Module Expr Str Import alias ImportFrom alias ImportFrom alias ImportFrom alias Assign NameStore Num Assign NameStore Num ClassDef bases AttributeLoad NameLoad attr body Expr Str FunctionDef arguments args NameParam defaults body Assign AttributeStore NameLoad attr Num decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Num Assign AttributeStore NameLoad attr Call NameLoad Str keyword ListLoad Str Str Str Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Assign NameStore BinOpAdd BinOpAdd BinOpAdd SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Num keyword AttributeLoad NameLoad attr keyword Str Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad NameLoad keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Num Assign AttributeStore NameLoad attr Call NameLoad Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad NameLoad attr NameLoad Num keyword AttributeLoad NameLoad attr keyword Str Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad NameLoad keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Num Assign AttributeStore NameLoad attr Call NameLoad Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad NameLoad attr NameLoad Num keyword AttributeLoad NameLoad attr keyword Str Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad NameLoad keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Num Assign AttributeStore NameLoad attr Call NameLoad Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad NameLoad attr NameLoad Num keyword AttributeLoad NameLoad attr keyword Str Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad NameLoad keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Num Assign AttributeStore NameLoad attr Call NameLoad Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad NameLoad attr NameLoad Num keyword AttributeLoad NameLoad attr keyword Str Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad NameLoad keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Num Assign AttributeStore NameLoad attr Call NameLoad Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad NameLoad attr NameLoad Num keyword AttributeLoad NameLoad attr keyword Str Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad NameLoad keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Num Assign AttributeStore NameLoad attr Call NameLoad Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad NameLoad attr NameLoad Num keyword AttributeLoad NameLoad attr keyword Str Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad NameLoad keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Num Assign AttributeStore NameLoad attr Call NameLoad Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad NameLoad attr NameLoad Num keyword AttributeLoad NameLoad attr keyword Str Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad NameLoad keyword Str decorator_list decorator_list ClassDef bases AttributeLoad NameLoad attr body Expr Str FunctionDef arguments args NameParam defaults body Assign AttributeStore NameLoad attr Num decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr Num Assign SubscriptStore NameLoad Index Num Num Assign SubscriptStore NameLoad Index Num Num Assign SubscriptStore NameLoad Index Num Num Assign SubscriptStore NameLoad Index Num Num Assign AttributeStore NameLoad attr Call NameLoad Str keyword ListLoad Str Str Str Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr BinOpDiv Num Num Num Assign AttributeStore NameLoad attr Call NameLoad Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr ListLoad Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Assign AttributeStore NameLoad attr Call NameLoad Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr ListLoad Num Num Num Num Assign AttributeStore NameLoad attr Call NameLoad Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore ListLoad BinOpDiv Num Num Num Num Num Num Num Num Num Num Num BinOpDiv Num Num Num BinOpDiv Num Num Num Num Num Num Num Num Num Assign AttributeStore NameLoad attr Call NameLoad Str keyword ListLoad Str Str Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr ListLoad Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Assign AttributeStore NameLoad attr Call NameLoad Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr BinOpDiv Num Num Num Assign AttributeStore NameLoad attr Call NameLoad Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore ListLoad Num Num Num Num Assign AttributeStore NameLoad attr Call NameLoad Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr Num Num Assign AttributeStore NameLoad attr Call NameLoad Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword Str decorator_list decorator_list ClassDef bases AttributeLoad NameLoad attr body Expr Str FunctionDef arguments args NameParam defaults body Assign AttributeStore NameLoad attr Num decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr Num Assign SubscriptStore NameLoad Index Num Num Assign AttributeStore NameLoad attr Call NameLoad Str keyword Dict Str Num Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr Num Assign SubscriptStore NameLoad Index Num Num Assign SubscriptStore NameLoad Index Num Num Assign SubscriptStore NameLoad Index Num Num Assign SubscriptStore NameLoad Index Num Num Assign AttributeStore NameLoad attr Call NameLoad Str keyword Dict Str Str Str Str Num Num Num Num Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr Num Assign SubscriptStore NameLoad Index Num Num Assign AttributeStore NameLoad attr Call NameLoad Str keyword Dict Str Num Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr Num Assign SubscriptStore NameLoad Index Num Num Assign SubscriptStore NameLoad Index Num Num Assign AttributeStore NameLoad attr Call NameLoad Str keyword Dict Str Str Num Num Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr Num Assign SubscriptStore NameLoad Index Num Num Assign SubscriptStore NameLoad Index Num Num Assign SubscriptStore NameLoad Index Num Num Assign AttributeStore NameLoad attr Call NameLoad Str keyword Dict Str Str Str Num Num Num Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr Num Assign SubscriptStore NameLoad Index Num Num Assign AttributeStore NameLoad attr Call NameLoad Str keyword Dict Str Num Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr Num Assign SubscriptStore NameLoad Index Num Num Assign SubscriptStore NameLoad Index Num Num Assign SubscriptStore NameLoad Index Num Num Assign SubscriptStore NameLoad Index Num Num Assign AttributeStore NameLoad attr Call NameLoad Str keyword Dict Str Str Str Str Num Num Num Num Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore ListLoad Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Assign AttributeStore NameLoad attr Call NameLoad Str keyword Dict Str Str Num Num Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword Str decorator_list decorator_list ClassDef bases AttributeLoad NameLoad attr body Expr Str FunctionDef arguments args NameParam defaults body Assign AttributeStore NameLoad attr Num decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr ListLoad BinOpDiv Num Num BinOpDiv Num Num BinOpDiv Num Num BinOpDiv Num Num Assign AttributeStore NameLoad attr Call NameLoad Str keyword Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr ListLoad BinOpDiv Num Num BinOpDiv Num Num Num Num Assign AttributeStore NameLoad attr Call NameLoad Str keyword ListLoad Num Num Num keyword Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr ListLoad Num Num Num Num Num BinOpDiv Num Num Num Num Num Num Num Num Num Num BinOpDiv Num Num Num Num Num Num Num BinOpDiv Num Num BinOpDiv Num Num Num Num Num Num BinOpDiv Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num BinOpDiv Num Num BinOpDiv Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num BinOpDiv Num Num Assign AttributeStore NameLoad attr Call NameLoad Str keyword Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr ListLoad Num Num Num Num Num BinOpDiv Num Num Num Num Num Num Num Num Num Num BinOpDiv Num Num Num Num Num Num Num BinOpDiv Num Num BinOpDiv Num Num Num Num Num Num BinOpDiv Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num BinOpDiv Num Num Assign AttributeStore NameLoad attr Call NameLoad Str keyword ListLoad Num Num Num keyword Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr ListLoad Num Num Num Num BinOpDiv Num Num Num Num Num Num Num BinOpDiv Num Num Num BinOpDiv Num Num Num BinOpDiv Num Num Num BinOpDiv Num Num BinOpDiv Num Num Num Num Assign AttributeStore NameLoad attr Call NameLoad Str keyword Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr ListLoad Num Num Num Num BinOpDiv Num Num Num Num Num Num Num BinOpDiv Num Num Num BinOpDiv Num Num Num BinOpDiv Num Num Num BinOpDiv Num Num Num Num Num Assign AttributeStore NameLoad attr Call NameLoad Str keyword ListLoad Num Num Num keyword Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr ListLoad BinOpDiv Num Num BinOpDiv Num Num BinOpDiv Num Num BinOpDiv Num Num Assign AttributeStore NameLoad attr Call NameLoad Str keyword Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr ListLoad BinOpDiv Num Num BinOpDiv Num Num BinOpDiv Num Num BinOpDiv Num Num Assign AttributeStore NameLoad attr Call NameLoad Str keyword ListLoad Num Num Num keyword Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr ListLoad BinOpDiv Num Num BinOpDiv Num Num BinOpDiv Num Num BinOpDiv Num Num BinOpDiv Num Num BinOpDiv Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Assign AttributeStore NameLoad attr Call NameLoad Str keyword Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr ListLoad BinOpDiv Num Num Num Num BinOpDiv Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Assign AttributeStore NameLoad attr Call NameLoad Str keyword ListLoad Num Num Num keyword Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr ListLoad Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Assign AttributeStore NameLoad attr Call NameLoad Str keyword Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad NameLoad attr ListLoad Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num BinOpDiv Num Num Num BinOpDiv Num Num Num BinOpDiv Num Num BinOpDiv Num Num BinOpDiv Num Num BinOpDiv Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Num Assign AttributeStore NameLoad attr Call NameLoad Str keyword ListLoad Num Num Num keyword Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword Str decorator_list decorator_list
N/A N/A  Suite of unit tests for state_freqs module. N/A unittest Bio Seq Bio.Alphabet generic_dna pyvolve * N/A ZERO 1e-08 N/A DECIMAL 8 state_freqs_RandomFrequencies_Tests N/A N/A unittest TestCase N/A N/A  Set of "unittests" for the EqualFrequencies subclass of StateFrequencies. Note that since random, cannot test exact values. setUp N/A N/A self N/A N/A N/A N/A self dec 8 N/A test_RandomFrequencies_calculate_freqs_bycodon_typecodon_restriction N/A N/A self N/A N/A N/A correct_len 61 N/A N/A self rFreqs N/A RandomFrequencies codon restrict N/A AGG CCT GCG TGC N/A freqs N/A N/A N/A self rFreqs compute_frequencies type codon N/A sum N/A N/A N/A N/A freqs N/A 10 N/A freqs N/A 23 N/A freqs N/A 38 N/A freqs N/A 54 N/A N/A N/A N/A np testing assert_almost_equal sum 1.0 decimal N/A self dec err_msg RandomFrequencies do not sum to 1 for  codon, type=codon, with restriction. N/A N/A N/A self assertEqual N/A len freqs correct_len msg RandomFrequencies has incorrect size for  codon, type=codon. N/A test_RandomFrequencies_calculate_freqs_bycodon_typecodon N/A N/A self N/A N/A N/A correct_len 61 N/A N/A self rFreqs N/A RandomFrequencies codon N/A freqs N/A N/A N/A self rFreqs compute_frequencies type codon N/A N/A N/A N/A np testing assert_almost_equal N/A N/A np sum freqs 1.0 decimal N/A self dec err_msg RandomFrequencies do not sum to 1 for  codon, type=codon. N/A N/A N/A self assertEqual N/A len freqs correct_len msg RandomFrequencies has incorrect size for  codon, type=codon. N/A test_RandomFrequencies_calculate_freqs_bycodon_typeamino N/A N/A self N/A N/A N/A correct_len 20 N/A N/A self rFreqs N/A RandomFrequencies codon N/A freqs N/A N/A N/A self rFreqs compute_frequencies type amino_acid N/A N/A N/A N/A np testing assert_almost_equal N/A N/A np sum freqs 1.0 decimal N/A self dec err_msg RandomFrequencies do not sum to 1 for  codon, type=amino_acid. N/A N/A N/A self assertEqual N/A len freqs correct_len msg RandomFrequencies has incorrect size for  codon, type=codon. N/A test_RandomFrequencies_calculate_freqs_bycodon_typenuc N/A N/A self N/A N/A N/A correct_len 4 N/A N/A self rFreqs N/A RandomFrequencies codon N/A freqs N/A N/A N/A self rFreqs compute_frequencies type nucleotide N/A N/A N/A N/A np testing assert_almost_equal N/A N/A np sum freqs 1.0 decimal N/A self dec err_msg RandomFrequencies do not sum to 1 for  codon, type=nucleotide. N/A N/A N/A self assertEqual N/A len freqs correct_len msg RandomFrequencies has incorrect size for  codon, type=codon. N/A test_RandomFrequencies_calculate_freqs_byamino_typecodon N/A N/A self N/A N/A N/A correct_len 61 N/A N/A self rFreqs N/A RandomFrequencies amino_acid N/A freqs N/A N/A N/A self rFreqs compute_frequencies type codon N/A N/A N/A N/A np testing assert_almost_equal N/A N/A np sum freqs 1.0 decimal N/A self dec err_msg RandomFrequencies do not sum to 1 for  amino, type=codon. N/A N/A N/A self assertEqual N/A len freqs correct_len msg RandomFrequencies has incorrect size for  amino, type=codon. N/A test_RandomFrequencies_calculate_freqs_byamino_typeamino N/A N/A self N/A N/A N/A correct_len 20 N/A N/A self rFreqs N/A RandomFrequencies amino_acid N/A freqs N/A N/A N/A self rFreqs compute_frequencies type amino_acid N/A N/A N/A N/A np testing assert_almost_equal N/A N/A np sum freqs 1.0 decimal N/A self dec err_msg RandomFrequencies do not sum to 1 for  amino, type=amino. N/A N/A N/A self assertEqual N/A len freqs correct_len msg RandomFrequencies has incorrect size for  amino, type=amino. N/A test_RandomFrequencies_calculate_freqs_byamino_typenuc N/A N/A self N/A N/A N/A correct_len 4 N/A N/A self rFreqs N/A RandomFrequencies amino_acid N/A freqs N/A N/A N/A self rFreqs compute_frequencies type nucleotide N/A N/A N/A N/A np testing assert_almost_equal N/A N/A np sum freqs 1.0 decimal N/A self dec err_msg RandomFrequencies do not sum to 1 for  amino, type=nuc. N/A N/A N/A self assertEqual N/A len freqs correct_len msg RandomFrequencies has incorrect size for  amino, type=nuc. N/A test_RandomFrequencies_calculate_freqs_bynuc_typenuc N/A N/A self N/A N/A N/A correct_len 4 N/A N/A self rFreqs N/A RandomFrequencies nucleotide N/A freqs N/A N/A N/A self rFreqs compute_frequencies type nucleotide N/A N/A N/A N/A np testing assert_almost_equal N/A N/A np sum freqs 1.0 decimal N/A self dec err_msg RandomFrequencies do not sum to 1 for  nuc, type=nuc. N/A N/A N/A self assertEqual N/A len freqs correct_len msg RandomFrequencies has incorrect size for  nuc, type=nuc. N/A N/A state_freqs_EqualFrequencies_Tests N/A N/A unittest TestCase N/A N/A  Set of "unittests" for the EqualFrequencies subclass of StateFrequencies. setUp N/A N/A self N/A N/A N/A N/A self dec 8 N/A test_EqualFrequencies_calculate_freqs_bycodon_typecodon_restrict N/A N/A self N/A N/A N/A correct N/A N/A np zeros 61 N/A N/A correct N/A 10 0.25 N/A N/A correct N/A 23 0.25 N/A N/A correct N/A 38 0.25 N/A N/A correct N/A 54 0.25 N/A N/A self eqFreqs N/A EqualFrequencies codon restrict N/A AGG CCT GCG TGC N/A freqs N/A N/A N/A self eqFreqs compute_frequencies type codon N/A N/A N/A N/A np testing assert_array_almost_equal correct freqs decimal N/A self dec err_msg EqualFrequencies not calculated properly for  codon, type=codon with restriction. N/A test_EqualFrequencies_calculate_freqs_bycodon_typecodon N/A N/A self N/A N/A N/A correct N/A N/A np array N/A N/A np repeat N/A 1.0 61.0 61 N/A N/A self eqFreqs N/A EqualFrequencies codon N/A freqs N/A N/A N/A self eqFreqs compute_frequencies type codon N/A N/A N/A N/A np testing assert_array_almost_equal correct freqs decimal N/A self dec err_msg EqualFrequencies not calculated properly for  codon, type=codon. N/A test_EqualFrequencies_calculate_freqs_bycodon_typeamino N/A N/A self N/A N/A N/A correct N/A N/A np array N/A 0.0655737704918 0.0327868852459 0.0327868852459 0.0327868852459 0.0327868852459 0.0655737704918 0.0327868852459 0.0491803278689 0.0327868852459 0.0983606557377 0.016393442623 0.0327868852459 0.0655737704918 0.0327868852459 0.0983606557377 0.0983606557377 0.0655737704918 0.0655737704918 0.016393442623 0.0327868852459 N/A N/A self eqFreqs N/A EqualFrequencies codon N/A freqs N/A N/A N/A self eqFreqs compute_frequencies type amino_acid N/A N/A N/A N/A np testing assert_array_almost_equal correct freqs decimal N/A self dec err_msg EqualFrequencies not calculated properly for  codon, type=amino. N/A test_EqualFrequencies_calculate_freqs_bycodon_typenuc N/A N/A self N/A N/A N/A correct N/A N/A np array N/A 0.24043715847 0.262295081967 0.251366120219 0.245901639344 N/A N/A self eqFreqs N/A EqualFrequencies codon N/A freqs N/A N/A N/A self eqFreqs compute_frequencies type nucleotide N/A N/A N/A N/A np testing assert_array_almost_equal correct freqs decimal N/A self dec err_msg EqualFrequencies not calculated properly for  codon, type=nuc. N/A test_EqualFrequencies_calculate_freqs_byamino_typeamino_restrict N/A N/A self N/A N/A N/A correct N/A N/A 1.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 N/A 1.0 3.0 0.0 N/A 1.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 N/A N/A self eqFreqs N/A EqualFrequencies amino_acid restrict N/A A M P N/A freqs N/A N/A N/A self eqFreqs compute_frequencies type amino_acid N/A N/A N/A N/A np testing assert_array_almost_equal correct freqs decimal N/A self dec err_msg EqualFrequencies not calculated properly for  amino, type=amino with restriction. N/A test_EqualFrequencies_calculate_freqs_byamino_typecodon N/A N/A self N/A N/A N/A correct N/A N/A np array N/A 0.025 0.025 0.025 0.025 0.0125 0.0125 0.0125 0.0125 0.00833333 0.00833333 0.00833333 0.00833333 0.01666667 0.01666667 0.05 0.01666667 0.025 0.025 0.025 0.025 0.0125 0.0125 0.0125 0.0125 0.00833333 0.00833333 0.00833333 0.00833333 0.00833333 0.00833333 0.00833333 0.00833333 0.025 0.025 0.025 0.025 0.0125 0.0125 0.0125 0.0125 0.0125 0.0125 0.0125 0.0125 0.0125 0.0125 0.0125 0.0125 0.025 0.025 0.00833333 0.00833333 0.00833333 0.00833333 0.025 0.05 0.025 0.00833333 0.025 0.00833333 0.025 N/A N/A self eqFreqs N/A EqualFrequencies amino_acid N/A freqs N/A N/A N/A self eqFreqs compute_frequencies type codon N/A N/A N/A N/A np testing assert_array_almost_equal correct freqs decimal N/A self dec err_msg EqualFrequencies not calculated properly for  amino, type=codon. N/A test_EqualFrequencies_calculate_freqs_byamino_typeamino N/A N/A self N/A N/A N/A correct N/A N/A np array N/A N/A np repeat N/A 1.0 20.0 20 N/A N/A self eqFreqs N/A EqualFrequencies amino_acid N/A freqs N/A N/A N/A self eqFreqs compute_frequencies type amino_acid N/A N/A N/A N/A np testing assert_array_almost_equal correct freqs decimal N/A self dec err_msg EqualFrequencies not calculated properly for  amino, type=amino. N/A test_EqualFrequencies_calculate_freqs_byamino_typenuc N/A N/A self N/A N/A N/A correct N/A 0.27638889 0.22083333 0.24861111 0.25416667 N/A N/A self eqFreqs N/A EqualFrequencies amino_acid N/A freqs N/A N/A N/A self eqFreqs compute_frequencies type nucleotide N/A N/A N/A N/A np testing assert_array_almost_equal correct freqs decimal N/A self dec err_msg EqualFrequencies not calculated properly for  amino, type=nuc. N/A test_EqualFrequencies_calculate_freqs_bynuc_typenuc N/A N/A self N/A N/A N/A correct N/A N/A np array N/A N/A np repeat 0.25 4 N/A N/A self eqFreqs N/A EqualFrequencies nucleotide N/A freqs N/A N/A N/A self eqFreqs compute_frequencies type nucleotide N/A N/A N/A N/A np testing assert_array_almost_equal correct freqs decimal N/A self dec err_msg EqualFrequencies not calculated properly for  nuc, type=nuc. N/A N/A state_freqs_CustomFrequencies_Tests N/A N/A unittest TestCase N/A N/A  Set of "unittests" for the CustomFrequencies subclass of StateFrequencies. setUp N/A N/A self N/A N/A N/A N/A self dec 8 N/A test_CustomFrequencies_calculate_freqs_bynuc_typenuc_singlenuc N/A N/A self N/A N/A N/A correct N/A N/A np zeros 4 N/A N/A correct N/A 1 1.0 N/A N/A self uFreqs N/A CustomFrequencies nucleotide freq_dict N/A C 1.0 N/A freqs N/A N/A N/A self uFreqs compute_frequencies type nucleotide N/A N/A N/A N/A np testing assert_array_almost_equal correct freqs decimal N/A self dec err_msg CustomFrequencies not calculated properly  nuc, type=nuc with single nucleotide freq specified. N/A test_CustomFrequencies_calculate_freqs_bynuc_typenuc_multiplenuc N/A N/A self N/A N/A N/A correct N/A N/A np zeros 4 N/A N/A correct N/A 0 0.25 N/A N/A correct N/A 1 0.25 N/A N/A correct N/A 2 0.25 N/A N/A correct N/A 3 0.25 N/A N/A self uFreqs N/A CustomFrequencies nucleotide freq_dict N/A A C G T 0.25 0.25 0.25 0.25 N/A freqs N/A N/A N/A self uFreqs compute_frequencies type nucleotide N/A N/A N/A N/A np testing assert_array_almost_equal correct freqs decimal N/A self dec err_msg CustomFrequencies not calculated properly  nuc, type=nuc with multiple nucleotide freqs specified. N/A test_CustomFrequencies_calculate_freqs_bycodon_typecodon_singlecodon N/A N/A self N/A N/A N/A correct N/A N/A np zeros 61 N/A N/A correct N/A 1 1.0 N/A N/A self uFreqs N/A CustomFrequencies codon freq_dict N/A AAC 1.0 N/A freqs N/A N/A N/A self uFreqs compute_frequencies type codon N/A N/A N/A N/A np testing assert_array_almost_equal correct freqs decimal N/A self dec err_msg CustomFrequencies not calculated properly for  codon, type=codon, single codon freq specified. N/A test_CustomFrequencies_calculate_freqs_bycodon_typecodon_multiplecodons N/A N/A self N/A N/A N/A correct N/A N/A np zeros 61 N/A N/A correct N/A 1 0.5 N/A N/A correct N/A 2 0.5 N/A N/A self uFreqs N/A CustomFrequencies codon freq_dict N/A AAC AAG 0.5 0.5 N/A freqs N/A N/A N/A self uFreqs compute_frequencies type codon N/A N/A N/A N/A np testing assert_array_almost_equal correct freqs decimal N/A self dec err_msg CustomFrequencies not calculated properly for  codon, type=codon, multiple codon freqs specified. N/A test_CustomFrequencies_calculate_freqs_bycodon_typeamino N/A N/A self N/A N/A N/A correct N/A N/A np zeros 20 N/A N/A correct N/A 8 0.5 N/A N/A correct N/A 9 0.25 N/A N/A correct N/A 10 0.25 N/A N/A self uFreqs N/A CustomFrequencies codon freq_dict N/A AAA ATG CTT 0.5 0.25 0.25 N/A freqs N/A N/A N/A self uFreqs compute_frequencies type amino_acid N/A N/A N/A N/A np testing assert_array_almost_equal correct freqs decimal N/A self dec err_msg CustomFrequencies not calculated properly for  codon, type=amino, multiple codon freqs specified. N/A test_CustomFrequencies_calculate_freqs_byamino_typeamino_singleaa N/A N/A self N/A N/A N/A correct N/A N/A np zeros 20 N/A N/A correct N/A 1 1.0 N/A N/A self uFreqs N/A CustomFrequencies amino_acid freq_dict N/A C 1.0 N/A freqs N/A N/A N/A self uFreqs compute_frequencies type amino_acid N/A N/A N/A N/A np testing assert_array_almost_equal correct freqs decimal N/A self dec err_msg CustomFrequencies not calculated properly for  amino, type=amino with single aa specified. N/A test_CustomFrequencies_calculate_freqs_byamino_typeamino_multipleaa N/A N/A self N/A N/A N/A correct N/A N/A np zeros 20 N/A N/A correct N/A 1 0.25 N/A N/A correct N/A 2 0.25 N/A N/A correct N/A 3 0.25 N/A N/A correct N/A 4 0.25 N/A N/A self uFreqs N/A CustomFrequencies amino_acid freq_dict N/A C D E F 0.25 0.25 0.25 0.25 N/A freqs N/A N/A N/A self uFreqs compute_frequencies type amino_acid N/A N/A N/A N/A np testing assert_array_almost_equal correct freqs decimal N/A self dec err_msg CustomFrequencies not calculated properly for  amino, type=amino with multiple aas specified. N/A test_CustomFrequencies_calculate_freqs_byamino_typecodon_multipleaa N/A N/A self N/A N/A N/A correct N/A 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.08333333 0.08333333 0.08333333 0.08333333 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.125 0.125 0.125 0.125 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.08333333 0.0 0.08333333 0.0 N/A N/A self uFreqs N/A CustomFrequencies amino_acid freq_dict N/A L V 0.5 0.5 N/A freqs N/A N/A N/A self uFreqs compute_frequencies type codon N/A N/A N/A N/A np testing assert_array_almost_equal correct freqs decimal N/A self dec err_msg CustomFrequencies not calculated properly for  amino, type=amino with multiple aas specified. N/A N/A state_freqs_ReadFrequencies_Tests N/A N/A unittest TestCase N/A N/A  Set of "unittests" for the ReadFrequencies subclass of StateFrequencies. setUp N/A N/A self N/A N/A N/A N/A self dec 8 N/A test_ReadFrequencies_calculate_freqs_bynuc_typenuc_nocol N/A N/A self N/A N/A N/A correct N/A N/A np array N/A N/A 5.0 54.0 N/A 12.0 54.0 N/A 18.0 54.0 N/A 19.0 54.0 N/A N/A self rFreqs N/A ReadFrequencies nucleotide file tests/freqFiles/testFreq_codon_aln.fasta N/A freqs N/A N/A N/A self rFreqs compute_frequencies type nucleotide N/A N/A N/A N/A np testing assert_array_almost_equal correct freqs decimal N/A self dec err_msg ReadFrequencies not calculated properly for  nuc, type=nuc, no columns. N/A test_ReadFrequencies_calculate_freqs_bynuc_typenuc_col N/A N/A self N/A N/A N/A correct N/A N/A np array N/A N/A 2.0 9.0 N/A 7.0 9.0 0 0 N/A N/A self rFreqs N/A ReadFrequencies nucleotide columns N/A 1 2 3 file tests/freqFiles/testFreq_codon_aln.fasta N/A freqs N/A N/A N/A self rFreqs compute_frequencies type nucleotide N/A N/A N/A N/A np testing assert_array_almost_equal correct freqs decimal N/A self dec err_msg ReadFrequencies not calculated properly for  nuc, type=nuc, with columns. N/A test_ReadFrequencies_calculate_freqs_bycodon_typecodon_nocol N/A N/A self N/A N/A N/A correct N/A N/A np array N/A 0 0 0 0 0 N/A 1.0 18.0 0 0 0 0 0 0 0 0 N/A 1.0 6.0 0 0 0 0 0 N/A 1.0 18.0 N/A 1.0 18.0 0 0 0 0 N/A 1.0 9.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 N/A 1.0 6.0 N/A 2.0 9.0 0 0 0 0 0 0 0 0 0 0 0 0 0 N/A 1.0 6.0 N/A N/A self rFreqs N/A ReadFrequencies codon file tests/freqFiles/testFreq_codon_aln.fasta N/A freqs N/A N/A N/A self rFreqs compute_frequencies type codon N/A N/A N/A N/A np testing assert_array_almost_equal correct freqs decimal N/A self dec err_msg ReadFrequencies not calculated properly for  codon, type=codon, no columns. N/A test_ReadFrequencies_calculate_freqs_bycodon_typecodon_col N/A N/A self N/A N/A N/A correct N/A N/A np array N/A 0 0 0 0 0 N/A 1.0 9.0 0 0 0 0 0 0 0 0 N/A 1.0 3.0 0 0 0 0 0 N/A 1.0 9.0 N/A 1.0 9.0 0 0 0 0 N/A 1.0 9.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 N/A 2.0 9.0 N/A N/A self rFreqs N/A ReadFrequencies codon columns N/A 1 2 3 file tests/freqFiles/testFreq_codon_aln.fasta N/A freqs N/A N/A N/A self rFreqs compute_frequencies type codon N/A N/A N/A N/A np testing assert_array_almost_equal correct freqs decimal N/A self dec err_msg ReadFrequencies not calculated properly for  codon, type=codon, with columns. N/A test_ReadFrequencies_calculate_freqs_bycodon_typeamino_nocol N/A N/A self N/A N/A N/A correct N/A N/A np array N/A 0 0 0 0 N/A 1.0 6.0 0 0 0 0 0 N/A 1.0 6.0 0 N/A 1.0 9.0 0 N/A 1.0 9.0 0 N/A 1.0 18.0 N/A 7.0 18.0 0 0 N/A N/A self rFreqs N/A ReadFrequencies codon file tests/freqFiles/testFreq_codon_aln.fasta N/A freqs N/A N/A N/A self rFreqs compute_frequencies type amino_acid N/A N/A N/A N/A np testing assert_array_almost_equal correct freqs decimal N/A self dec err_msg ReadFrequencies not calculated properly for  codon, type=amino, no columns. N/A test_ReadFrequencies_calculate_freqs_bycodon_typeamino_col N/A N/A self N/A N/A N/A correct N/A N/A np array N/A 0 0 0 0 N/A 2.0 9.0 0 0 0 0 0 N/A 1.0 3.0 0 N/A 2.0 9.0 0 N/A 1.0 9.0 0 N/A 1.0 9.0 0 0 0 N/A N/A self rFreqs N/A ReadFrequencies codon columns N/A 1 2 3 file tests/freqFiles/testFreq_codon_aln.fasta N/A freqs N/A N/A N/A self rFreqs compute_frequencies type amino_acid N/A N/A N/A N/A np testing assert_array_almost_equal correct freqs decimal N/A self dec err_msg ReadFrequencies not calculated properly for  codon, type=amino, with columns. N/A test_ReadFrequencies_calculate_freqs_bycodon_typenuc_nocol N/A N/A self N/A N/A N/A correct N/A N/A np array N/A N/A 5.0 54.0 N/A 12.0 54.0 N/A 18.0 54.0 N/A 19.0 54.0 N/A N/A self rFreqs N/A ReadFrequencies codon file tests/freqFiles/testFreq_codon_aln.fasta N/A freqs N/A N/A N/A self rFreqs compute_frequencies type nucleotide N/A N/A N/A N/A np testing assert_array_almost_equal correct freqs decimal N/A self dec err_msg ReadFrequencies not calculated properly for  codon, type=nuc, no columns. N/A test_ReadFrequencies_calculate_freqs_bycodon_typenuc_col N/A N/A self N/A N/A N/A correct N/A N/A np array N/A N/A 5.0 27.0 N/A 8.0 27.0 N/A 5.0 27.0 N/A 9.0 27.0 N/A N/A self rFreqs N/A ReadFrequencies codon columns N/A 1 2 3 file tests/freqFiles/testFreq_codon_aln.fasta N/A freqs N/A N/A N/A self rFreqs compute_frequencies type nucleotide N/A N/A N/A N/A np testing assert_array_almost_equal correct freqs decimal N/A self dec err_msg ReadFrequencies not calculated properly for  codon, type=nuc, with columns. N/A test_ReadFrequencies_calculate_freqs_byamino_typeamino_nocol N/A N/A self N/A N/A N/A correct N/A N/A np array N/A N/A 1.0 6.0 N/A 1.0 6.0 N/A 1.0 6.0 N/A 1.0 6.0 N/A 1.0 6.0 N/A 1.0 6.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 N/A N/A self rFreqs N/A ReadFrequencies amino_acid file tests/freqFiles/testFreq_amino_aln.fasta N/A freqs N/A N/A N/A self rFreqs compute_frequencies type amino_acid N/A N/A N/A N/A np testing assert_array_almost_equal correct freqs decimal N/A self dec err_msg ReadFrequencies not calculated properly for  amino, type=amino, no columns. N/A test_ReadFrequencies_calculate_freqs_byamino_typeamino_col N/A N/A self N/A N/A N/A correct N/A N/A np array N/A N/A 2.0 3.0 0 0 N/A 1.0 3.0 0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 N/A N/A self rFreqs N/A ReadFrequencies amino_acid columns N/A 1 2 3 file tests/freqFiles/testFreq_amino_aln.fasta N/A freqs N/A N/A N/A self rFreqs compute_frequencies type amino_acid N/A N/A N/A N/A np testing assert_array_almost_equal correct freqs decimal N/A self dec err_msg ReadFrequencies not calculated properly for  amino, type=amino, with columns. N/A test_ReadFrequencies_calculate_freqs_byamino_typecodon_nocol N/A N/A self N/A N/A N/A correct N/A N/A np array N/A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.08333333 0.08333333 0.08333333 0.08333333 0.04166667 0.04166667 0.04166667 0.04166667 0.04166667 0.04166667 0.04166667 0.04166667 0 0 0 0 0 0 0 0 0 0 0.08333333 0 0.08333333 0 0.08333333 0 0.08333333 N/A N/A self rFreqs N/A ReadFrequencies amino_acid file tests/freqFiles/testFreq_amino_aln.fasta N/A freqs N/A N/A N/A self rFreqs compute_frequencies type codon N/A N/A N/A N/A np testing assert_array_almost_equal correct freqs decimal N/A self dec err_msg ReadFrequencies not calculated properly for  amino, type=codon, no columns. N/A test_ReadFrequencies_calculate_freqs_byamino_typecodon_col N/A N/A self N/A N/A N/A correct N/A N/A np array N/A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 N/A 1.0 6.0 0 N/A 1.0 6.0 0 N/A 1.0 6.0 N/A 1.0 6.0 N/A 1.0 6.0 N/A 1.0 6.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 N/A N/A self rFreqs N/A ReadFrequencies amino_acid columns N/A 1 2 3 file tests/freqFiles/testFreq_amino_aln.fasta N/A freqs N/A N/A N/A self rFreqs compute_frequencies type codon N/A N/A N/A N/A np testing assert_array_almost_equal correct freqs decimal N/A self dec err_msg ReadFrequencies not calculated properly for  amino, type=codon, with columns. N/A N/A