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BF updates
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@spond
spond committed Dec 12, 2023
1 parent 0622be2 commit 1bb5353
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Showing 2 changed files with 21 additions and 7 deletions.
20 changes: 17 additions & 3 deletions res/TemplateBatchFiles/SelectionAnalyses/RELAX.bf
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Original file line number Diff line number Diff line change
Expand Up @@ -43,19 +43,21 @@ relax.analysis_description = {
Version 3.1 adds LHC + Nedler-Mead initial fit phase and keyword support.
Version 3.1.1 adds some bug fixes for better convergence.
Version 4.0 adds support for synonymous rate variation.
Version 4.1 adds further support for multiple hit models",
Version 4.1 adds further support for multiple hit models.
Version 4.1.1 adds reporting for convergence diagnostics",
terms.io.version : "3.1.1",
terms.io.reference : "RELAX: Detecting Relaxed Selection in a Phylogenetic Framework (2015). Mol Biol Evol 32 (3): 820-832",
terms.io.authors : "Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution g",
terms.io.contact : "[email protected]",
terms.io.requirements : "in-frame codon alignment and a phylogenetic tree, with at least two groups of branches defined using the {} notation (one group can be defined as all unlabeled branches)"
terms.io.requirements : "in-frame codon alignment and a phylogenetic tree, with at least two groups of branches defined using the {} notation (one group can be defined as all unlabeled branches)",
terms.settings: {}
};

relax.json = { terms.json.analysis: relax.analysis_description,
terms.json.input: {},
terms.json.fits : {},
terms.json.timers : {},
terms.json.test_results : {}
terms.json.test_results : {},
};

relax.relaxation_parameter = "relax.K";
Expand Down Expand Up @@ -1001,6 +1003,9 @@ function relax.FitMainTestPair (prompt) {


if (Abs (relax.best_samples[1] - relax.best_samples[0]) < 5.) { // could be diagnostic of convergence problems
selection.io.json_store_setting (relax.json, "convergence-flat-surface", relax.best_samples[1] - relax.best_samples[0]);


io.ReportProgressMessageMD("RELAX", "alt-2", "* Potential convergence issues due to flat likelihood surfaces; checking to see whether K > 1 or K < 1 is robustly inferred");
if (relax.fitted.K > 1) {
parameters.SetRange (model.generic.GetGlobalParameter (relax.model_object_map ["relax.test"] , terms.relax.k), terms.range01);
Expand All @@ -1022,6 +1027,8 @@ function relax.FitMainTestPair (prompt) {


if (relax.alternative_model.fit.take2 [terms.fit.log_likelihood] > relax.alternative_model.fit[terms.fit.log_likelihood]) {
relax.stash_fitted_K = relax.fitted.K;


io.ReportProgressMessageMD("RELAX", "alt-2", "\n### Potential for highly unreliable K inference due to multiple local maxima in the likelihood function, treat results with caution ");
io.ReportProgressMessageMD("RELAX", "alt-2", "> Relaxation parameter reset to opposite mode of evolution from that obtained in the initial optimization.");
Expand All @@ -1032,6 +1039,11 @@ function relax.FitMainTestPair (prompt) {
relax.inferred_distribution = parameters.GetStickBreakingDistribution (models.codon.BS_REL.ExtractMixtureDistribution (relax.model_object_map ["relax.test"])) % 0;
selection.io.report_dnds (relax.inferred_distribution);

selection.io.json_store_setting (relax.json, "convergence-unstable", {
{relax.fitted.K, relax.alternative_model.fit.take2 [terms.fit.log_likelihood]}
{relax.stash_fitted_K, relax.alternative_model.fit [terms.fit.log_likelihood]}

});

io.ReportProgressMessageMD("RELAX", "alt-2", "* The following rate distribution was inferred for **reference** branches");
relax.inferred_distribution_ref = parameters.GetStickBreakingDistribution (models.codon.BS_REL.ExtractMixtureDistribution (relax.model_object_map ["relax.reference"])) % 0;
Expand Down Expand Up @@ -1182,6 +1194,8 @@ do {

if (relax.LRT [terms.LRT] < 0) {
io.ReportProgressMessageMD("RELAX", "refit", "* Detected convergence issues (negative LRT). Refitting the alterative/null model pair from a new starting point");
selection.io.json_store_setting (relax.json, "convergence-negative-lrt", relax.loop_passes);

relax.general_descriptive.fit = relax.null_model.fit; // reset initial conditions
for (relax.k = 1; relax.k < relax.numbers_of_tested_groups; relax.k += 1) { // remove constraints on K
relax.model_nmsp = relax.model_namespaces[relax.k ];
Expand Down
8 changes: 4 additions & 4 deletions res/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf
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Original file line number Diff line number Diff line change
Expand Up @@ -69,11 +69,11 @@ absrel.display_orders = {terms.original_name: -1,
absrel.analysis_description = {terms.io.info : "aBSREL (Adaptive branch-site random effects likelihood)
uses an adaptive random effects branch-site model framework
to test whether each branch has evolved under positive selection,
using a procedure which infers an optimal number of rate categories per branch. v2.3 adds support for SRV. v2.5 adds support for ancestral state reconstruction, identification of sites contributing to selection signal, and some diagnostics. ",
using a procedure which infers an optimal number of rate categories per branch. v2.2 adds support for multiple-hit models. v2.3 adds support for SRV. v2.5 adds support for ancestral state reconstruction, identification of sites contributing to selection signal, and some diagnostics. ",
terms.io.version : "2.5",
terms.io.reference : "
Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection (2015).
Mol Biol Evol 32 (5): 1342-1353. v2.2 adds support for multiple-hit models.
Mol Biol Evol 32 (5): 1342-1353.
",
terms.io.authors : "Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group",
terms.io.contact : "[email protected]",
Expand Down Expand Up @@ -703,12 +703,12 @@ for (absrel.branch_id = 0; absrel.branch_id < absrel.branch_count; absrel.branch

if (absrel.multi_hit == "Double" || absrel.multi_hit == "Double+Triple") {
absrel.report.row [4] = (absrel.final_estimates[utility.getGlobalValue ("terms.parameters.multiple_hit_rate")])[utility.getGlobalValue ("terms.fit.MLE")];
absrel.branch.delta [absrel.current_branch] = absrel.report.row [3];
absrel.branch.delta [absrel.current_branch] = absrel.report.row [4];
absrel.offset = 1;
}
if (absrel.multi_hit == "Double+Triple") {
absrel.report.row [5] = (absrel.final_estimates[utility.getGlobalValue ("terms.parameters.triple_hit_rate")])[utility.getGlobalValue ("terms.fit.MLE")];
absrel.branch.psi [absrel.current_branch] = absrel.report.row [4];
absrel.branch.psi [absrel.current_branch] = absrel.report.row [5];
absrel.offset += 1;
}

Expand Down

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