@staticmethod<EOL><INDENT>def _refine_j(seq, species):<DEDENT>
jgerm = germlines.get_germline(seq['<STR_LIT>']['<STR_LIT>'], species)<EOL>aln = global_alignment(seq['<STR_LIT>'], jgerm)<EOL>append = '<STR_LIT>'<EOL>for s, g in zip(aln.aligned_query[::-<NUM_LIT:1>], aln.aligned_target[::-<NUM_LIT:1>]):<EOL><INDENT>if s != '<STR_LIT:->':<EOL><INDENT>break<EOL><DEDENT>else:<EOL><INDENT>append += g<EOL><DEDENT><DEDENT>seq['<STR_LIT>'] = seq['<STR_LIT>'] + append[::-<NUM_LIT:1>]<EOL>
Completes the 3' end of a a truncated sequence with germline nucleotides.
Input is a MongoDB dict (seq) and the species.