io.py 文件源码

def gfa1_to_gapped_transcript(
    gfa_in, fasta_out, number_of_ns=100, soft_mask_overlaps=False, hard_mask_overlaps=False):

    if soft_mask_overlaps == True and hard_mask_overlaps == True:
        raise Exception("I can't soft mask and hard mask at the same time, dude!")

    # Process
    gfa1 = read_gfa1(gfa_in)
    exon_dict = _segments_to_exon_dict(gfa1["segments"])
    coordinate_dict = _containments_to_coordinate_dict(gfa1["containments"])
    overlap_dict = _links_to_overlap_dict(gfa1["links"])
    path_dict = _paths_to_path_dict(gfa1["paths"])


    # Mask if necessary
    _mask(exon_dict, overlap_dict, soft_mask_overlaps, hard_mask_overlaps)

    composed_paths = _compose_paths(exon_dict, path_dict, number_of_ns)

    # Write
    SeqIO.write(format="fasta", sequences=composed_paths, handle=fasta_out)