#NEWLINE# def test_arg_mismatch_score( self ) : #NEWLINE# #INDENT# query_sequences = [ 'TTATAATTAATTCTTATTATTATCAATATTTATAATTTGATTTTGTTGTAAT' , 'AGTCGAAGGGTAAGGGGTATAGGCGTGTCACCTA' , 'AGTCGAAGGGTAATA' , 'CTGCCTCAGGGGCGAGGAAAGCGTCAGCGCGGCTGCCGTCGGCGCAGGGGC' , 'AGGGTAATTAGCGCGTGTTCACCTA' ] #NEWLINE# target_sequences = self #NEWLINE# self . _check_argument_with_inequality_on_optimal_align_score ( query_sequences = query_sequences , target_sequences = target_sequences , arg = 'mismatch_score' , default = ( - 3 ) , i_range = range ( ( - 6 ) , 1 ) , compare_lt = self . assertLessEqual , compare_gt = self . assertGreaterEqual ) #NEWLINE# expected = { #NEWLINE# #INDENT# 'optimal_alignment_score' : 8 , #NEWLINE# 'suboptimal_alignment_score' : 0 , #NEWLINE# 'query_begin' : 5 , #NEWLINE# 'query_end' : 8 , #NEWLINE# 'target_begin' : 10 , #NEWLINE# 'target_end_optimal' : 13 , #NEWLINE# 'target_end_suboptimal' : 0 , #NEWLINE# 'cigar' : '4M' , #NEWLINE# 'query_sequence' : 'AGAGGGTAATCAGCCGTGTCCACCGGAACACAACGCTATCGGGCGA' , #NEWLINE# 'target_sequence' : 'GTTCGCCCCAGTAAAGTTGCTACCAAATCCGCATG' , #NEWLINE# #UNINDENT# } #NEWLINE# query = StripedSmithWaterman ( expected [ 'query_sequence' ] , mismatch_score = ( - 8 ) ) #NEWLINE# alignment = query ( expected [ 'target_sequence' ] ) #NEWLINE# self . _check_alignment ( alignment , expected )