gfa.py 文件源码

def gfa1_write_graph(f: TextIO, g: AssemblyGraph,
                     with_orig_segments: SegmentMapping=None):
    f.write(gfa_header("1.0"))

    segments = set()
    for n in g.nodes_iter():
        segment_name = str(n)[:-1]
        if segment_name in segments:
            continue

        segments.add(segment_name)

        if with_orig_segments and segment_name in with_orig_segments:
            n = with_orig_segments[segment_name]

        parts = ["S", segment_name, "*", "LN:i:{}".format(n.length)]
        f.write(gfa_line(*parts))

    for u, v, d in g.edges_iter(data=True):
        uid = str(u)[:-1]
        u_strand = str(u)[-1:]
        vid = str(v)[:-1]
        v_strand = str(v)[-1:]

        # Fake CIGAR string just indicating overlap length
        overlap = str(d['overlap_len'])+"M"

        parts = ["L", uid, u_strand, vid, v_strand, overlap]
        f.write(gfa_line(*parts))