Module Import alias Import alias identifier ImportFrom alias alias alias alias ImportFrom alias ImportFrom alias ImportFrom alias ClassDef bases AttributeLoad NameLoad attr body FunctionDef arguments args NameParam defaults body Assign AttributeStore NameLoad attr Call NameLoad ListLoad NameLoad Lambda arguments args NameParam defaults Call AttributeLoad NameLoad attr NameLoad keyword Str Lambda arguments args NameParam defaults Call AttributeLoad NameLoad attr NameLoad keyword AttributeLoad NameLoad attr Assign NameStore Str Assign NameStore Str Assign NameStore Str Assign NameStore Str Assign NameStore Str Assign NameStore Str Assign NameStore Call NameLoad Call NameLoad Call NameLoad NameLoad Assign AttributeStore NameLoad attr TupleLoad NameLoad NameLoad Assign AttributeStore NameLoad attr TupleLoad NameLoad NameLoad Assign NameStore BinOpAdd AttributeLoad NameLoad attr TupleLoad NameLoad Assign NameStore BinOpAdd AttributeLoad NameLoad attr TupleLoad NameLoad Assign NameStore BinOpAdd NameLoad TupleLoad NameLoad Assign NameStore BinOpAdd NameLoad TupleLoad NameLoad Assign AttributeStore NameLoad attr TupleLoad NameLoad NameLoad Assign NameStore BinOpAdd AttributeLoad NameLoad attr TupleLoad NameLoad Assign NameStore BinOpAdd AttributeLoad NameLoad attr TupleLoad NameLoad Assign AttributeStore NameLoad attr TupleLoad NameLoad NameLoad Assign NameStore BinOpAdd NameLoad TupleLoad NameLoad Assign NameStore BinOpAdd NameLoad TupleLoad NameLoad Assign AttributeStore NameLoad attr TupleLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body ClassDef bases NameLoad body Pass decorator_list With Call AttributeLoad NameLoad attr NameLoad NameStore body Expr Call NameLoad Expr Call AttributeLoad NameLoad attr Str Call NameLoad AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Str Call NameLoad AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore TupleLoad NameLoad Str Assign NameStore TupleLoad NameLoad Str For TupleStore NameStore NameStore TupleLoad NameLoad NameLoad body Assign NameStore Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr AttributeLoad Call NameLoad Str attr NameLoad Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore TupleLoad NameLoad Str Assign NameStore TupleLoad NameLoad Str For TupleStore NameStore NameStore TupleLoad NameLoad NameLoad body Assign NameStore Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr AttributeLoad Call NameLoad Str attr NameLoad Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore TupleLoad NameLoad Dict Str Str Str Str Str Str Str Str Str Str Str Call NameLoad ListLoad Str Str Str Call NameLoad ListLoad Str Str Str Call NameLoad ListLoad Str Str Str Call NameLoad ListLoad Str Str Call NameLoad ListLoad Str Str Call NameLoad ListLoad Str Str Str Str Call NameLoad ListLoad Str Str Call NameLoad ListLoad Str Str Call NameLoad ListLoad Str Str Call NameLoad ListLoad Str Str Str Call NameLoad ListLoad Str Str Assign NameStore TupleLoad NameLoad Dict Str Str Str Str Str Str Str Str Str Str Str Call NameLoad ListLoad Str Str Str Call NameLoad ListLoad Str Str Str Call NameLoad ListLoad Str Str Str Call NameLoad ListLoad Str Str Call NameLoad ListLoad Str Str Call NameLoad ListLoad Str Str Str Str Call NameLoad ListLoad Str Str Call NameLoad ListLoad Str Str Call NameLoad ListLoad Str Str Call NameLoad ListLoad Str Str Str Call NameLoad ListLoad Str Str For TupleStore NameStore NameStore TupleLoad NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr AttributeLoad Call NameLoad Str attr NameLoad Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore TupleLoad NameLoad Dict Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Assign NameStore TupleLoad NameLoad Dict Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str Str For TupleStore NameStore NameStore TupleLoad NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr AttributeLoad Call NameLoad Str attr NameLoad Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr NameLoad Assign SubscriptStore AttributeLoad NameLoad attr Index Str Str Assign SubscriptStore AttributeLoad NameLoad attr Index Str Str Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr NameLoad With Call AttributeLoad NameLoad attr NameLoad body Assign AttributeStore Call NameLoad Str attr Dict Str Str decorator_list FunctionDef arguments args NameParam defaults body For NameStore TupleLoad Call NameLoad Str Call NameLoad Str body Assign NameStore Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr NameLoad Call NameLoad Str Assign NameStore Call AttributeLoad NameLoad attr Num Expr Call AttributeLoad NameLoad attr NameLoad Call NameLoad Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call NameLoad BinOpMult Str Num BinOpMult Str Num For NameStore TupleLoad Call NameLoad Str Call NameLoad Str body Assign NameStore Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Call NameLoad Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call NameLoad Str For NameStore TupleLoad Call NameLoad Str Call NameLoad Str body Assign NameStore Call AttributeLoad NameLoad attr Num keyword Num keyword Str keyword Str Expr Call AttributeLoad NameLoad attr NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr keyword Num keyword Num keyword Str keyword Str Expr Call AttributeLoad NameLoad attr NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr Num Num Str Str Expr Call AttributeLoad NameLoad attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Dict Str Str Str Num Assign NameStore Dict Str Call NameLoad Num For NameStore TupleLoad Call NameLoad Str keyword NameLoad keyword NameLoad Call NameLoad Str keyword NameLoad keyword NameLoad body Assign NameStore Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr NameLoad Call NameLoad Str keyword Dict Str Str Str Num decorator_list FunctionDef arguments args NameParam defaults body For NameStore TupleLoad Call NameLoad Str Call NameLoad Str body With Call AttributeLoad NameLoad attr NameLoad Str body Expr Call AttributeLoad NameLoad attr Num decorator_list FunctionDef arguments args NameParam defaults body For NameStore TupleLoad Call NameLoad Str Call NameLoad Str body Assign NameStore Call NameLoad Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr NameLoad ListLoad Call NameLoad Str Call NameLoad Str Call NameLoad Str Call NameLoad Str Call NameLoad Str Call NameLoad Str Assign NameStore Call NameLoad Call AttributeLoad NameLoad attr Num Expr Call AttributeLoad NameLoad attr NameLoad ListLoad Call NameLoad Str Call NameLoad Str Call NameLoad Str Call NameLoad Str Call NameLoad Str Call NameLoad Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call NameLoad BinOpMult Str Num BinOpMult Str Num For NameStore TupleLoad Call NameLoad Str Call NameLoad Str body Assign NameStore Call NameLoad Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr NameLoad ListLoad Call NameLoad Str Call NameLoad Str Call NameLoad Str Call NameLoad Str Call NameLoad Str Call NameLoad Str decorator_list FunctionDef arguments args NameParam defaults body For NameStore TupleLoad Call NameLoad Str Call NameLoad Str body Assign NameStore Call NameLoad Call AttributeLoad NameLoad attr Num keyword Str keyword Str Expr Call AttributeLoad NameLoad attr NameLoad Call NameLoad Str Assign NameStore Call NameLoad Call AttributeLoad NameLoad attr keyword Num keyword Str keyword Str Expr Call AttributeLoad NameLoad attr NameLoad Call NameLoad Str Assign NameStore Call NameLoad Call AttributeLoad NameLoad attr Num Str Str Expr Call AttributeLoad NameLoad attr NameLoad Call NameLoad Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Dict Str Str Str Num Assign NameStore Dict Str Call NameLoad Num For NameStore TupleLoad Call NameLoad Str keyword NameLoad keyword NameLoad Call NameLoad Str keyword NameLoad keyword NameLoad body Assign NameStore SubscriptLoad Call NameLoad Call AttributeLoad NameLoad attr Slice Num Expr Call AttributeLoad NameLoad attr NameLoad ListLoad Call NameLoad Str keyword Dict Str Str Str Num Call NameLoad Str keyword Dict Str Str Str Num decorator_list FunctionDef arguments args NameParam defaults body For NameStore TupleLoad Call NameLoad Str Call NameLoad Str body With Call AttributeLoad NameLoad attr NameLoad Str body Expr Call AttributeLoad NameLoad attr Num decorator_list FunctionDef arguments args NameParam defaults body For NameStore TupleLoad Call NameLoad Str Call NameLoad Str body Assign NameStore Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Str NameLoad Expr Call AttributeLoad NameLoad attr Str NameLoad For NameStore TupleLoad Call NameLoad Str Call NameLoad Str body Assign NameStore Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Str NameLoad Expr Call AttributeLoad NameLoad attr Str NameLoad For NameStore TupleLoad Call NameLoad Str Call NameLoad Str body Assign NameStore Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Str NameLoad Expr Call AttributeLoad NameLoad attr Str NameLoad For NameStore TupleLoad Call NameLoad Str Call NameLoad Str body Assign NameStore Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Str NameLoad Expr Call AttributeLoad NameLoad attr Str NameLoad For NameStore TupleLoad Call NameLoad Str Call NameLoad Str body Assign NameStore Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Str NameLoad Expr Call AttributeLoad NameLoad attr Str NameLoad decorator_list FunctionDef arguments args NameParam defaults body For NameStore TupleLoad NameLoad NameLoad body Assign NameStore Call AttributeLoad Call NameLoad Str attr Expr Call AttributeLoad NameLoad attr NameLoad Call NameLoad Str Assign NameStore Call AttributeLoad Call NameLoad Str keyword Dict Str Str Str Str keyword Dict Str ListLoad attr Expr Call AttributeLoad NameLoad attr NameLoad Call NameLoad Str keyword Dict Str Str Str Str keyword Dict Str ListLoad decorator_list FunctionDef arguments args NameParam defaults body For TupleStore NameStore NameStore NameStore NameStore AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad Call NameLoad NameLoad attr Expr Call AttributeLoad NameLoad attr NameLoad Call NameLoad NameLoad Assign NameStore Call AttributeLoad Call NameLoad NameLoad keyword Dict Str Str Str Str keyword Dict Str NameLoad attr Expr Call AttributeLoad NameLoad attr NameLoad Call NameLoad NameLoad keyword Dict Str Str Str Str keyword Dict Str NameLoad decorator_list FunctionDef arguments args NameParam defaults body For NameStore TupleLoad NameLoad NameLoad body Assign NameStore Call AttributeLoad Call NameLoad Str attr keyword NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Call NameLoad Str Assign NameStore Call AttributeLoad Call NameLoad Str keyword Dict Str Str Str Str keyword Dict Str ListLoad attr keyword NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Call NameLoad Str keyword Dict Str Str Str Str keyword Dict Str ListLoad decorator_list FunctionDef arguments args NameParam defaults body For TupleStore NameStore NameStore NameStore NameStore AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad Call NameLoad NameLoad attr keyword NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Call NameLoad NameLoad Assign NameStore Call AttributeLoad Call NameLoad NameLoad keyword Dict Str Str Str Str keyword Dict Str NameLoad attr keyword NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Call NameLoad NameLoad keyword Dict Str Str Str Str keyword Dict Str SubscriptLoad Call NameLoad NameLoad Slice Num decorator_list FunctionDef arguments args NameParam defaults body For TupleStore NameStore NameStore NameStore NameStore AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad Call NameLoad NameLoad keyword Dict Str Str Str Str keyword Dict Str NameLoad attr Expr Call AttributeLoad NameLoad attr NameLoad Call NameLoad NameLoad keyword Dict Str Str Str Str keyword Dict Str SubscriptLoad Call NameLoad NameLoad Slice Num decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Num For TupleStore NameStore NameStore NameStore AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr Call NameLoad ListLoad NameLoad For NameStore NameLoad body AugAssignAdd NameStore Num Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Num decorator_list FunctionDef arguments args NameParam defaults body For NameStore TupleLoad NameLoad NameLoad body Assign NameStore Call NameLoad Str Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call NameLoad Str keyword Dict Str Str Str Str keyword Dict Str Call AttributeLoad NameLoad attr ListLoad keyword AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body For TupleStore NameStore NameStore NameStore NameStore AttributeLoad NameLoad attr body Assign NameStore Call NameLoad NameLoad Assign NameStore Call NameLoad NameLoad keyword Dict Str Str Str Str keyword Dict Str NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body For NameStore TupleLoad NameLoad NameLoad body Assign NameStore Call NameLoad Str Assign NameStore Call NameLoad Str Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call NameLoad Str Assign NameStore Call NameLoad Str Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body For NameStore TupleLoad NameLoad NameLoad body ClassDef bases NameLoad body FunctionDef arguments args NameParam defaults body Return Dict Str Call NameLoad Str decorator_list NameLoad FunctionDef arguments args NameParam defaults body Return Call NameLoad Str decorator_list NameLoad FunctionDef arguments args NameParam defaults body Return Str decorator_list NameLoad FunctionDef arguments args NameParam defaults body Return Call NameLoad Str decorator_list NameLoad decorator_list Assign NameStore Call NameLoad Str Assign NameStore Call NameLoad Str With Call AttributeLoad NameLoad attr NameLoad Str body Expr Call AttributeLoad NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore TupleLoad NameLoad Str Str Assign NameStore TupleLoad NameLoad Str Str Assign NameStore TupleLoad NameLoad NameLoad For TupleStore NameStore NameStore NameStore NameLoad body Assign NameStore Call NameLoad Str Expr Call AttributeLoad NameLoad attr Call NameLoad Call AttributeLoad NameLoad attr Str ListLoad Assign NameStore Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Call NameLoad Call AttributeLoad NameLoad attr Str ListLoad Call NameLoad Num Num Call NameLoad Num Num Assign NameStore Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Call NameLoad Call AttributeLoad NameLoad attr Str keyword Num keyword Call AttributeLoad NameLoad attr ListLoad Call NameLoad Num Num decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore TupleLoad NameLoad Str Str Assign NameStore TupleLoad NameLoad Str Str Assign NameStore TupleLoad NameLoad NameLoad For TupleStore NameStore NameStore NameStore NameLoad body Assign NameStore Call NameLoad Str Expr Call AttributeLoad NameLoad attr Call NameLoad Call AttributeLoad NameLoad attr Str ListLoad Assign NameStore Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Call NameLoad Call AttributeLoad NameLoad attr Str ListLoad Call NameLoad Num Num Call NameLoad Num Num Assign NameStore Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Call NameLoad Call AttributeLoad NameLoad attr Str keyword Num keyword Call AttributeLoad NameLoad attr ListLoad Call NameLoad Num Num decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore TupleLoad TupleLoad Str Num Num TupleLoad Str Num Num TupleLoad Str Num Num TupleLoad Str Num Num TupleLoad Str Num Num TupleLoad Str Num Num TupleLoad Str Num Num TupleLoad Str Num Num TupleLoad Str Num Num TupleLoad Str Num Num TupleLoad Str Num Num TupleLoad Str Num Num Assign NameStore TupleLoad NameLoad BinOpAdd NameLoad TupleLoad TupleLoad Str Num Num Assign NameStore TupleLoad NameLoad BinOpAdd NameLoad TupleLoad TupleLoad Str Num Num For TupleStore NameStore NameStore TupleLoad NameLoad NameLoad body For TupleStore NameStore NameStore NameStore NameLoad body Assign NameStore Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr NameLoad Call AttributeLoad NameLoad attr keyword NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Call AttributeLoad NameLoad attr keyword NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Call AttributeLoad NameLoad attr decorator_list decorator_list If CompareEq NameLoad Str body Expr Call AttributeLoad NameLoad attr
N/A N/A unittest N/A numpy np skbio DNA RNA Protein GeneticCode skbio.sequence._nucleotide_mixin NucleotideMixin skbio.sequence GrammaredSequence skbio.util classproperty TestNucelotideSequence N/A N/A unittest TestCase N/A setUp N/A N/A self N/A N/A N/A N/A self sequence_kinds N/A frozenset N/A str N/A N/A N/A s N/A N/A N/A np fromstring s dtype |S1 N/A N/A N/A s N/A N/A N/A np fromstring s dtype N/A np uint8 N/A dna_str ACGTMRWSYKVHDBN.- N/A dna_comp_str TGCAKYWSRMBDHVN.- N/A dna_rev_comp_str -.NVHDBMRSWYKACGT N/A rna_str ACGUMRWSYKVHDBN.- N/A rna_comp_str UGCAKYWSRMBDHVN.- N/A rna_rev_comp_str -.NVHDBMRSWYKACGU N/A qual N/A tuple N/A range N/A len dna_str N/A N/A self dna N/A DNA dna_str N/A N/A self rna N/A RNA rna_str N/A dna_comp N/A N/A self dna N/A dna_comp_str N/A rna_comp N/A N/A self rna N/A rna_comp_str N/A dna_comp_qual N/A dna_comp N/A qual N/A rna_comp_qual N/A rna_comp N/A qual N/A N/A self all_combos_comp_qual N/A dna_comp_qual rna_comp_qual N/A dna_rev_comp N/A N/A self dna N/A dna_rev_comp_str N/A rna_rev_comp N/A N/A self rna N/A rna_rev_comp_str N/A N/A self all_combos_rev_comp N/A dna_rev_comp rna_rev_comp N/A dna_rev_comp_qual N/A dna_rev_comp N/A qual N/A rna_rev_comp_qual N/A rna_rev_comp N/A qual N/A N/A self all_combos_rev_comp_qual N/A dna_rev_comp_qual rna_rev_comp_qual N/A test_instantiation_with_no_implementation N/A N/A self N/A N/A NucleotideSequenceSubclassNoImplementation N/A NucleotideMixin N/A N/A N/A N/A N/A N/A self assertRaises TypeError cm N/A N/A N/A NucleotideSequenceSubclassNoImplementation N/A N/A N/A self assertIn abstract class N/A str N/A cm exception N/A N/A N/A self assertIn complement_map N/A str N/A cm exception N/A test_nondegenerate_chars N/A N/A self N/A N/A N/A dna N/A DNA ACGT N/A rna N/A RNA ACGU N/A N/A constructor nondegenerate N/A dna rna N/A N/A exp N/A set nondegenerate N/A N/A N/A self assertEqual N/A N/A constructor nondegenerate_chars exp N/A N/A N/A self assertEqual N/A constructor nondegenerate_chars exp N/A test_definite_chars N/A N/A self N/A N/A N/A dna N/A DNA ACGT N/A rna N/A RNA ACGU N/A N/A constructor definite_char N/A dna rna N/A N/A exp N/A set definite_char N/A N/A N/A self assertEqual N/A N/A constructor definite_chars exp N/A N/A N/A self assertEqual N/A constructor definite_chars exp N/A test_degenerate_map N/A N/A self N/A N/A N/A dna_exp N/A DNA N/A B D H K M N S R W V Y N/A set N/A C T G N/A set N/A A T G N/A set N/A A C T N/A set N/A T G N/A set N/A A C N/A set N/A A C T G N/A set N/A C G N/A set N/A A G N/A set N/A A T N/A set N/A A C G N/A set N/A C T N/A rna_exp N/A RNA N/A B D H K M N S R W V Y N/A set N/A C U G N/A set N/A A U G N/A set N/A A C U N/A set N/A U G N/A set N/A A C N/A set N/A A C U G N/A set N/A C G N/A set N/A A G N/A set N/A A U N/A set N/A A C G N/A set N/A C U N/A N/A constructor degenerate N/A dna_exp rna_exp N/A N/A N/A N/A self assertEqual N/A N/A constructor degenerate_map degenerate N/A N/A N/A self assertEqual N/A constructor degenerate_map degenerate N/A test_complement_map N/A N/A self N/A N/A N/A dna_exp N/A DNA N/A - . A C B D G H K M N S R T W V Y - . T G V H C D M K N S Y A W B R N/A rna_exp N/A RNA N/A - . A C B D G H K M N S R U W V Y - . U G V H C D M K N S Y A W B R N/A N/A constructor comp_map N/A dna_exp rna_exp N/A N/A N/A N/A self assertEqual N/A N/A constructor complement_map comp_map N/A N/A N/A self assertEqual N/A constructor complement_map comp_map N/A N/A N/A constructor complement_map N/A A X N/A N/A N/A constructor complement_map N/A C W N/A N/A N/A self assertEqual N/A constructor complement_map comp_map N/A N/A N/A self assertRaises AttributeError N/A N/A N/A N/A constructor complement_map N/A W X N/A test_translate_ncbi_table_id N/A N/A self N/A N/A N/A seq N/A N/A RNA AAAUUUAUGCAU N/A DNA AAATTTATGCAT N/A N/A obs N/A N/A seq translate N/A N/A N/A self assertEqual obs N/A Protein KFMH N/A obs N/A N/A seq translate 9 N/A N/A N/A self assertEqual obs N/A Protein NFMH N/A test_translate_genetic_code_object N/A N/A self N/A N/A N/A gc N/A GeneticCode N/A M 64 N/A - 64 N/A seq N/A N/A RNA AAAUUUAUGCAU N/A DNA AAATTTATGCAT N/A N/A obs N/A N/A seq translate gc N/A N/A N/A self assertEqual obs N/A Protein MMMM N/A test_translate_passes_parameters_through N/A N/A self N/A N/A N/A exp N/A Protein MW N/A seq N/A N/A RNA UAAAUUGUGGUAA N/A DNA TAAATTGTGGTAA N/A N/A obs N/A N/A seq translate 13 reading_frame 2 start require stop require N/A N/A N/A self assertEqual obs exp N/A obs N/A N/A seq translate genetic_code 13 reading_frame 2 start require stop require N/A N/A N/A self assertEqual obs exp N/A obs N/A N/A seq translate 13 2 require require N/A N/A N/A self assertEqual obs exp N/A test_translate_preserves_metadata N/A N/A self N/A N/A N/A metadata N/A foo baz bar 42 N/A positional_metadata N/A foo N/A range 3 N/A seq N/A N/A RNA AUG metadata metadata positional_metadata positional_metadata N/A DNA ATG metadata metadata positional_metadata positional_metadata N/A N/A obs N/A N/A seq translate N/A N/A N/A self assertEqual obs N/A Protein M metadata N/A foo baz bar 42 N/A test_translate_invalid_id N/A N/A self N/A N/A N/A seq N/A N/A RNA AUG N/A DNA ATG N/A N/A N/A N/A self assertRaisesRegex ValueError table_id.*42 N/A N/A N/A N/A seq translate 42 N/A test_translate_six_frames_ncbi_table_id N/A N/A self N/A N/A N/A seq N/A N/A RNA AAAUUG N/A DNA AAATTG N/A N/A obs N/A list N/A N/A seq translate_six_frames N/A N/A N/A self assertEqual obs N/A N/A Protein KL N/A Protein N N/A Protein I N/A Protein QF N/A Protein N N/A Protein I N/A obs N/A list N/A N/A seq translate_six_frames 9 N/A N/A N/A self assertEqual obs N/A N/A Protein NL N/A Protein N N/A Protein I N/A Protein QF N/A Protein N N/A Protein I N/A test_translate_six_frames_genetic_code_object N/A N/A self N/A N/A N/A gc N/A GeneticCode N/A M 64 N/A - 64 N/A seq N/A N/A RNA AAAUUG N/A DNA AAATTG N/A N/A obs N/A list N/A N/A seq translate_six_frames gc N/A N/A N/A self assertEqual obs N/A N/A Protein MM N/A Protein M N/A Protein M N/A Protein MM N/A Protein M N/A Protein M N/A test_translate_six_frames_passes_parameters_through N/A N/A self N/A N/A N/A seq N/A N/A RNA UUUAUGUGGUGA N/A DNA TTTATGTGGTGA N/A N/A obs N/A next N/A N/A seq translate_six_frames 11 start require stop require N/A N/A N/A self assertEqual obs N/A Protein MW N/A obs N/A next N/A N/A seq translate_six_frames genetic_code 11 start require stop require N/A N/A N/A self assertEqual obs N/A Protein MW N/A obs N/A next N/A N/A seq translate_six_frames 11 require require N/A N/A N/A self assertEqual obs N/A Protein MW N/A test_translate_six_frames_preserves_metadata N/A N/A self N/A N/A N/A metadata N/A foo baz bar 42 N/A positional_metadata N/A foo N/A range 3 N/A seq N/A N/A RNA AUG metadata metadata positional_metadata positional_metadata N/A DNA ATG metadata metadata positional_metadata positional_metadata N/A N/A obs N/A N/A list N/A N/A seq translate_six_frames N/A 2 N/A N/A N/A self assertEqual obs N/A N/A Protein M metadata N/A foo baz bar 42 N/A Protein metadata N/A foo baz bar 42 N/A test_translate_six_frames_invalid_id N/A N/A self N/A N/A N/A seq N/A N/A RNA AUG N/A DNA ATG N/A N/A N/A N/A self assertRaisesRegex ValueError table_id.*42 N/A N/A N/A N/A seq translate_six_frames 42 N/A test_repr N/A N/A self N/A N/A N/A seq N/A N/A DNA N/A RNA N/A N/A obs N/A repr seq N/A N/A N/A self assertIn has gaps: False obs N/A N/A N/A self assertIn GC-content: 0.00% obs N/A seq N/A N/A DNA ACGT N/A RNA ACGU N/A N/A obs N/A repr seq N/A N/A N/A self assertIn has gaps: False obs N/A N/A N/A self assertIn GC-content: 50.00% obs N/A seq N/A N/A DNA CST N/A RNA CSU N/A N/A obs N/A repr seq N/A N/A N/A self assertIn has gaps: False obs N/A N/A N/A self assertIn GC-content: 66.67% obs N/A seq N/A N/A DNA GCSSCG N/A RNA GCSSCG N/A N/A obs N/A repr seq N/A N/A N/A self assertIn has gaps: False obs N/A N/A N/A self assertIn GC-content: 100.00% obs N/A seq N/A N/A DNA -GCSSCG. N/A RNA -GCSSCG. N/A N/A obs N/A repr seq N/A N/A N/A self assertIn has gaps: True obs N/A N/A N/A self assertIn GC-content: 100.00% obs N/A test_complement_without_reverse_empty N/A N/A self N/A N/A N/A constructor N/A DNA RNA N/A N/A comp N/A N/A N/A constructor complement N/A N/A N/A self assertEqual comp N/A constructor N/A comp N/A N/A N/A constructor metadata N/A id description foo bar positional_metadata N/A quality N/A complement N/A N/A N/A self assertEqual comp N/A constructor metadata N/A id description foo bar positional_metadata N/A quality N/A N/A test_complement_without_reverse_non_empty N/A N/A self N/A N/A N/A N/A constructor seq_str comp_str qual N/A self all_combos_comp_qual N/A N/A comp N/A N/A N/A constructor seq_str complement N/A N/A N/A self assertEqual comp N/A constructor comp_str N/A comp N/A N/A N/A constructor seq_str metadata N/A id description foo bar positional_metadata N/A quality qual complement N/A N/A N/A self assertEqual comp N/A constructor comp_str metadata N/A id description foo bar positional_metadata N/A quality qual N/A test_complement_with_reverse_empty N/A N/A self N/A N/A N/A constructor N/A DNA RNA N/A N/A rc N/A N/A N/A constructor complement reverse True N/A N/A N/A self assertEqual rc N/A constructor N/A rc N/A N/A N/A constructor metadata N/A id description foo bar positional_metadata N/A quality N/A complement reverse True N/A N/A N/A self assertEqual rc N/A constructor metadata N/A id description foo bar positional_metadata N/A quality N/A N/A test_complement_with_reverse_non_empty N/A N/A self N/A N/A N/A N/A constructor seq_str rev_comp_str qual N/A self all_combos_rev_comp_qual N/A N/A rc N/A N/A N/A constructor seq_str complement reverse True N/A N/A N/A self assertEqual rc N/A constructor rev_comp_str N/A rc N/A N/A N/A constructor seq_str metadata N/A id description foo bar positional_metadata N/A quality qual complement reverse True N/A N/A N/A self assertEqual rc N/A constructor rev_comp_str metadata N/A id description foo bar positional_metadata N/A quality N/A N/A list qual N/A -1 N/A test_reverse_complement N/A N/A self N/A N/A N/A N/A constructor seq_str rev_comp_str qual N/A self all_combos_rev_comp_qual N/A N/A rc N/A N/A N/A constructor seq_str metadata N/A id description foo bar positional_metadata N/A quality qual reverse_complement N/A N/A N/A self assertEqual rc N/A constructor rev_comp_str metadata N/A id description foo bar positional_metadata N/A quality N/A N/A list qual N/A -1 N/A test_is_reverse_complement_varied_types N/A N/A self N/A N/A N/A tested 0 N/A N/A constructor seq_str rev_comp_str N/A self all_combos_rev_comp N/A N/A seq_kinds N/A N/A N/A self sequence_kinds union N/A frozenset N/A constructor N/A sequence seq_kinds N/A N/A tested 1 N/A seq1 N/A constructor seq_str N/A seq2 N/A sequence rev_comp_str N/A N/A N/A self assertTrue N/A N/A seq1 is_reverse_complement seq2 N/A N/A N/A self assertEqual tested 8 N/A test_is_reverse_complement_empty N/A N/A self N/A N/A N/A constructor N/A DNA RNA N/A N/A seq1 N/A constructor N/A N/A N/A self assertTrue N/A N/A seq1 is_reverse_complement seq1 N/A seq2 N/A constructor metadata N/A id description foo bar positional_metadata N/A quality N/A N/A np array N/A dtype N/A np int64 N/A N/A N/A self assertTrue N/A N/A seq2 is_reverse_complement seq2 N/A N/A N/A self assertTrue N/A N/A seq1 is_reverse_complement seq2 N/A N/A N/A self assertTrue N/A N/A seq2 is_reverse_complement seq1 N/A test_is_reverse_complement_metadata_ignored N/A N/A self N/A N/A N/A N/A constructor seq_str rev_comp_str qual N/A self all_combos_rev_comp_qual N/A N/A seq1 N/A constructor seq_str N/A seq2 N/A constructor rev_comp_str metadata N/A id description foo bar positional_metadata N/A quality qual N/A N/A N/A self assertFalse N/A N/A seq1 is_reverse_complement seq1 N/A N/A N/A self assertFalse N/A N/A seq2 is_reverse_complement seq2 N/A N/A N/A self assertTrue N/A N/A seq1 is_reverse_complement seq2 N/A N/A N/A self assertTrue N/A N/A seq2 is_reverse_complement seq1 N/A test_is_reverse_complement_non_reverse_complements N/A N/A self N/A N/A N/A constructor N/A DNA RNA N/A N/A seq1 N/A constructor ACAG N/A seq2 N/A constructor AAAA N/A N/A N/A self assertFalse N/A N/A seq1 is_reverse_complement seq1 N/A N/A N/A self assertFalse N/A N/A seq2 is_reverse_complement seq2 N/A N/A N/A self assertFalse N/A N/A seq1 is_reverse_complement seq2 N/A N/A N/A self assertFalse N/A N/A seq2 is_reverse_complement seq1 N/A seq1 N/A constructor ACAG N/A seq2 N/A constructor AAAAA N/A N/A N/A self assertFalse N/A N/A seq1 is_reverse_complement seq1 N/A N/A N/A self assertFalse N/A N/A seq2 is_reverse_complement seq2 N/A N/A N/A self assertFalse N/A N/A seq1 is_reverse_complement seq2 N/A N/A N/A self assertFalse N/A N/A seq2 is_reverse_complement seq1 N/A test_is_reverse_complement_type_mismatch N/A N/A self N/A N/A N/A Class N/A DNA RNA N/A DifferentSequenceClass N/A GrammaredSequence N/A degenerate_map N/A N/A cls N/A N/A N/A N/A X N/A set AB N/A classproperty definite_chars N/A N/A cls N/A N/A N/A N/A set ABC N/A classproperty default_gap_char N/A N/A cls N/A N/A N/A - N/A classproperty gap_chars N/A N/A cls N/A N/A N/A N/A set -. N/A classproperty N/A N/A seq1 N/A Class ABC N/A seq2 N/A DifferentSequenceClass ABC N/A N/A N/A self assertRaisesRegex TypeError Cannot use.*and DifferentSequenceClass together N/A N/A N/A N/A seq1 is_reverse_complement seq2 N/A test_motif_purine_run N/A N/A self N/A N/A N/A dna N/A DNA AARC--TCRG AA-RC--TCR-G N/A rna N/A RNA AARC--UCRG AA-RC--UCR-G N/A all_sets N/A dna rna N/A N/A constructor run1 run2 all_sets N/A N/A seq N/A constructor N/A N/A N/A self assertEqual N/A list N/A N/A seq find_motifs purine-run N/A N/A seq N/A constructor run1 N/A N/A N/A self assertEqual N/A list N/A N/A seq find_motifs purine-run N/A N/A slice 0 3 N/A slice 8 10 N/A seq N/A constructor run2 N/A N/A N/A self assertEqual N/A list N/A N/A seq find_motifs purine-run min_length 3 ignore N/A N/A seq gaps N/A N/A slice 0 4 N/A test_motif_pyrimidine_run N/A N/A self N/A N/A N/A dna N/A DNA AARC--TCRA AA-RC--TCR-A N/A rna N/A RNA AARC--UCRG AA-RC--UCR-G N/A all_sets N/A dna rna N/A N/A constructor run1 run2 all_sets N/A N/A seq N/A constructor N/A N/A N/A self assertEqual N/A list N/A N/A seq find_motifs pyrimidine-run N/A N/A seq N/A constructor run1 N/A N/A N/A self assertEqual N/A list N/A N/A seq find_motifs pyrimidine-run N/A N/A slice 3 4 N/A slice 6 8 N/A seq N/A constructor run2 N/A N/A N/A self assertEqual N/A list N/A N/A seq find_motifs pyrimidine-run min_length 3 ignore N/A N/A seq gaps N/A N/A slice 4 9 N/A test_gc_frequency_and_gc_content N/A N/A self N/A N/A N/A universal_sets N/A N/A 0 0.0 N/A ADDDH 0 0.0 N/A ACGA 2 0.5 N/A ACGS 3 0.75 N/A AAAAAAAG 1 0.125 N/A CCC 3 1.0 N/A GGG 3 1.0 N/A SSS 3 1.0 N/A CGS 3 1.0 N/A ----.... 0 0.0 N/A G--.. 1 1.0 N/A ACGA 2 0.5 N/A dna N/A DNA N/A universal_sets N/A N/A ATMRWYKVHDBN.- 0 0.0 N/A rna N/A RNA N/A universal_sets N/A N/A AUMRWYKVHDBN.- 0 0.0 N/A N/A constructor current_set N/A dna rna N/A N/A N/A seq_str count ratio current_set N/A N/A seq N/A constructor seq_str N/A N/A N/A self assertEqual count N/A N/A seq gc_frequency N/A N/A N/A self assertEqual count N/A N/A seq gc_frequency relative False N/A N/A N/A self assertEqual ratio N/A N/A seq gc_frequency relative True N/A N/A N/A self assertEqual ratio N/A N/A seq gc_content N/A N/A N/A N/A __name__ __main__ N/A N/A N/A N/A unittest main