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Merge pull request #1239 from veg/develop
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2.5.21
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@spond
spond authored Oct 29, 2020
2 parents f12276c + 89c6820 commit 1c6e1d7
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Showing 27 changed files with 1,351 additions and 1,130 deletions.
3 changes: 2 additions & 1 deletion CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -588,6 +588,7 @@ add_test (BGM HYPHYMP tests/hbltests/libv3/BGM.wbf)
add_test (CONTRAST-FEL HYPHYMP tests/hbltests/libv3/CFEL.wbf)
add_test (GARD HYPHYMP tests/hbltests/libv3/GARD.wbf)
add_test (FADE HYPHYMP tests/hbltests/libv3/FADE.wbf)
add_test (NAME ABSREL COMMAND HYPHYMP tests/hbltests/libv3/ABSREL.wbf)
add_test (ABSREL HYPHYMP tests/hbltests/libv3/ABSREL.wbf)
add_test (FMM HYPHYMP tests/hbltests/libv3/FMM.wbf)
#add_test (NAME ABSREL-MH COMMAND HYPHYMP tests/hbltests/libv3/ABSREL-MH.wbf)

3 changes: 2 additions & 1 deletion res/TemplateBatchFiles/ConvertDataFile.bf
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Expand Up @@ -32,7 +32,8 @@ ChoiceList (DATA_FILE_PRINT_FORMAT,"Output Format",1,SKIP_NONE,
/* 8 */ "CSV", "Comma separated characters",
/* 9 */ "FASTA sequential","FASTA Sequential Format.",
/* 10 */ "FASTA interleaved","FASTA Interleaved Format.",
/* 11 */ "PAML compatible", "PAML Compatible PHYLIP-like format");
/* 11 */ "PAML compatible", "PAML Compatible PHYLIP-like format",
/* 12 */ "STOCKHOLM", "STOCKHOLM format");

if (DATA_FILE_PRINT_FORMAT<0)
{
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57 changes: 36 additions & 21 deletions res/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf
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@@ -1,4 +1,4 @@
RequireVersion ("2.5.12");
RequireVersion ("2.5.21");


LoadFunctionLibrary("libv3/all-terms.bf"); // must be loaded before CF3x4
Expand Down Expand Up @@ -214,9 +214,7 @@ busted.model_generator = "models.codon.BS_REL.ModelDescription";


if (busted.do_srv) {

if (busted.do_bs_srv) {
busted.model_generator = "busted.model.with.GDD";
busted.model_generator = "models.codon.BS_REL_SRV.ModelDescription";
busted.rate_class_arguments = {{busted.synonymous_rate_classes__,busted.rate_classes__}};
} else {
Expand Down Expand Up @@ -262,15 +260,20 @@ busted.background.bsrel_model = model.generic.DefineMixtureModel(busted.model_g
models.BindGlobalParameters ({"0" : busted.test.bsrel_model, "1" : busted.background.bsrel_model}, terms.nucleotideRate("[ACGT]","[ACGT]"));


/*if (busted.do_srv) {
if (busted.do_srv) {
if (busted.do_bs_srv) {
models.BindGlobalParameters ({"0" : busted.test.bsrel_model, "1" : busted.background.bsrel_model}, "Mean scaler variable for");
for (description,var_id; in; (busted.background.bsrel_model[terms.parameters])[terms.global]) {
if (regexp.Find (description, terms.parameters.synonymous_rate + " for category")) {
var_id_2 = utility.GetByKey ((busted.test.bsrel_model[terms.parameters])[terms.global], description, "String");
if (None != var_id_2) {
parameters.SetConstraint (var_id, var_id_2, terms.global);
}
}
}

models.BindGlobalParameters ({"0" : busted.test.bsrel_model, "1" : busted.background.bsrel_model}, terms.AddCategory (utility.getGlobalValue("terms.mixture.mixture_aux_weight"), "SRV [0-9]+"));
} else {
models.BindGlobalParameters ({"0" : busted.test.bsrel_model, "1" : busted.background.bsrel_model}, "GDD rate category");
models.BindGlobalParameters ({"0" : busted.test.bsrel_model, "1" : busted.background.bsrel_model}, utility.getGlobalValue("terms.mixture.mixture_aux_weight") + " for GDD category ");
}
}*/
}
}

busted.distribution = models.codon.BS_REL.ExtractMixtureDistribution(busted.test.bsrel_model);

Expand Down Expand Up @@ -408,8 +411,8 @@ busted.grid_search.results = estimators.FitLF (busted.filter_names, busted.tree
terms.search_grid : busted.initial_grid,
terms.search_restarts : busted.N.initial_guesses
});


busted.full_model = estimators.FitLF (busted.filter_names, busted.trees, busted.model_map, busted.grid_search.results, busted.model_object_map, {
"retain-lf-object": TRUE,
terms.run_options.optimization_settings :
Expand All @@ -426,11 +429,6 @@ io.SpoolLFToPath(busted.full_model[terms.likelihood_function], io.PromptUserForF

io.ReportProgressMessageMD("BUSTED", "main", "* " + selection.io.report_fit (busted.full_model, 9, busted.codon_data_info[terms.data.sample_size]));

if (busted.do_srv_hmm) {
busted.hmm_lambda = selection.io.extract_global_MLE (busted.full_model, terms.rate_variation.hmm_lambda);
io.ReportProgressMessageMD("BUSTED", "main", "* HMM switching rate = " + Format (busted.hmm_lambda, 8, 3));

}


io.ReportProgressMessageMD("BUSTED", "main", "* For *test* branches, the following rate distribution for branch-site combinations was inferred");
Expand All @@ -448,9 +446,7 @@ busted.distribution_for_json = {busted.FG : utility.Map (utility.Range (busted.r
terms.json.proportion : busted.inferred_test_distribution [_index_][1]}")
};

if (busted.do_srv_hmm) {
busted.distribution_for_json [terms.rate_variation.hmm_lambda] = busted.hmm_lambda;
}


if (busted.has_background) {
io.ReportProgressMessageMD("BUSTED", "main", "* For *background* branches, the following rate distribution for branch-site combinations was inferred");
Expand All @@ -464,6 +460,19 @@ if (busted.has_background) {

if (busted.do_srv) {

if (busted.do_srv_hmm) {
busted.hmm_lambda = selection.io.extract_global_MLE (busted.full_model, terms.rate_variation.hmm_lambda);
busted.hmm_lambda.CI = parameters.GetProfileCI(((busted.full_model[terms.global])[terms.rate_variation.hmm_lambda])[terms.id],
busted.full_model[terms.likelihood_function], 0.95);
io.ReportProgressMessageMD("BUSTED", "main", "* HMM switching rate = " + Format (busted.hmm_lambda, 8, 3));

io.ReportProgressMessageMD ("BUSTED", "main", "* HMM switching rate = " + Format (busted.hmm_lambda,8,4) +
" (95% profile CI " + Format ((busted.hmm_lambda.CI )[terms.lower_bound],8,4) + "-" + Format ((busted.hmm_lambda.CI )[terms.upper_bound],8,4) + ")");

busted.distribution_for_json [terms.rate_variation.hmm_lambda] = busted.hmm_lambda.CI;
}


if (busted.do_bs_srv) {
busted.srv_info = parameters.GetStickBreakingDistribution ( busted.srv_rate_reporting) % 0
} else {
Expand Down Expand Up @@ -560,10 +569,16 @@ if (!busted.run_test) {

if (busted.do_srv) {
if (busted.do_bs_srv) {
busted.srv_info = parameters.GetStickBreakingDistribution ( busted.srv_rate_reporting) % 0
busted.srv_info = parameters.GetStickBreakingDistribution ( busted.srv_rate_reporting) % 0;
} else {
busted.srv_info = Transpose((rate_variation.extract_category_information(busted.test.bsrel_model))["VALUEINDEXORDER"][0])%0;
}
if (busted.do_srv_hmm) {
busted.hmm_lambda = selection.io.extract_global_MLE (busted.full_model, terms.rate_variation.hmm_lambda);
io.ReportProgressMessageMD("BUSTED", "main", "* HMM switching rate = " + Format (busted.hmm_lambda, 8, 3));
busted.distribution_for_json [terms.rate_variation.hmm_lambda] = busted.hmm_lambda;
}

io.ReportProgressMessageMD("BUSTED", "main", "* The following rate distribution for site-to-site **synonymous** rate variation was inferred");
selection.io.report_distribution (busted.srv_info);

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5 changes: 4 additions & 1 deletion res/TemplateBatchFiles/SelectionAnalyses/FEL.bf
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Original file line number Diff line number Diff line change
Expand Up @@ -162,7 +162,10 @@ io.ReportProgressMessageMD ("fel", "codon-refit", "Improving branch lengths, nuc
fel.final_partitioned_mg_results = estimators.FitMGREV (fel.filter_names, fel.trees, fel.codon_data_info [terms.code], {
terms.run_options.model_type: terms.local,
terms.run_options.partitioned_omega: fel.selected_branches,
terms.run_options.retain_lf_object: TRUE
terms.run_options.retain_lf_object: TRUE,
terms.run_options.optimization_settings: {
"OPTIMIZATION_METHOD" : "coordinate-wise"
}
}, fel.partitioned_mg_results);


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