def _refine_v(seq, species):
        '''
        Completes the 5' end of a a truncated sequence with germline nucleotides.
        Input is a MongoDB dict (seq) and the species.
        '''
        vgerm = germlines.get_germline(seq['v_gene']['full'], species)
        aln = global_alignment(seq['vdj_nt'], vgerm)
        prepend = ''
        for s, g in zip(aln.aligned_query, aln.aligned_target):
            if s != '-':
                break
            else:
                prepend += g
        seq['vdj_nt'] = prepend + seq['vdj_nt']
Completes the 5' end of a a truncated sequence with germline nucleotides.
        Input is a MongoDB dict (seq) and the species.