalind_2391': 'AAATTTT',
     'Rosalind_5013': 'GGGTGGG'}
    
    def is_k_overlap(s1, s2, k):
        return s1[-k:] == s2[:k]
    
    
    import itertools
    def k_edges(data, k):
        edges = []
        for u,v in itertools.combinations(data, 2):  # data 里面任意取两个比较
            u_dna, v_dna = data[u], data[v]
            print u_dna, v_dna
            if is_k_overlap(u_dna, v_dna, k):
                edges.append((u,v))
    
            if is_k_overlap(v_dna, u_dna, k):
                edges.append((v,u))
    
        return edges
    
    print k_edges(data, 3)
    

      方法二:

    # coding=utf-8
    ### 12. Overlap Graphs ###
    from collections import OrderedDict
    import re
    
    
    def overlap_graph(dna, n):
        edges = []
        for ke1, val1 in dna:
            for ke2, val2 in dna:
                if ke1 != ke2 and val1[-n:] == val2[:n]:
                    edges.append(ke1 + '	' + ke2)
        return edges
    
    
    dna = OrderedDict()
    with open('12.txt') as f:
        for line in f:
            line = line.rstrip()
            if line.startswith('>'):
                seqName = re.sub('>', '', line)
                dna[seqName] = ''
                continue
            dna[seqName] += line.upper()
    
    fh = open('rosalind_grph_output.txt', 'wt')
    for x in overlap_graph(dna.items(), 3):
        fh.write(x + '
    ')
    
    fh.close()
    

      方法三

    # coding=utf-8
    seq_list = []
    stseq = ''
    for line in open('12.txt'):
        if line[0] == '>':
            if stseq != '':
                seq_list.append([stname, stseq])
                stseq = ''
            stname = line[1:-1]
        else:
            stseq = stseq + line.strip('
    ')
    seq_list.append([stname, stseq])
    l = len(seq_list)
    
    for i in range(0, l):
        for j in range(0, i):
            if seq_list[i][1] == seq_list[j][1]:
                continue
            if seq_list[i][1][0:3] == seq_list[j][1][-3:]:
                print seq_list[j][0], seq_list[i][0]
            if seq_list[i][1][-3:] == seq_list[j][1][0:3]:
                print seq_list[i][0], seq_list[j][0]
    

      

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  • 原文地址:https://www.cnblogs.com/think-and-do/p/7277822.html
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