Module Expr Str Import alias Import alias identifier ImportFrom alias Assign NameStore Call NameLoad Assign NameStore Num Assign NameStore Num ClassDef bases AttributeLoad NameLoad attr body Expr Str FunctionDef arguments args NameParam defaults body Assign NameStore Dict Str Call AttributeLoad NameLoad attr Num Num Assign NameStore Call NameLoad Str NameLoad keyword Num Expr Call AttributeLoad NameLoad attr NameLoad Lambda arguments args defaults Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Dict Assign NameStore Call NameLoad Str NameLoad keyword Num Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad AttributeLoad NameLoad attr attr SubscriptLoad AttributeLoad NameLoad attr Index Str Call AttributeLoad NameLoad attr ListLoad Num Num Num Num keyword NameLoad keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Dict Str ListLoad Num Num Num Num Assign NameStore Call NameLoad Str NameLoad keyword Num Expr Call AttributeLoad NameLoad attr NameLoad Lambda arguments args defaults Call AttributeLoad NameLoad attr 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 NameStore Dict Assign NameStore Call NameLoad Str NameLoad keyword Num Expr Call AttributeLoad NameLoad attr keyword NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr SubscriptLoad AttributeLoad NameLoad attr Index Str NameLoad keyword NameLoad 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 Assign NameStore Dict Assign NameStore Call NameLoad Str NameLoad keyword Num Expr Call AttributeLoad NameLoad attr keyword NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr SubscriptLoad AttributeLoad NameLoad attr Index Str NameLoad keyword NameLoad keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore ListLoad Num Num Num Num 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 NameStore Dict Str NameLoad Assign NameStore Call NameLoad Str NameLoad keyword Num Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad AttributeLoad NameLoad attr attr SubscriptLoad AttributeLoad NameLoad attr Index Str NameLoad keyword NameLoad keyword Str decorator_list decorator_list ClassDef bases AttributeLoad NameLoad attr body Expr Str FunctionDef arguments args NameParam defaults body Assign NameStore Dict Str Str Call AttributeLoad NameLoad attr Num Num Dict Str Str Str Str Str Str Num Num Num Num Num Num Assign NameStore Call NameLoad Str NameLoad Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr CompareEq SubscriptLoad AttributeLoad NameLoad attr Index Str Dict Str Str Str Str Str Str Str Str Str Str Str Str Num Num Num Num Num Num Num Num Num Num Num Num keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Dict Str Str Call AttributeLoad NameLoad attr Num Num Dict Str Str Str Str Str Num Num Num Num Num Assign NameStore Call NameLoad Str NameLoad Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr CompareEq SubscriptLoad AttributeLoad NameLoad attr Index Str Dict Str Str Str Str Str Str Str Str Str Str Str Str Num Num Num Num Num Num Num Num Num Num Num Num keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Dict Str Str Call AttributeLoad NameLoad attr Num Num Num Assign NameStore Call NameLoad Str NameLoad Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr CompareEq SubscriptLoad AttributeLoad NameLoad attr Index Str Dict Str Str Str Str Str Str Str Str Str Str Str Str Num Num Num Num Num Num Num Num Num Num Num Num keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Dict Str Call AttributeLoad NameLoad attr Num Num Assign NameStore Call NameLoad Str NameLoad Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr CompareEq SubscriptLoad AttributeLoad NameLoad attr Index Str Dict Str Str Str Str Str Str Str Str Str Str Str Str Num Num Num Num Num Num Num Num Num Num Num Num keyword Str decorator_list decorator_list ClassDef bases AttributeLoad NameLoad attr body Expr Str FunctionDef arguments args NameParam defaults body Assign NameStore Dict Assign NameStore Call NameLoad Str NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Lambda arguments args defaults Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Dict Str Num Assign NameStore Call NameLoad Str NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Lambda arguments args defaults Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Dict Str Num Assign NameStore Call NameLoad Str NameLoad Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr SubscriptLoad AttributeLoad NameLoad attr Index Str Num keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Dict Str Num Assign NameStore Call NameLoad Str NameLoad Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr SubscriptLoad AttributeLoad NameLoad attr Index Str Num keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Dict Str ListLoad Num Num Num Assign NameStore Call NameLoad Str NameLoad Assign AttributeStore NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad AttributeLoad NameLoad attr attr SubscriptLoad AttributeLoad NameLoad attr Index Str Call AttributeLoad NameLoad attr Num keyword NameLoad keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Dict Str Str ListLoad Num Num Num Num Assign NameStore Call NameLoad Str NameLoad Assign AttributeStore NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Lambda arguments args defaults Call AttributeLoad NameLoad attr decorator_list decorator_list ClassDef bases AttributeLoad NameLoad attr body Expr Str FunctionDef arguments args NameParam defaults body Assign NameStore Call Call NameLoad Str Dict keyword Num Expr Call AttributeLoad NameLoad attr BoolOpAnd CompareEq SubscriptLoad NameLoad Index Str Num CompareEq SubscriptLoad NameLoad Index Str Num keyword Str Expr Call AttributeLoad NameLoad attr BoolOpAnd CompareEq SubscriptLoad NameLoad Index Str Num CompareEq SubscriptLoad NameLoad Index Str Num keyword Str decorator_list decorator_list ClassDef bases AttributeLoad NameLoad attr body Expr Str 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 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 NameStore Call NameLoad Str Dict Str NameLoad Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr SubscriptLoad AttributeLoad NameLoad attr Index Str keyword Str Expr Call AttributeLoad NameLoad attr SubscriptLoad AttributeLoad NameLoad attr Index Str keyword Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr SubscriptLoad AttributeLoad NameLoad attr Index Str NameLoad keyword NameLoad 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 NameStore Call NameLoad Str Dict Str NameLoad Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr SubscriptLoad AttributeLoad NameLoad attr Index Str keyword Str Expr Call AttributeLoad NameLoad attr SubscriptLoad AttributeLoad NameLoad attr Index Str 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 NameStore Call NameLoad Str Dict Str NameLoad Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr SubscriptLoad AttributeLoad NameLoad attr Index Str keyword Str Expr Call AttributeLoad NameLoad attr SubscriptLoad AttributeLoad NameLoad attr Index Str keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore ListLoad Num Num Num Num Assign NameStore Call NameLoad Str Dict Str NameLoad Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr SubscriptLoad AttributeLoad NameLoad attr Index Str keyword Str Expr Call AttributeLoad NameLoad attr SubscriptLoad AttributeLoad NameLoad attr Index Str keyword Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore ListLoad Num Num Num Num Assign NameStore Call NameLoad Str Dict Str NameLoad Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr SubscriptLoad AttributeLoad NameLoad attr Index Str keyword Str Expr Call AttributeLoad NameLoad attr SubscriptLoad AttributeLoad NameLoad attr Index Str keyword Str decorator_list decorator_list
N/A N/A  Suite of unit tests for parameters_sanity module. N/A unittest N/A numpy np pyvolve * N/A MOLECULES N/A Genetics N/A ZERO 1e-08 N/A DECIMAL 8 ParametersSanity_sanity_freqs N/A N/A unittest TestCase N/A N/A  
        Set of unittests for state frequency sanity testing.
     test_sanity_state_freqs_incorrect_size N/A N/A self N/A N/A N/A params N/A state_freqs N/A N/A np repeat 0.05 20 N/A pm N/A Nucleotide_Sanity nucleotide params size 4 N/A N/A N/A self assertRaises AssertionError N/A N/A N/A N/A N/A N/A pm _sanity_state_freqs N/A test_sanity_state_freqs_missing N/A N/A self N/A N/A N/A params N/A N/A pm N/A Nucleotide_Sanity nucleotide params size 4 N/A N/A N/A pm _sanity_state_freqs N/A N/A N/A N/A np testing assert_array_almost_equal N/A N/A pm params N/A state_freqs N/A N/A np array N/A 0.25 0.25 0.25 0.25 decimal DECIMAL err_msg state_freqs not set to equal when not provided in params dict. N/A test_sanity_state_freqs_incorrect_sum N/A N/A self N/A N/A N/A params N/A state_freqs N/A 0.1 0.2 0.1 0.3 N/A pm N/A Nucleotide_Sanity nucleotide params size 4 N/A N/A N/A self assertRaises AssertionError N/A N/A N/A N/A N/A N/A pm _sanity_state_freqs N/A test_sanity_state_freqs_ecm N/A N/A self N/A N/A N/A ecmrest_freqs N/A 0.03000113 0.02017108 0.02634411 0.02300609 0.01552806 0.02020108 0.01214205 0.01342405 0.01037204 0.01167905 0.00819503 0.01014204 0.01355105 0.02344109 0.02010208 0.0255761 0.01607606 0.01170305 0.02021108 0.01109704 0.01064204 0.01010004 0.01184305 0.01000704 0.00480002 0.01414806 0.00783703 0.00831103 0.00760003 0.01738607 0.02883912 0.01446706 0.03322313 0.0245321 0.03187813 0.02819811 0.01590806 0.02830711 0.01885308 0.01900508 0.01579606 0.02298209 0.01019104 0.01685207 0.01090104 0.01893808 0.02274709 0.01904708 0.01578206 0.01596506 0.00975004 0.01113104 0.00895604 0.01188005 0.00702903 0.01188005 0.00602502 0.01638707 0.02138309 0.01542506 0.02210309 N/A params N/A N/A pm N/A ECM_Sanity ecmrest params size 61 N/A N/A N/A pm _sanity_state_freqs empirical True N/A N/A N/A N/A np testing assert_array_almost_equal N/A N/A pm params N/A state_freqs ecmrest_freqs decimal DECIMAL err_msg ECMrest default state_freqs not set up properly. N/A test_sanity_state_freqs_aminoacid N/A N/A self N/A N/A N/A wag_freqs N/A 0.086628 0.0193078 0.0570451 0.0580589 0.0384319 0.0832518 0.0244313 0.048466 0.0620286 0.086209 0.0195027 0.0390894 0.0457631 0.0367281 0.043972 0.0695179 0.0610127 0.0708956 0.0143859 0.0352742 N/A params N/A N/A pm N/A ECM_Sanity wag params size 20 N/A N/A N/A pm _sanity_state_freqs empirical True N/A N/A N/A N/A np testing assert_array_almost_equal N/A N/A pm params N/A state_freqs wag_freqs decimal DECIMAL err_msg WAG (aa model) default state_freqs not set up properly. N/A test_sanity_state_freqs_MG_provided_codon N/A N/A self N/A N/A N/A mg_nuc N/A 0.23577944 0.2426595 0.28132983 0.24023122 N/A mg_codon N/A 0.00648685834 0.0256846182 0.0362821504 0.0178992022 0.00378995203 0.0127376858 0.0111733512 0.00277350952 0.032135792 0.0115713167 0.00135629025 0.0218752127 2.501683e-05 0.0310876439 0.0337328837 0.0165327942 0.00821428969 0.0155572812 0.017629382 0.0229747386 0.00173289159 0.0113379531 0.0159673812 0.0297921605 0.0352280293 0.0094272491 0.0248052302 0.0147583962 0.0196410901 0.00933795423 6.06200346e-05 0.0111892264 0.0118844724 0.017517364 0.0277504624 0.0190563757 0.0316335607 0.0145931598 0.0142666011 0.0296971714 0.0190421569 0.003335634 0.00294568624 0.0340917454 0.0132157035 0.0194067362 0.0183063743 0.0103705727 0.0109380931 0.00607488829 0.0117862027 0.00453122192 0.0249775815 0.00896308703 0.0310326855 0.0294072089 0.0193306945 0.00342785939 0.0224745563 0.00787119137 0.0192728016 N/A params N/A state_freqs mg_codon N/A pm N/A MechCodon_Sanity mg params size 61 N/A N/A N/A pm _sanity_state_freqs_MG N/A N/A N/A N/A np testing assert_array_almost_equal N/A N/A pm params N/A nuc_freqs mg_nuc decimal DECIMAL err_msg Nucleotide frequencies not properly calc'd from codon frequencies for an MG model. N/A N/A ParametersSanity_sanity_mutation N/A N/A unittest TestCase N/A N/A  
        Set of unittests for mutation rate sanity testing.
     test_sanity_mutation_rates_missing_reverse N/A N/A self N/A N/A N/A params N/A state_freqs mu N/A N/A np repeat 0.25 4 N/A AC AG AT CG CT GT 1.0 2.5 1.0 1.0 2.5 1.0 N/A pm N/A Nucleotide_Sanity nucleotide params N/A N/A N/A pm _sanity_mutation_rates N/A N/A N/A self assertTrue N/A N/A N/A pm params N/A mu N/A AC CA AG GA AT TA CG GC CT TC GT TG 1.0 1.0 2.5 2.5 1.0 1.0 1.0 1.0 2.5 2.5 1.0 1.0 msg Backward mutation rates not properly assigned when all forward rates given. N/A test_sanity_mutation_rates_missing_some N/A N/A self N/A N/A N/A params N/A state_freqs mu N/A N/A np repeat 0.25 4 N/A AG AT CG CT GT 2.5 1.0 1.0 2.5 1.0 N/A pm N/A Nucleotide_Sanity nucleotide params N/A N/A N/A pm _sanity_mutation_rates N/A N/A N/A self assertTrue N/A N/A N/A pm params N/A mu N/A AC CA AG GA AT TA CG GC CT TC GT TG 1.0 1.0 2.5 2.5 1.0 1.0 1.0 1.0 2.5 2.5 1.0 1.0 msg Missing mutation rates not filled in when all but 1 pair provided. N/A test_sanity_mutation_rates_kappa N/A N/A self N/A N/A N/A params N/A state_freqs kappa N/A N/A np repeat 0.25 4 2.5 N/A pm N/A Nucleotide_Sanity nucleotide params N/A N/A N/A pm _sanity_mutation_rates N/A N/A N/A self assertTrue N/A N/A N/A pm params N/A mu N/A AC CA AG GA AT TA CG GC CT TC GT TG 1.0 1.0 2.5 2.5 1.0 1.0 1.0 1.0 2.5 2.5 1.0 1.0 msg Missing mutation rates wrong when only kappa provided. N/A test_sanity_mutation_rates_all_missing N/A N/A self N/A N/A N/A params N/A state_freqs N/A N/A np repeat 0.25 4 N/A pm N/A Nucleotide_Sanity nucleotide params N/A N/A N/A pm _sanity_mutation_rates N/A N/A N/A self assertTrue N/A N/A N/A pm params N/A mu N/A AC CA AG GA AT TA CG GC CT TC GT TG 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 msg Missing mutation rates not added in when none provided. N/A N/A ParametersSanity_sanity_dnds N/A N/A unittest TestCase N/A N/A  
        Set of unittests for dN/dS rate sanity testing.
     test_sanity_MechCodon_homo_dNdSmissing N/A N/A self N/A N/A N/A params N/A N/A pm N/A MechCodon_Sanity gy params N/A N/A N/A self assertRaises KeyError N/A N/A N/A N/A N/A N/A pm _sanity_dnds N/A test_sanity_MechCodon_homo_dNmissing N/A N/A self N/A N/A N/A params N/A alpha 1.5 N/A pm N/A MechCodon_Sanity gy params N/A N/A N/A self assertRaises KeyError N/A N/A N/A N/A N/A N/A pm _sanity_dnds N/A test_sanity_MechCodon_homo_dSmissing N/A N/A self N/A N/A N/A params N/A beta 1.5 N/A pm N/A MechCodon_Sanity gy params N/A N/A N/A pm _sanity_dnds N/A N/A N/A self assertEqual N/A N/A pm params N/A alpha 1.0 msg dS (alpha key) not set to 1 when not provided. N/A test_sanity_MechCodon_homo_omega N/A N/A self N/A N/A N/A params N/A omega 0.1 N/A pm N/A MechCodon_Sanity gy params N/A N/A N/A pm _sanity_dnds N/A N/A N/A self assertEqual N/A N/A pm params N/A beta 0.1 msg 'omega' key not converted to 'beta' key in codon model sanity. N/A test_sanity_MechCodon_hetero_dSmissing N/A N/A self N/A N/A N/A params N/A beta N/A 0.2 0.3 0.4 N/A pm N/A MechCodon_Sanity gy params N/A N/A pm hetmodel True N/A N/A N/A pm _sanity_dnds N/A N/A N/A N/A np testing assert_array_almost_equal N/A N/A pm params N/A alpha N/A N/A np ones 3 decimal DECIMAL err_msg dS not properly filled in when not provided for a heterogeneous codon model. N/A test_sanity_MechCodon_hetero_bad_dNdS_combo N/A N/A self N/A N/A N/A params N/A beta alpha N/A 0.2 0.3 0.4 9.0 N/A pm N/A MechCodon_Sanity gy params N/A N/A pm hetmodel True N/A N/A N/A self assertRaises TypeError N/A N/A N/A N/A N/A N/A pm _sanity_dnds N/A N/A ParametersSanity_ECM N/A N/A unittest TestCase N/A N/A  
        Unittest for ECM_Sanity.
     test_sanity_ECM N/A N/A self N/A N/A N/A newp N/A N/A ECM_Sanity ecmrest N/A size 61 N/A N/A N/A self assertTrue N/A N/A N/A newp N/A beta 1.0 N/A N/A newp N/A alpha 1.0 msg dN, dS not properly filled in as 1 when missing from params dictionary for ECM model. N/A N/A N/A self assertTrue N/A N/A N/A newp N/A k_ti 1.0 N/A N/A newp N/A k_tv 1.0 msg kappa params not properly initialized to 1. when not provided for ECM model. N/A N/A ParametersSanity_MutSel N/A N/A unittest TestCase N/A N/A  
        Unittest for MutSel_Sanity.
     test_sanity_MutSel_aa_fitness N/A N/A self N/A N/A N/A aa_fitness N/A N/A np array N/A -1.309 -0.881 0.662 -1.245 3.909 3.276 3.578 0.785 -0.957 2.862 2.919 2.174 2.907 1.438 3.231 0.733 3.098 2.505 1.47 0.0 N/A codon_from_aa_fitness N/A N/A np array N/A -0.957 2.174 -0.957 2.174 3.098 3.098 3.098 3.098 3.231 0.733 3.231 0.733 0.785 0.785 2.919 0.785 1.438 3.578 1.438 3.578 2.907 2.907 2.907 2.907 3.231 3.231 3.231 3.231 2.862 2.862 2.862 2.862 -1.245 0.662 -1.245 0.662 -1.309 -1.309 -1.309 -1.309 3.276 3.276 3.276 3.276 2.505 2.505 2.505 2.505 0.0 0.0 0.733 0.733 0.733 0.733 -0.881 1.47 -0.881 2.862 3.909 2.862 3.909 N/A pm N/A MutSel_Sanity mutsel N/A fitness aa_fitness N/A N/A N/A pm _sanity_state_freqs_fitness N/A N/A N/A self assertTrue N/A N/A pm params N/A codon_model msg MutSel model not recognized as codon model when amino acid fitnesses provided. N/A N/A N/A self assertFalse N/A N/A pm params N/A calc_by_freqs msg MutSel model didnt set calc_by_freqs as False when amino acid fitnesses provided. N/A N/A N/A N/A np testing assert_array_almost_equal N/A N/A pm params N/A fitness codon_from_aa_fitness decimal DECIMAL err_msg Mutsel amino acid fitness not properly converted to codon fitness. N/A test_sanity_MutSel_codon_fitness N/A N/A self N/A N/A N/A codon_fitness N/A N/A np array N/A -0.957 2.174 -0.957 2.174 3.098 3.098 3.098 3.098 3.231 0.733 3.231 0.733 0.785 0.785 2.919 0.785 1.438 3.578 1.438 3.578 2.907 2.907 2.907 2.907 3.231 3.231 3.231 3.231 2.862 2.862 2.862 2.862 -1.245 0.662 -1.245 0.662 -1.309 -1.309 -1.309 -1.309 3.276 3.276 3.276 3.276 2.505 2.505 2.505 2.505 0.0 0.0 0.733 0.733 0.733 0.733 -0.881 1.47 -0.881 2.862 3.909 2.862 3.909 N/A pm N/A MutSel_Sanity mutsel N/A fitness codon_fitness N/A N/A N/A pm _sanity_state_freqs_fitness N/A N/A N/A self assertTrue N/A N/A pm params N/A codon_model msg MutSel model not recognized as codon model when codon fitnesses provided. N/A N/A N/A self assertFalse N/A N/A pm params N/A calc_by_freqs msg MutSel model didnt set calc_by_freqs as False when codon fitnesses provided. N/A test_sanity_MutSel_codon_frequencies N/A N/A self N/A N/A N/A codon_freqs N/A 0.01372832 0.01412889 0.01638048 0.0139875 0.01412889 0.01454117 0.01685846 0.01439566 0.01638048 0.01685846 0.01954503 0.01668976 0.0139875 0.01439566 0.01668976 0.0142516 0.01412889 0.01454117 0.01685846 0.01439566 0.01454117 0.01496548 0.01735039 0.01481573 0.01685846 0.01735039 0.02011536 0.01717677 0.01439566 0.01481573 0.01717677 0.01466747 0.01638048 0.01685846 0.01954503 0.01668976 0.01685846 0.01735039 0.02011536 0.01717677 0.01954503 0.02011536 0.02332095 0.01991406 0.01668976 0.01717677 0.01991406 0.01700488 0.01439566 0.0142516 0.01439566 0.01481573 0.01717677 0.01466747 0.01717677 0.01991406 0.01700488 0.0142516 0.01466747 0.01700488 0.01452069 N/A pm N/A MutSel_Sanity mutsel N/A state_freqs codon_freqs N/A N/A N/A pm _sanity_state_freqs_fitness N/A N/A N/A self assertTrue N/A N/A pm params N/A codon_model msg MutSel model not recognized as codon model when codon frequencies provided. N/A N/A N/A self assertTrue N/A N/A pm params N/A calc_by_freqs msg MutSel model didnt set calc_by_freqs as True when codon frequencies provided. N/A test_sanity_MutSel_nuc_fitness N/A N/A self N/A N/A N/A nuc_fitness N/A 0.2 0.4 1.6 1.5 N/A pm N/A MutSel_Sanity mutsel N/A fitness nuc_fitness N/A N/A N/A pm _sanity_state_freqs_fitness N/A N/A N/A self assertFalse N/A N/A pm params N/A codon_model msg MutSel model recognized as codon model when nucleotide fitness provided. N/A N/A N/A self assertFalse N/A N/A pm params N/A calc_by_freqs msg MutSel model didnt set calc_by_freqs as False when nucleotide fitnss provided. N/A test_sanity_MutSel_nuc_frequencies N/A N/A self N/A N/A N/A nuc_freqs N/A 0.25 0.25 0.25 0.25 N/A pm N/A MutSel_Sanity mutsel N/A state_freqs nuc_freqs N/A N/A N/A pm _sanity_state_freqs_fitness N/A N/A N/A self assertFalse N/A N/A pm params N/A codon_model msg MutSel model not recognized as codon model when nucleotide frequencies provided. N/A N/A N/A self assertTrue N/A N/A pm params N/A calc_by_freqs msg MutSel model didnt set calc_by_freqs as True when nucleotide frequencies provided. N/A N/A