io.py 文件源码

def gfa1_to_exons(gfa_in_fn, fasta_out_fn, soft_mask_overlaps=False, hard_mask_overlaps=False):

    gfa1 = read_gfa1(gfa_in_fn)

    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)

    # Add coordinate information to description
    for exon_id, exon_record in exon_dict.items():
        exon_record.description = " ".join(coordinate_dict[exon_id])

    # Write to fasta
    SeqIO.write(format="fasta", handle=fasta_out_fn, sequences=exon_dict.values())