#NEWLINE# def test_align_with_N_in_nucleotide_sequence( self ) : #NEWLINE# #INDENT# expected = { #NEWLINE# #INDENT# 'optimal_alignment_score' : 9 , #NEWLINE# 'suboptimal_alignment_score' : 0 , #NEWLINE# 'query_begin' : 0 , #NEWLINE# 'query_end' : 8 , #NEWLINE# 'target_begin' : 0 , #NEWLINE# 'target_end_optimal' : 9 , #NEWLINE# 'target_end_suboptimal' : 0 , #NEWLINE# 'cigar' : '4M1D5M' , #NEWLINE# 'query_sequence' : 'ACTCANNATCGANCTAGC' , #NEWLINE# 'target_sequence' : 'ACTCGAAAATGTNNGCA' , #NEWLINE# #UNINDENT# } #NEWLINE# query = StripedSmithWaterman ( expected [ 'query_sequence' ] ) #NEWLINE# alignment = query ( expected [ 'target_sequence' ] ) #NEWLINE# self . _check_alignment ( query , expected )