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']
def _refine_v ( seq , 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.