Module ImportFrom alias alias ImportFrom alias alias alias alias alias alias ImportFrom alias alias ImportFrom alias ClassDef bases NameLoad body Assign NameStore ListLoad Str Str Str Str Str Str Str Str Str Str FunctionDef arguments args NameParam NameParam NameParam defaults body For NameStore AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr TupleLoad SubscriptLoad NameLoad Index Str SubscriptLoad NameLoad Index NameLoad TupleLoad SubscriptLoad NameLoad Index Str SubscriptLoad NameLoad Index NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam defaults NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad body Assign NameStore Dict Assign NameStore Dict Assign SubscriptStore NameLoad Index NameLoad NameLoad For NameStore NameLoad body For NameStore NameLoad body For NameStore NameLoad body Assign SubscriptStore NameLoad Index NameLoad NameLoad Assign NameStore Call NameLoad NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad NameLoad Assign NameStore Call NameLoad NameLoad If CompareEq NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr If CompareLt NameLoad NameLoad body Expr Call NameLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr If CompareGt NameLoad NameLoad body Expr Call NameLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam defaults NameLoad NameLoad ListLoad ListLoad body Assign NameStore Dict FunctionDef arguments args NameParam NameParam defaults body If CompareIs Call NameLoad SubscriptLoad NameLoad Index NameLoad NameLoad body Return CompareLt SubscriptLoad NameLoad Index NameLoad Num orelse Return UnaryOpNot SubscriptLoad NameLoad Index NameLoad decorator_list For NameStore NameLoad body For NameStore NameLoad body For TupleStore NameStore NameStore NameLoad body Assign SubscriptStore NameLoad Index NameLoad NameLoad Assign NameStore Call NameLoad NameLoad NameLoad Assign NameStore Call NameLoad NameLoad For NameStore NameLoad body Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad NameLoad For NameStore ListComp NameLoad comprehension NameStore AttributeLoad NameLoad attr CompareNotIn NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad NameLoad decorator_list decorator_list ClassDef bases NameLoad body FunctionDef arguments args NameParam defaults body Assign NameStore Str Assign NameStore ListLoad Dict Str Str Str Str Str Str Str Str Str Str Num Num Num Num Num Num Num Str NameLoad Str Dict Str Str Str Str Str Str Str Str Str Str Num Num Num Num Num Num Num Str NameLoad Str Dict Str Str Str Str Str Str Str Str Str Str Num Num Num Num Num Num Num Str NameLoad Str Dict Str Str Str Str Str Str Str Str Str Str Num Num Num Num Num Num Num Str NameLoad Str Dict Str Str Str Str Str Str Str Str Str Str Num Num Num Num Num Num Num Str NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore ListLoad For NameStore NameLoad body Assign NameStore Call NameLoad SubscriptLoad NameLoad Index Str Expr Call AttributeLoad NameLoad attr NameLoad For TupleStore NameStore NameStore Call NameLoad NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Dict Str Str Str Str Str Str Str Str Str Str Num Num Num Num Num Num Num Str Str Str Assign NameStore Call NameLoad SubscriptLoad NameLoad Index Str keyword Num keyword Num keyword Num keyword Num keyword NameLoad keyword NameLoad keyword NameLoad keyword NameLoad keyword NameLoad keyword NameLoad keyword Num keyword Num keyword NameLoad keyword NameLoad keyword NameLoad Assign NameStore Call NameLoad SubscriptLoad NameLoad Index Str Expr Call AttributeLoad NameLoad attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Dict Str Str Str Str Str Str Str Str Str Str Num Num Num Num Num Num Num Str Str Str Assign NameStore Call NameLoad SubscriptLoad NameLoad Index Str keyword NameLoad keyword NameLoad Assign NameStore Call NameLoad SubscriptLoad NameLoad Index Str Expr Call AttributeLoad NameLoad attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Dict Str Str Str Str Str Str Str Str Str Str Num Num Num Num Num Num Num Str Str Str Assign NameStore Call NameLoad SubscriptLoad NameLoad Index Str Assign NameStore Call NameLoad SubscriptLoad NameLoad Index Str Expr Call AttributeLoad NameLoad attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Dict Str Str Str Str Str Str Str Str Str Str Num Num Num Num Num Num Num Str Str Str Assign NameStore Call NameLoad SubscriptLoad NameLoad Index Str Assign NameStore Call NameLoad SubscriptLoad NameLoad Index Str Expr Call AttributeLoad NameLoad attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore ListLoad Str Str Str Str Str Assign NameStore NameLoad Expr Call AttributeLoad NameLoad attr keyword NameLoad keyword NameLoad keyword Str keyword Num keyword Call NameLoad Num Num keyword AttributeLoad NameLoad attr keyword AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore ListLoad Str Str Str Str Str Assign NameStore NameLoad Expr Call AttributeLoad NameLoad attr keyword NameLoad keyword NameLoad keyword Str keyword Num keyword Call NameLoad Num Num keyword AttributeLoad NameLoad attr keyword AttributeLoad NameLoad attr Assign NameStore Dict Str Str Str Str Str Str Str Str Str Str Num Num Num Num Num Num Num Str Str Str Assign NameStore Call NameLoad SubscriptLoad NameLoad Index Str keyword Num Assign NameStore Call NameLoad SubscriptLoad NameLoad Index Str Expr Call AttributeLoad NameLoad attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore ListLoad Str Str Str Str Str Assign NameStore NameLoad Assign NameStore Dict Str Str Str Str Str Dict Str Str Str Str Str Num Num Num Num Num Dict Str Str Str Str Str Num Num Num Num Num Dict Str Str Str Str Str Num Num Num Num Num Dict Str Str Str Str Str Num Num Num Num Num Dict Str Str Str Str Str Num Num Num Num Num For NameStore NameLoad body For NameStore NameLoad body Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad keyword NameLoad Assign NameStore Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore ListLoad Str Str Str Str Str Assign NameStore NameLoad Expr Call AttributeLoad NameLoad attr keyword NameLoad keyword NameLoad keyword Str keyword Num keyword Call NameLoad Num Num keyword AttributeLoad NameLoad attr keyword AttributeLoad NameLoad attr Assign NameStore Dict Str Str Str Str Str Str Str Str Str Str Num Num Num Num Num Num Num Str Str Str Assign NameStore Call NameLoad SubscriptLoad NameLoad Index Str keyword Num Assign NameStore Call NameLoad SubscriptLoad NameLoad Index Str Expr Call AttributeLoad NameLoad attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore ListLoad Str Str Str Str Str Assign NameStore NameLoad Expr Call AttributeLoad NameLoad attr keyword NameLoad keyword NameLoad keyword Str keyword Num keyword Call NameLoad Num Num keyword AttributeLoad NameLoad attr keyword AttributeLoad NameLoad attr Assign NameStore Dict Str Str Str Str Str Str Str Str Str Str Num Num Num Num Num Num Num Str Str Str Assign NameStore Call NameLoad SubscriptLoad NameLoad Index Str keyword Num Assign NameStore Call NameLoad SubscriptLoad NameLoad Index Str Expr Call AttributeLoad NameLoad attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore ListLoad Str Str Str Str Str Assign NameStore NameLoad Expr Call AttributeLoad NameLoad attr keyword NameLoad keyword NameLoad keyword ListLoad TupleLoad Str NameLoad keyword ListLoad Str Str Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore ListLoad Str Str Str Str Str Assign NameStore NameLoad Expr Call AttributeLoad NameLoad attr keyword NameLoad keyword NameLoad keyword ListLoad TupleLoad Str Num keyword ListLoad Str Str Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore ListLoad Str Str Str Str Str Assign NameStore NameLoad Expr Call AttributeLoad NameLoad attr keyword NameLoad keyword NameLoad keyword ListLoad TupleLoad Str Num keyword ListLoad Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore ListLoad Str Str Str Str Str Assign NameStore NameLoad Expr Call AttributeLoad NameLoad attr keyword NameLoad keyword NameLoad keyword ListLoad TupleLoad Str NameLoad TupleLoad Str Num keyword ListLoad Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore ListLoad TupleLoad Dict Str Str Str Str Str Str Str Str Str Str Num Num Num Num Num Num Num Str Str Str NameLoad TupleLoad Dict Str Str Str Str Str Str Str Str Str Str Num Num Num Num Num Num Num Str Str Str NameLoad For TupleStore NameStore NameStore NameLoad body Assign NameStore Call NameLoad SubscriptLoad NameLoad Index Str keyword NameLoad Assign NameStore Call NameLoad SubscriptLoad NameLoad Index Str Expr Call AttributeLoad NameLoad attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Dict Str Str Str Str Str Str Str Str Str Str Num Num Num Num Num Num Num Str Str Str Assign NameStore Call NameLoad Str keyword NameLoad Assign NameStore Call NameLoad Str Expr Call AttributeLoad NameLoad attr NameLoad NameLoad decorator_list decorator_list ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam NameParam NameParam defaults body Assign TupleStore NameStore NameStore NameStore NameLoad Expr Call AttributeLoad NameLoad attr NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr NameLoad Call NameLoad ListLoad Call NameLoad AttributeLoad NameLoad attr Call NameLoad AttributeLoad NameLoad attr If CompareEq AttributeLoad NameLoad attr Num body Expr Call AttributeLoad NameLoad attr NameLoad NameLoad orelse For TupleStore TupleStore NameStore NameStore TupleStore NameStore NameStore Call NameLoad NameLoad ListLoad TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Str Assign NameStore Str Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad Call NameLoad NameLoad Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Str Assign NameStore Str Assign NameStore Call NameLoad NameLoad keyword NameLoad keyword NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad Call NameLoad NameLoad Call NameLoad NameLoad keyword NameLoad Expr Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Dict Assign SubscriptStore NameLoad Index Str Num Assign SubscriptStore NameLoad Index Str Num Assign NameStore Str Assign NameStore Str Assign NameStore Call NameLoad NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad Call NameLoad NameLoad Call NameLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body With Call AttributeLoad NameLoad attr NameLoad Str body Expr Call NameLoad Call NameLoad Str Call NameLoad Str With Call AttributeLoad NameLoad attr NameLoad Str body Expr Call NameLoad Str Call NameLoad Str decorator_list FunctionDef arguments args NameParam defaults body With Call AttributeLoad NameLoad attr NameLoad Str body Expr Call NameLoad Call NameLoad Str Call NameLoad Str decorator_list decorator_list ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam defaults body ClassDef bases NameLoad body FunctionDef arguments args NameParam NameParam NameParam NameParam defaults body For NameStore NameLoad body Expr Call NameLoad NameLoad NameLoad SubscriptLoad NameLoad Index NameLoad decorator_list decorator_list Return Call NameLoad NameLoad NameLoad Num decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Str Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad Str For NameStore AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad NameLoad SubscriptLoad NameLoad Index NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore ListLoad TupleLoad Dict Str Str Str Str NameLoad TupleLoad Dict Str Str Str Str NameLoad For TupleStore NameStore NameStore NameLoad body Assign NameStore Call NameLoad SubscriptLoad NameLoad Index Str keyword NameLoad Assign NameStore Call NameLoad SubscriptLoad NameLoad Index Str Expr Call AttributeLoad NameLoad attr NameLoad Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore ListLoad TupleLoad Dict Str Str Str Str NameLoad TupleLoad Dict Str Str Str Str NameLoad For TupleStore NameStore NameStore NameLoad body Assign NameStore Call NameLoad SubscriptLoad NameLoad Index Str keyword NameLoad Assign NameStore Call NameLoad SubscriptLoad NameLoad Index Str Expr Call AttributeLoad NameLoad attr UnaryOpNot NameLoad Expr Call AttributeLoad NameLoad attr UnaryOpNot NameLoad Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Str Assign NameStore ListLoad Dict Str Str Str Str Str ListLoad TupleLoad Num Str TupleLoad Num Str TupleLoad Num Str TupleLoad Num Str Num Num Str Str Dict Str Str Str Str Str ListLoad TupleLoad Num Str Num Num Str Str Dict Str Str Str Str Str ListLoad TupleLoad Num Str TupleLoad Num Str TupleLoad Num Str TupleLoad Num Str Num Num Str Str Dict Str Str Str Str Str ListLoad TupleLoad Num Str TupleLoad Num Str TupleLoad Num Str TupleLoad Num Str Num Num Str Str Dict Str Str Str Str Str ListLoad TupleLoad Num Str TupleLoad Num Str TupleLoad Num Str TupleLoad Num Str TupleLoad Num Str TupleLoad Num Str TupleLoad Num Str TupleLoad Num Str TupleLoad Num Str Num Num Str Str For NameStore NameLoad body Assign NameStore Call AttributeLoad NameLoad attr Dict Assign NameStore BinOpAdd BinOpAdd BinOpSub SubscriptLoad NameLoad Index Str Num SubscriptLoad NameLoad Index Str Call NameLoad ListComp IfExp CompareEq NameLoad Str NameLoad Num comprehension TupleStore NameStore NameStore SubscriptLoad NameLoad Index Str Expr Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Index Str Call AttributeLoad NameLoad attr NameLoad NameLoad SubscriptLoad NameLoad Index Str SubscriptLoad NameLoad Index Str NameLoad SubscriptLoad NameLoad Index Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call NameLoad Str Assign NameStore Call NameLoad Str Expr Call AttributeLoad NameLoad attr Str AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Str AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call NameLoad Str keyword NameLoad Assign NameStore Call NameLoad Str Expr Call AttributeLoad NameLoad attr NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr NameLoad AttributeLoad NameLoad attr decorator_list decorator_list If CompareEq NameLoad Str body Expr Call NameLoad
N/A unittest TestCase main skbio local_pairwise_align_ssw Sequence DNA RNA Protein TabularMSA skbio.alignment StripedSmithWaterman AlignmentStructure skbio.alignment._pairwise blosum50 TestSSW N/A TestCase N/A N/A align_attributes N/A optimal_alignment_score suboptimal_alignment_score target_begin target_end_optimal target_end_suboptimal query_begin query_end cigar query_sequence target_sequence _check_alignment N/A N/A self alignment expected N/A N/A N/A attribute N/A self align_attributes N/A N/A N/A N/A self assertEqual N/A N/A expected N/A target_sequence N/A expected N/A attribute N/A N/A alignment N/A target_sequence N/A alignment N/A attribute N/A _check_argument_with_inequality_on_optimal_align_score N/A N/A self query_sequences target_sequences arg default i_range compare_lt compare_gt N/A None None None None None None None N/A N/A iterable_kwarg N/A N/A default_kwarg N/A N/A N/A default_kwarg N/A arg default N/A query_sequence query_sequences N/A N/A target_sequence target_sequences N/A N/A i i_range N/A N/A N/A iterable_kwarg N/A arg i N/A query1 N/A StripedSmithWaterman query_sequence iterable_kwarg N/A align1 N/A query1 target_sequence N/A query2 N/A StripedSmithWaterman query_sequence default_kwarg N/A align2 N/A query2 target_sequence N/A N/A i default N/A N/A N/A N/A self assertEqual N/A align1 optimal_alignment_score N/A align2 optimal_alignment_score N/A N/A i default N/A N/A N/A compare_lt N/A align1 optimal_alignment_score N/A align2 optimal_alignment_score N/A N/A i default N/A N/A N/A compare_gt N/A align1 optimal_alignment_score N/A align2 optimal_alignment_score N/A _check_bit_flag_sets_properties_falsy_or_negative N/A N/A self query_sequences target_sequences arg_settings properties_to_null N/A None None N/A N/A N/A N/A kwarg N/A falsy_or_negative N/A N/A alignment prop N/A N/A N/A N/A N/A type N/A alignment N/A prop int N/A N/A N/A N/A alignment N/A prop 0 N/A N/A N/A N/A alignment N/A prop N/A N/A query_sequence query_sequences N/A N/A target_sequence target_sequences N/A N/A N/A arg setting arg_settings N/A N/A N/A kwarg N/A arg setting N/A query N/A StripedSmithWaterman query_sequence kwarg N/A alignment N/A query target_sequence N/A prop properties_to_null N/A N/A N/A N/A self assertTrue N/A falsy_or_negative alignment prop N/A prop N/A p N/A p N/A self align_attributes N/A p properties_to_null N/A N/A N/A N/A self assertFalse N/A falsy_or_negative alignment prop N/A N/A TestStripedSmithWaterman N/A TestSSW N/A test_object_is_reusable N/A N/A self N/A N/A N/A q_seq AGGGTAATTAGGCGTGTTCACCTA N/A expected_alignments N/A N/A optimal_alignment_score suboptimal_alignment_score query_begin query_end target_begin target_end_optimal target_end_suboptimal cigar query_sequence target_sequence 10 10 4 8 3 7 34 5M q_seq TTATAATTTTCTTATTATTATCAATATTTATAATTTGATTTTGTTGTAAT N/A optimal_alignment_score suboptimal_alignment_score query_begin query_end target_begin target_end_optimal target_end_suboptimal cigar query_sequence target_sequence 36 16 0 23 6 29 13 8M1D8M1I7M q_seq AGTCGAAGGGTAATATAGGCGTGTCACCTA N/A optimal_alignment_score suboptimal_alignment_score query_begin query_end target_begin target_end_optimal target_end_suboptimal cigar query_sequence target_sequence 16 0 0 7 6 13 0 8M q_seq AGTCGAAGGGTAATA N/A optimal_alignment_score suboptimal_alignment_score query_begin query_end target_begin target_end_optimal target_end_suboptimal cigar query_sequence target_sequence 8 8 0 3 7 10 42 4M q_seq CTGCCTCAGGGGGAGGAAAGCGTCAGCGCGGCTGCCGTCGGCGCAGGGGC N/A optimal_alignment_score suboptimal_alignment_score query_begin query_end target_begin target_end_optimal target_end_suboptimal cigar query_sequence target_sequence 48 16 0 23 0 23 7 24M q_seq q_seq N/A query N/A StripedSmithWaterman q_seq N/A results N/A N/A expected expected_alignments N/A N/A alignment N/A query N/A expected N/A target_sequence N/A N/A N/A results append alignment N/A N/A result expected N/A zip results expected_alignments N/A N/A N/A N/A self _check_alignment result expected N/A test_regression_on_instantiation_arguments N/A N/A self N/A N/A N/A expected N/A optimal_alignment_score suboptimal_alignment_score query_begin query_end target_begin target_end_optimal target_end_suboptimal cigar query_sequence target_sequence 23 10 0 16 0 20 4 6M4D11M AAACGATAAATCCGCGTA AAACGACTACTAAATCCGCGTGATAGGGGA N/A query N/A StripedSmithWaterman N/A expected N/A query_sequence gap_open_penalty 5 gap_extend_penalty 2 score_size 2 mask_length 15 mask_auto True score_only False score_filter None distance_filter None override_skip_babp False protein False match_score 2 mismatch_score -3 substitution_matrix None suppress_sequences False zero_index True N/A alignment N/A query N/A expected N/A target_sequence N/A N/A N/A self _check_alignment alignment expected N/A test_protein_sequence_is_usable N/A N/A self N/A N/A N/A expected N/A optimal_alignment_score suboptimal_alignment_score query_begin query_end target_begin target_end_optimal target_end_suboptimal cigar query_sequence target_sequence 316 95 0 52 0 52 18 15M1D15M1I22M VHLTGEEKSAVAALWGKVNVDEVGGEALGRXLLVVYPWTQRFFESFSDLSTPDABVMSNPKVKAHGK VHLTPEEKSAVTALWBGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPD* N/A query N/A StripedSmithWaterman N/A expected N/A query_sequence protein True substitution_matrix blosum50 N/A alignment N/A query N/A expected N/A target_sequence N/A N/A N/A self _check_alignment alignment expected N/A test_lowercase_is_valid_sequence N/A N/A self N/A N/A N/A expected N/A optimal_alignment_score suboptimal_alignment_score query_begin query_end target_begin target_end_optimal target_end_suboptimal cigar query_sequence target_sequence 23 10 0 16 0 20 4 6M4D11M aaacgataaatccgcgta aaacgactactaaatccgcgtgatagggga N/A query N/A StripedSmithWaterman N/A expected N/A query_sequence N/A alignment N/A query N/A expected N/A target_sequence N/A N/A N/A self _check_alignment alignment expected N/A test_align_with_N_in_nucleotide_sequence N/A N/A self N/A N/A N/A expected N/A optimal_alignment_score suboptimal_alignment_score query_begin query_end target_begin target_end_optimal target_end_suboptimal cigar query_sequence target_sequence 9 0 0 8 0 9 0 4M1D5M ACTCANNATCGANCTAGC ACTCGAAAATGTNNGCA N/A query N/A StripedSmithWaterman N/A expected N/A query_sequence N/A alignment N/A query N/A expected N/A target_sequence N/A N/A N/A self _check_alignment alignment expected N/A test_arg_match_score N/A N/A self N/A N/A N/A query_sequences N/A TTTTTTCTTATTATTATCAATATTTATAATTTGATTTTGTTGTAAT AGTCGAAGGGTCAATATAGGCGTGTCACCTA AGTCGAAGGGTAATA CTGCCTCAAGGGGGAGGAAAGCGTCAGCGCGGCTGCCGTCGGCGCAGGGGC AGGGTAATTTTAGGCGTGTTCACCTA N/A target_sequences query_sequences N/A N/A N/A self _check_argument_with_inequality_on_optimal_align_score query_sequences query_sequences target_sequences target_sequences arg match_score default 2 i_range N/A range 0 5 compare_lt N/A self assertLess compare_gt N/A self assertGreater N/A test_arg_mismatch_score N/A N/A self N/A N/A N/A query_sequences N/A TTATAATTAATTCTTATTATTATCAATATTTATAATTTGATTTTGTTGTAAT AGTCGAAGGGTAAGGGGTATAGGCGTGTCACCTA AGTCGAAGGGTAATA CTGCCTCAGGGGCGAGGAAAGCGTCAGCGCGGCTGCCGTCGGCGCAGGGGC AGGGTAATTAGCGCGTGTTCACCTA N/A target_sequences query_sequences N/A N/A N/A self _check_argument_with_inequality_on_optimal_align_score query_sequences query_sequences target_sequences target_sequences arg mismatch_score default -3 i_range N/A range -6 1 compare_lt N/A self assertLessEqual compare_gt N/A self assertGreaterEqual N/A expected N/A optimal_alignment_score suboptimal_alignment_score query_begin query_end target_begin target_end_optimal target_end_suboptimal cigar query_sequence target_sequence 8 0 5 8 10 13 0 4M AGAGGGTAATCAGCCGTGTCCACCGGAACACAACGCTATCGGGCGA GTTCGCCCCAGTAAAGTTGCTACCAAATCCGCATG N/A query N/A StripedSmithWaterman N/A expected N/A query_sequence mismatch_score -8 N/A alignment N/A query N/A expected N/A target_sequence N/A N/A N/A self _check_alignment alignment expected N/A test_arg_matrix_overrides_match_and_mismatch N/A N/A self N/A N/A N/A query_sequences N/A TTATAATTAATTCTTATTATTATCAATATTTATAATTTGATTTTGTTGTAAT AGTCGAAGGGTAAGGGGTATAGGCGTGTCACCTA AGTCGAAGGGTAATA CTGCCTCAGGGGCGAGGAAAGCGTCAGCGCGGCTGCCGTCGGCGCAGGGGC AGGGTAATTAGCGCGTGTTCACCTA N/A target_sequences query_sequences N/A matrix N/A A T C G N N/A A T C G N 4 -1 -2 -3 4 N/A A T C G N -1 1 -1 -4 1 N/A A T C G N -2 -1 10 1 1 N/A A T C G N -3 -4 1 3 1 N/A A T C G N 4 1 1 1 0 N/A query_sequence query_sequences N/A N/A target_sequence target_sequences N/A N/A query1 N/A StripedSmithWaterman query_sequence N/A align1 N/A query1 target_sequence N/A query2 N/A StripedSmithWaterman query_sequence substitution_matrix matrix N/A align2 N/A query2 target_sequence N/A N/A N/A self assertNotEqual N/A align1 optimal_alignment_score N/A align2 optimal_alignment_score N/A test_arg_gap_open_penalty N/A N/A self N/A N/A N/A query_sequences N/A TTATAATTTTCTTAGTTATTATCAATATTTATAATTTGATTTTGTTGTAAT AGTCCGAAGGGTAATATAGGCGTGTCACCTA AGTCGAAGGCGGTAATA CTGCCTCGGCAGGGGGAGGAAAGCGTCAGCGCGGCTGCCGTCGGCGCAGGGGC AGGGTAATTAAAGGCGTGTTCACCTA N/A target_sequences query_sequences N/A N/A N/A 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 N/A range 1 12 compare_lt N/A self assertGreaterEqual compare_gt N/A self assertLessEqual N/A expected N/A optimal_alignment_score suboptimal_alignment_score query_begin query_end target_begin target_end_optimal target_end_suboptimal cigar query_sequence target_sequence 51 20 0 37 0 29 9 5M4I3M3I1M1I21M TAGAGATTAATTGCCACATTGCCACTGCCAAAATTCTG TAGAGATTAATTGCCACTGCCAAAATTCTG N/A query N/A StripedSmithWaterman N/A expected N/A query_sequence gap_open_penalty 1 N/A alignment N/A query N/A expected N/A target_sequence N/A N/A N/A self _check_alignment alignment expected N/A test_arg_gap_extend_penalty N/A N/A self N/A N/A N/A query_sequences N/A TTATAATTTTCTTATTATTATCAATATTTATAATTTGATTTTGTTGTAAT AGTCGAAGGGTAATACTAGGCGTGTCACCTA AGTCGAAGGGTAATA CTGCCTCAGGGGGAGGCAAAGCGTCAGCGCGGCTGCCGTCGGCGCAGGGGC AGGGTAATTAGGCGTGTTCACCTA N/A target_sequences query_sequences N/A N/A N/A self _check_argument_with_inequality_on_optimal_align_score query_sequences query_sequences target_sequences target_sequences arg gap_extend_penalty default 2 i_range N/A range 1 10 compare_lt N/A self assertGreaterEqual compare_gt N/A self assertLessEqual N/A expected N/A optimal_alignment_score suboptimal_alignment_score query_begin query_end target_begin target_end_optimal target_end_suboptimal cigar query_sequence target_sequence 9 8 6 12 7 13 38 7M TCTATAAGATTCCGCATGCGTTACTTATAAGATGTCTCAACGG GCCCAGTAGCTTCCCAATATGAGAGCATCAATTGTAGATCGGGCC N/A query N/A StripedSmithWaterman N/A expected N/A query_sequence gap_extend_penalty 10 N/A alignment N/A query N/A expected N/A target_sequence N/A N/A N/A self _check_alignment alignment expected N/A test_arg_score_only N/A N/A self N/A N/A N/A query_sequences N/A TTATCGTGATTATTATCAATATTTATAATTTGATTTTGTTGTAAT AGTCGAAGGGTAATACTATAAGGCGTGTCACCTA AGTCGAAGGGTAATA AGGGTAATTAGGCGTGCGTGCGTGTTCACCTA AGGGTATTAGGCGTGTTCACCTA N/A target_sequences query_sequences N/A N/A N/A self _check_bit_flag_sets_properties_falsy_or_negative query_sequences query_sequences target_sequences target_sequences arg_settings N/A N/A score_only True properties_to_null N/A query_begin target_begin cigar N/A test_arg_score_filter_is_used N/A N/A self N/A N/A N/A query_sequences N/A TTATCGTGATTATTATCAATATTTATAATTTGATTTTGTTGTAAT AGTCGAAGGGTAATACTATAAGGCGTGTCACCTA AGTCGAAGGGTAATA AGGGTAATTAGGCGTGCGTGCGTGTTCACCTA AGGGTATTAGGCGTGTTCACCTA N/A target_sequences query_sequences N/A N/A N/A self _check_bit_flag_sets_properties_falsy_or_negative query_sequences query_sequences target_sequences target_sequences arg_settings N/A N/A score_filter 9001 properties_to_null N/A query_begin target_begin cigar N/A test_arg_distance_filter_is_used N/A N/A self N/A N/A N/A query_sequences N/A TTATCGTGATTATTATCAATATTTATAATTTGATTTTGTTGTAAT AGTCGAAGGGTAATACTATAAGGCGTGTCACCTA AGTCGAAGGGTAATA AGGGTAATTAGGCGTGCGTGCGTGTTCACCTA AGGGTATTAGGCGTGTTCACCTA N/A target_sequences query_sequences N/A N/A N/A self _check_bit_flag_sets_properties_falsy_or_negative query_sequences query_sequences target_sequences target_sequences arg_settings N/A N/A distance_filter 1 properties_to_null N/A cigar N/A test_arg_override_skip_babp N/A N/A self N/A N/A N/A query_sequences N/A TTATCGTGATTATTATCAATATTTATAATTTGATTTTGTTGTAAT AGTCGAAGGGTAATACTATAAGGCGTGTCACCTA AGTCGAAGGGTAATA AGGGTAATTAGGCGTGCGTGCGTGTTCACCTA AGGGTATTAGGCGTGTTCACCTA N/A target_sequences query_sequences N/A N/A N/A self _check_bit_flag_sets_properties_falsy_or_negative query_sequences query_sequences target_sequences target_sequences arg_settings N/A N/A override_skip_babp True N/A score_filter 9001 properties_to_null N/A cigar N/A test_arg_zero_index_changes_base_of_index_to_0_or_1 N/A N/A self N/A N/A N/A expected_alignments N/A N/A N/A optimal_alignment_score suboptimal_alignment_score query_begin query_end target_begin target_end_optimal target_end_suboptimal cigar query_sequence target_sequence 100 44 5 54 0 49 21 50M AGTCACGCGCGCCGCCGGGGGGCCGGCCGGCGCCGGGGGGCGCCCCGGGCGGGGC CGCGCGCCGCCGGGGGGCCGGCCGGCGCCGGGGGGCGCCCCGGGCGGGGC True N/A N/A optimal_alignment_score suboptimal_alignment_score query_begin query_end target_begin target_end_optimal target_end_suboptimal cigar query_sequence target_sequence 100 44 6 55 1 50 22 50M AGTCACGCGCGCCGCCGGGGGGCCGGCCGGCGCCGGGGGGCGCCCCGGGCGGGGC CGCGCGCCGCCGGGGGGCCGGCCGGCGCCGGGGGGCGCCCCGGGCGGGGC False N/A N/A expected z expected_alignments N/A N/A query N/A StripedSmithWaterman N/A expected N/A query_sequence zero_index z N/A alignment N/A query N/A expected N/A target_sequence N/A N/A N/A self _check_alignment alignment expected N/A test_arg_suppress_sequences N/A N/A self N/A N/A N/A expected N/A optimal_alignment_score suboptimal_alignment_score query_begin query_end target_begin target_end_optimal target_end_suboptimal cigar query_sequence target_sequence 100 44 5 54 0 49 21 50M N/A query N/A StripedSmithWaterman AGTCACGCGCGCCGCCGGGGGGCCGGCCGGCGCCGGGGGGCGCCCCGGGCGGGGC suppress_sequences True N/A alignment N/A query CGCGCGCCGCCGGGGGGCCGGCCGGCGCCGGGGGGCGCCCCGGGCGGGGC N/A N/A N/A self _check_alignment alignment expected N/A N/A TestAlignStripedSmithWaterman N/A TestSSW N/A _check_TabularMSA_to_AlignmentStructure N/A N/A self alignment structure expected_dtype N/A N/A N/A N/A msa score start_end alignment N/A N/A N/A self assertEqual score N/A structure optimal_alignment_score N/A N/A N/A self assertEqual msa N/A TabularMSA N/A N/A expected_dtype N/A structure aligned_query_sequence N/A expected_dtype N/A structure aligned_target_sequence N/A N/A N/A structure query_begin -1 N/A N/A N/A N/A self assertEqual start_end None N/A N/A N/A N/A start end N/A expected_start expected_end N/A zip start_end N/A N/A N/A structure query_begin N/A structure query_end N/A N/A structure target_begin N/A structure target_end_optimal N/A N/A N/A N/A self assertEqual start expected_start N/A N/A N/A self assertEqual end expected_end N/A test_same_as_using_StripedSmithWaterman_object_DNA N/A N/A self N/A N/A N/A query_sequence ATGGAAGCTATAAGCGCGGGTGAG N/A target_sequence AACTTATATAATAAAAATTATATATTCGTTGGGTTCTTTTGATATAAATC N/A query N/A StripedSmithWaterman query_sequence N/A align1 N/A query target_sequence N/A align2 N/A local_pairwise_align_ssw N/A DNA query_sequence N/A DNA target_sequence N/A N/A N/A self _check_TabularMSA_to_AlignmentStructure align2 align1 DNA N/A test_same_as_using_StripedSmithWaterman_object_Protein N/A N/A self N/A N/A N/A query_sequence HEAGAWGHEE N/A target_sequence PAWHEAE N/A query N/A StripedSmithWaterman query_sequence protein True substitution_matrix blosum50 N/A align1 N/A query target_sequence N/A align2 N/A local_pairwise_align_ssw N/A Protein query_sequence N/A Protein target_sequence substitution_matrix blosum50 N/A N/A N/A self _check_TabularMSA_to_AlignmentStructure align2 align1 Protein N/A test_kwargs_are_usable N/A N/A self N/A N/A N/A kwargs N/A N/A N/A kwargs N/A mismatch_score -2 N/A N/A kwargs N/A match_score 5 N/A query_sequence AGGGTAATTAGGCGTGTTCACCTA N/A target_sequence TACTTATAAGATGTCTCAACGGCATGCGCAACTTGTGAAGTG N/A query N/A StripedSmithWaterman query_sequence kwargs N/A align1 N/A query target_sequence N/A align2 N/A local_pairwise_align_ssw N/A DNA query_sequence N/A DNA target_sequence kwargs N/A N/A N/A self _check_TabularMSA_to_AlignmentStructure align2 align1 DNA N/A test_invalid_type N/A N/A self N/A N/A N/A N/A N/A self assertRaisesRegex TypeError not type 'Sequence' N/A N/A N/A local_pairwise_align_ssw N/A DNA ACGT N/A Sequence ACGT N/A N/A N/A self assertRaisesRegex TypeError not type 'str' N/A N/A N/A local_pairwise_align_ssw ACGU N/A RNA ACGU N/A test_type_mismatch N/A N/A self N/A N/A N/A N/A N/A self assertRaisesRegex TypeError same type: 'DNA' != 'RNA' N/A N/A N/A local_pairwise_align_ssw N/A DNA ACGT N/A RNA ACGU N/A N/A TestAlignmentStructure N/A TestSSW N/A mock_object_factory N/A N/A self dictionary N/A N/A MockAlignmentStructure N/A AlignmentStructure N/A __init__ N/A N/A self _a _b _c N/A N/A N/A key dictionary N/A N/A N/A setattr self key N/A dictionary N/A key N/A N/A N/A N/A MockAlignmentStructure None None 0 N/A test_works_for_dot_and_square_bracket_access N/A N/A self N/A N/A N/A q_seq AGGGTAATTAGGCGTGTTCACCTA N/A query N/A StripedSmithWaterman q_seq N/A alignment N/A query TACTTATAAGATGTCTCAACGGCATGCGCAACTTGTGAAGTG N/A accessible N/A self align_attributes N/A N/A N/A N/A self assertEqual N/A getattr alignment accessible N/A alignment N/A accessible N/A test_is_zero_based_returns_true_if_index_base_is_zero N/A N/A self N/A N/A N/A expected_alignments N/A N/A N/A query_sequence target_sequence AGTCACGCGCGCCGCCGGGGGGCCGGCCGGCGCCGGGGGGCGCCCCGGGCGGGGC CGCGCGCCGCCGGGGGGCCGGCCGGCGCCGGGGGGCGCCCCGGGCGGGGC True N/A N/A query_sequence target_sequence AGTCACGCGCGCCGCCGGGGGGCCGGCCGGCGCCGGGGGGCGCCCCGGGCGGGGC CGCGCGCCGCCGGGGGGCCGGCCGGCGCCGGGGGGCGCCCCGGGCGGGGC False N/A N/A expected z expected_alignments N/A N/A query N/A StripedSmithWaterman N/A expected N/A query_sequence zero_index z N/A alignment N/A query N/A expected N/A target_sequence N/A N/A N/A self assertEqual z N/A N/A alignment is_zero_based N/A test_set_zero_based_changes_the_index_base N/A N/A self N/A N/A N/A expected_alignments N/A N/A N/A query_sequence target_sequence AGTCACGCGCGCCGCCGGGGGGCCGGCCGGCGCCGGGGGGCGCCCCGGGCGGGGC CGCGCGCCGCCGGGGGGCCGGCCGGCGCCGGGGGGCGCCCCGGGCGGGGC True N/A N/A query_sequence target_sequence AGTCACGCGCGCCGCCGGGGGGCCGGCCGGCGCCGGGGGGCGCCCCGGGCGGGGC CGCGCGCCGCCGGGGGGCCGGCCGGCGCCGGGGGGCGCCCCGGGCGGGGC False N/A N/A expected z expected_alignments N/A N/A query N/A StripedSmithWaterman N/A expected N/A query_sequence zero_index z N/A alignment N/A query N/A expected N/A target_sequence N/A N/A N/A alignment set_zero_based N/A z N/A N/A N/A self assertEqual N/A z N/A N/A alignment is_zero_based N/A test__get_aligned_sequences N/A N/A self N/A N/A N/A generic_sequence 123456789abcdefghijklmnopqrstuvwxyz N/A tests N/A N/A cigar_tuples begin end_after_cigar gap_type expected N/A N/A 4 M N/A 3 I N/A 1 D N/A 15 M 4 2 I 5678---9abcdefghijklmnop N/A cigar_tuples begin end_after_cigar gap_type expected N/A N/A 12 M 10 0 D bcdefghijklm N/A cigar_tuples begin end_after_cigar gap_type expected N/A N/A 10 D N/A 1 M N/A 3 I N/A 2 M 0 5 I 1---2345678 N/A cigar_tuples begin end_after_cigar gap_type expected N/A N/A 10 D N/A 1 M N/A 3 I N/A 2 M 3 0 D ----------456 N/A cigar_tuples begin end_after_cigar gap_type expected N/A N/A 1 I N/A 4 M N/A 3 I N/A 1 D N/A 8 M N/A 8 D N/A 2 I N/A 6 M N/A 1 I 4 3 I -5678---9abcdefg--hijklm-nop N/A test tests N/A N/A mock_object N/A N/A self mock_object_factory N/A N/A end N/A N/A N/A N/A test N/A end_after_cigar 1 N/A test N/A begin N/A sum N/A N/A N/A t M le 0 N/A N/A le t N/A test N/A cigar_tuples N/A N/A N/A self assertEqual N/A test N/A expected N/A N/A AlignmentStructure _get_aligned_sequence mock_object generic_sequence N/A test N/A cigar_tuples N/A test N/A begin end N/A test N/A gap_type N/A test_aligned_query_target_sequence N/A N/A self N/A N/A N/A query N/A StripedSmithWaterman AGGGTAATTAGGCGTGTTCACCTA N/A alignment N/A query AGTCGAAGGGTAATATAGGCGTGTCACCTA N/A N/A N/A self assertEqual AGGGTAATATAGGCGT-GTCACCTA N/A alignment aligned_target_sequence N/A N/A N/A self assertEqual AGGGTAAT-TAGGCGTGTTCACCTA N/A alignment aligned_query_sequence N/A test_aligned_query_target_sequence_with_suppressed_sequences N/A N/A self N/A N/A N/A query N/A StripedSmithWaterman AGGGTAATTAGGCGTGTTCACCTA suppress_sequences True N/A alignment N/A query AGTCGAAGGGTAATATAGGCGTGTCACCTA N/A N/A N/A self assertEqual None N/A alignment aligned_target_sequence N/A N/A N/A self assertEqual None N/A alignment aligned_query_sequence N/A N/A N/A N/A __name__ __main__ N/A N/A N/A main