@staticmethod
def _get_assembled_reference_sequences(nucmer_hits, ref_sequence, assembly):
    """nucmer_hits =  hits made by self._parse_nucmer_coords_file.
           ref_gene = reference sequence (pyfastaq.sequences.Fasta object)
           assembly = dictionary of contig name -> contig.
           Makes a set of Fasta objects of each piece of assembly that
           corresponds to the reference sequeunce."""
    sequences = {}
    for contig in sorted(nucmer_hits):
        for hit in nucmer_hits[contig]:
            qry_coords = hit.qry_coords()
            fa = assembly[hit.qry_name].subseq(qry_coords.start, qry_coords
                .end + 1)
            if hit.on_same_strand():
                strand = '+'
            else:
                fa.revcomp()
                strand = '-'
            ref_coords = hit.ref_coords()
            fa.id = '.'.join([ref_sequence.id, str(ref_coords.start + 1),
                str(ref_coords.end + 1), contig, str(qry_coords.start + 1),
                str(qry_coords.end + 1), strand])
            if hit.hit_length_ref == hit.ref_length:
                fa.id += '.complete'
            sequences[fa.id] = fa
    return sequences
