#NEWLINE# def test_arg_gap_open_penalty( self ) : #NEWLINE# #INDENT# query_sequences = [ 'TTATAATTTTCTTAGTTATTATCAATATTTATAATTTGATTTTGTTGTAAT' , 'AGTCCGAAGGGTAATATAGGCGTGTCACCTA' , 'AGTCGAAGGCGGTAATA' , 'CTGCCTCGGCAGGGGGAGGAAAGCGTCAGCGCGGCTGCCGTCGGCGCAGGGGC' , 'AGGGTAATTAAAGGCGTGTTCACCTA' ] #NEWLINE# target_sequences = query_sequences #NEWLINE# self . _check_argument_with_inequality_on_optimal_align_score ( query_sequences = query_sequences , target_sequences = target_sequences , arg = 'gap_open_penalty' , default = 5 , i_range = range ( 1 , 12 ) , compare_lt = self . assertGreaterEqual , compare_gt = self . assertLessEqual ) #NEWLINE# expected = { #NEWLINE# #INDENT# 'optimal_alignment_score' : 51 , #NEWLINE# 'suboptimal_alignment_score' : 20 , #NEWLINE# 'query_begin' : 0 , #NEWLINE# 'query_end' : 37 , #NEWLINE# 'target_begin' : 0 , #NEWLINE# 'target_end_optimal' : 29 , #NEWLINE# 'target_end_suboptimal' : 9 , #NEWLINE# 'cigar' : '5M4I3M3I1M1I21M' , #NEWLINE# 'query_sequence' : 'TAGAGATTAATTGCCACATTGCCACTGCCAAAATTCTG' , #NEWLINE# 'target_sequence' : 'TAGAGATTAATTGCCACTGCCAAAATTCTG' , #NEWLINE# #UNINDENT# } #NEWLINE# query = StripedSmithWaterman ( expected [ 'query_sequence' ] , gap_open_penalty = 1 ) #NEWLINE# alignment = query ( target_sequences [ 'target_sequence' ] ) #NEWLINE# self . _check_alignment ( alignment , expected )