コード例 #1
0
ファイル: io.py プロジェクト: jim-bo/silp2
def gen_sam_pair(fpath1, fpath2, flip_1, flip_2):
    ''' pulls info from paired sam file '''
    fin1 = open(fpath1)
    fin2 = open(fpath2)
    for line1 in fin1:
        line2 = fin2.readline()

        # sanity.
        if line1[0] == "@":
            continue

        # tokenize.
        tok1 = line1.strip().split()
        tok2 = line2.strip().split()

        if len(tok1) < 2 or len(tok2) < 2:
            print tok1, tok2

        # simplify.
        if tok1[1] == '0':
            orien1 = 0
        else:
            orien1 = 1

        if tok2[1] == '0':
            orien2 = 0
        else:
            orien2 = 1

        if flip_1 == True:
            orien1 = 1 - orien1
        if flip_2 == True:
            orien2 = 1 - orien2

        ctg1 = tok1[2]
        ctg2 = tok2[2]

        left1 = int(tok1[3])
        left2 = int(tok2[3])

        right1 = left1 + len(tok1[9])
        right2 = left2 + len(tok2[9])

        print ctg1<ctg2, orien1, orien2
        state = misc.determine_state(ctg1, ctg2, orien1, orien2)

        # yield the info.
        yield ctg1, left1, right1, ctg2, left2, right2, state, tok1, tok2

    fin1.close()
    fin2.close()
コード例 #2
0
ファイル: graphs.py プロジェクト: jim-bo/silp2
def agp_graph_undirected(fpath):
    ''' returns agp graph '''

    # load agp array.
    agp_edges = load_agp(fpath)

    # make digraph.
    G = nx.Graph()

    # add nodes.
    for i in range(agp_edges.size):

        # skip contigs themselves.
        if agp_edges[i]['comp_type'] != 'W': continue

        # add node info.
        name = agp_edges[i]['comp_name']
        width = agp_edges[i]['comp_stop']
        orien = agp_edges[i]['comp_orien']

        G.add_node(agp_edges[i]['comp_name'], {'width':width, 'orien':orien})

    # add edges.
    for i in range(agp_edges.size):

        # skip contigs themselves.
        if agp_edges[i]['comp_type'] != 'N': continue
        if i == agp_edges.shape[0] - 1: continue

        # add sorted edges.
        ctg1 = agp_edges[i-1]['comp_name']
        ctg2 = agp_edges[i+1]['comp_name']
        o1 = G.node[ctg1]['orien']
        o2 = G.node[ctg2]['orien']
        gap = agp_edges[i]['comp_stop']
        state = misc.determine_state(ctg1, ctg2, o1, o2)

        G.add_edge(ctg1, ctg2, {'gap':gap, 'state':state})

    # done.
    return G