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2.6.65 #1778

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Dec 19, 2024
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2.6.65 #1778

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c1a2dd1
Issue 1777 fix
spond Dec 16, 2024
7f8963c
MSS improvements, RELAX bug fix, optimization procedure tweaks
spond Dec 17, 2024
b874817
Merge remote-tracking branch 'origin' into develop
spond Dec 18, 2024
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4 changes: 2 additions & 2 deletions CMakeLists.txt
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Expand Up @@ -685,7 +685,7 @@ makeLink(HYPHYMP hyphy hyphy)

add_test (NAME UNIT-TESTS COMMAND bash run_unit_tests.sh)
add_test (CODON HYPHYMP tests/hbltests/SimpleOptimizations/SmallCodon.bf)
add_test (PROTEIN HYPHYMP CPU=1 tests/hbltests/SimpleOptimizations/IntermediateProtein.bf)
add_test (PROTEIN HYPHYMP tests/hbltests/SimpleOptimizations/IntermediateProtein.bf)
add_test (MTCODON HYPHYMP tests/hbltests/libv3/mtDNA-code.wbf)
add_test (ALGAE HYPHYMP tests/hbltests/libv3/algae-mtDNA.wbf)
add_test (CILIATES HYPHYMP tests/hbltests/libv3/ciliate-code.wbf)
Expand All @@ -701,7 +701,7 @@ add_test (RELAX HYPHYMP tests/hbltests/libv3/RELAX.wbf)
add_test (FUBAR HYPHYMP tests/hbltests/libv3/FUBAR.wbf)
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 (GARD HYPHYMP tests/hbltests/libv3/GARD.wbf ENV="TOLERATE_NUMERICAL_ERRORS=1;")
add_test (FADE HYPHYMP tests/hbltests/libv3/FADE.wbf)
add_test (ABSREL HYPHYMP tests/hbltests/libv3/ABSREL.wbf)
#add_test (FMM HYPHYMP tests/hbltests/libv3/FMM.wbf)
Expand Down
2 changes: 1 addition & 1 deletion res/TemplateBatchFiles/SelectionAnalyses/RELAX.bf
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Expand Up @@ -276,7 +276,7 @@ relax.do_srv = io.SelectAnOption (
if (relax.do_srv == "Branch-site") {
relax.do_bs_srv = TRUE;
relax.do_srv = TRUE;
(relax.json[terms.json.analysis])[terms.settings] = "Branch-site synonymous rate variation";
selection.io.json_store_setting (relax.json, "SRV type", "Branch-site synonymous rate variation");
} else {
if (relax.do_srv == "Yes") {
relax.do_bs_srv = FALSE;
Expand Down
3 changes: 2 additions & 1 deletion res/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.bf
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Expand Up @@ -453,7 +453,8 @@ function doGTR (prefix) {
terms.nucleotideRate ("A","C") : { utility.getGlobalValue ("terms.fit.MLE") : 0.25} ,
terms.nucleotideRate ("A","T") : { utility.getGlobalValue ("terms.fit.MLE") : 0.25} ,
terms.nucleotideRate ("C","G") : { utility.getGlobalValue ("terms.fit.MLE") : 0.25} ,
terms.nucleotideRate ("G","T") : { utility.getGlobalValue ("terms.fit.MLE") : 0.25}
terms.nucleotideRate ("G","T") : { utility.getGlobalValue ("terms.fit.MLE") : 0.25} ,
terms.nucleotideRate ("C","T") : { utility.getGlobalValue ("terms.fit.MLE") : 1.00}
}
});

Expand Down
186 changes: 143 additions & 43 deletions res/TemplateBatchFiles/libv3/models/codon/MSS.bf
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Expand Up @@ -14,7 +14,9 @@ terms.model.MSS.syn_rate_within = " within codon class ";
terms.model.MSS.syn_rate_between = " between codon classes ";
terms.model.MSS.between = "synonymous rate between codon classes";
terms.model.MSS.neutral = "neutral reference";
terms.model.MSS.empirical = "empirical";
terms.model.MSS.codon_classes = "codon classes";
terms.model.MSS.codon_pairs = "codon pairs";
terms.model.MSS.normalize = "normalize rates";

//----------------------------------------------------------------------------------------------------------------
Expand All @@ -32,7 +34,9 @@ lfunction model.codon.MSS.prompt_and_define_freq (type, code, freq) {
{"SynREV2g", "Each pair of synonymous codons mapping to the same amino-acid class and separated by a transition have a separate substitution rate (Valine == neutral). All between-class synonymous substitutions share a rate."}
{"SynREVCodon", "Each codon pair that is exchangeable gets its own substitution rate (fully estimated, mean = 1)"}
{"Random", "Random partition (specify how many classes; largest class = neutral)"}
{"Empirical", "Load a TSV file with an empirical rate estimate for each codon pair"}
{"File", "Load a TSV partition from file (prompted for neutral class)"}
{"Codon-file", "Load a TSV partition for pairs of codons from a file (prompted for neutral class)"}
},
"Synonymous Codon Class Definitions");

Expand Down Expand Up @@ -182,6 +186,18 @@ lfunction model.codon.MSS.prompt_and_define_freq (type, code, freq) {
return models.codon.MSS.ModelDescription(type, code, models.codon.MSS.LoadClasses (null));
}

if (partitioning_option == "Codon-file") {
KeywordArgument ("mss-file", "File defining the model partition");
KeywordArgument ("mss-neutral", "Designation for the neutral substitution rate");
return models.codon.MSS.ModelDescription(type, code, models.codon.MSS.LoadClassesCodon (null));
}

if (partitioning_option == "Empirical") {
KeywordArgument ("mss-file", "File defining empirical rates for each pair of codons");
return models.codon.MSS.ModelDescription(type, code, models.codon.MSS.LoadEmpiricalRates (null));
}


return {};
}

Expand Down Expand Up @@ -209,6 +225,10 @@ lfunction models.codon.MSS.ModelDescription(type, code, codon_classes) {
m[utility.getGlobalValue("terms.model.q_ij")] = "models.codon.MSS._GenerateRate";
m[utility.getGlobalValue("terms.model.MSS.codon_classes")] = codon_classes [^"terms.model.MSS.codon_classes"];
m[utility.getGlobalValue("terms.model.MSS.neutral")] = codon_classes [^"terms.model.MSS.neutral"];
m[utility.getGlobalValue("terms.model.MSS.empirical")] = codon_classes [^"terms.model.MSS.empirical"];
m[utility.getGlobalValue("terms.model.MSS.codon_pairs")] = codon_classes [^"terms.model.MSS.codon_pairs"];


if (codon_classes/utility.getGlobalValue("terms.model.MSS.between")) {
m[^"terms.model.MSS.between"] = codon_classes [^"terms.model.MSS.between"];
}
Expand Down Expand Up @@ -257,6 +277,8 @@ lfunction models.codon.MSS._GenerateRate (fromChar, toChar, namespace, model_typ
alpha_term = utility.getGlobalValue ("terms.parameters.synonymous_rate");
beta_term = utility.getGlobalValue ("terms.parameters.nonsynonymous_rate");
nr = model[utility.getGlobalValue("terms.model.MSS.neutral")];
empirical = model[utility.getGlobalValue("terms.model.MSS.empirical")];
codon_pairs = model[utility.getGlobalValue("terms.model.MSS.codon_pairs")];
omega = "omega";
alpha = "alpha";
beta = "beta";
Expand Down Expand Up @@ -298,63 +320,86 @@ lfunction models.codon.MSS._GenerateRate (fromChar, toChar, namespace, model_typ
rate_entry += "*" + aa_rate;
} else {

class_from = (model[^"terms.model.MSS.codon_classes"])[fromChar];
class_to = (model[^"terms.model.MSS.codon_classes"])[toChar];


if ((Abs (class_from) && Abs (class_to)) == FALSE) {
class_from = (model[^"terms.model.MSS.codon_classes"])[fromChar+toChar];
class_to = class_from;
}

assert (Abs (class_from) && Abs (class_to), "The neutral class for `fromChar` to `toChar` is not specified in the model definition");

if (class_from == class_to) {
if (class_from == nr) {
if (model_type == utility.getGlobalValue("terms.local")) {
codon_rate = alpha + "_" + class_from;
(_GenerateRate.p[model_type])[alpha_term + ^"terms.model.MSS.syn_rate_within" + class_from] = codon_rate;
rate_entry += "*" + codon_rate;
} else {
rate_entry = nuc_rate;
}
if (empirical) {
if (fromChar < toChar) {
key = fromChar + "|" + toChar;
} else {
if (model_type == utility.getGlobalValue("terms.local")) {
codon_rate = alpha + "_" + class_from;
key = toChar + "|" + fromChar;
}

assert (model[^"terms.model.MSS.codon_classes"] / key, "Rate for codon pair `key` was missing from the empirical file definition");
rate_entry += "*" + (model[^"terms.model.MSS.codon_classes"])[key];

} else {
if (codon_pairs) {
if (fromChar < toChar) {
key = fromChar + "|" + toChar;
} else {
codon_rate = parameters.ApplyNameSpace(alpha + "_" + class_from, namespace);
key = toChar + "|" + fromChar;
}
(_GenerateRate.p[model_type])[alpha_term + ^"terms.model.MSS.syn_rate_within" + class_from] = codon_rate;
rate_entry += "*" + codon_rate;
assert (model[^"terms.model.MSS.codon_classes"] / key, "Rate for codon pair `key` was missing from the empirical file definition");
class_from = (model[^"terms.model.MSS.codon_classes"])[key];
class_to = class_from;
} else {
class_from = (model[^"terms.model.MSS.codon_classes"])[fromChar];
class_to = (model[^"terms.model.MSS.codon_classes"])[toChar];
}
} else {
if (class_from > class_to) {
codon_rate = class_to;


if ((Abs (class_from) && Abs (class_to)) == FALSE) {
class_from = (model[^"terms.model.MSS.codon_classes"])[fromChar+toChar];
class_to = class_from;
class_from = codon_rate;
}
if (Abs (between_rate)) {
if (model_type == utility.getGlobalValue("terms.local")) {
codon_rate = between_rate;

assert (Abs (class_from) && Abs (class_to), "The neutral class for `fromChar` to `toChar` is not specified in the model definition");

if (class_from == class_to) {
if (class_from == nr) {
if (model_type == utility.getGlobalValue("terms.local")) {
codon_rate = alpha + "_" + class_from;
(_GenerateRate.p[model_type])[alpha_term + ^"terms.model.MSS.syn_rate_within" + class_from] = codon_rate;
rate_entry += "*" + codon_rate;
} else {
rate_entry = nuc_rate;
}
} else {
codon_rate = parameters.ApplyNameSpace(between_rate, namespace);
if (model_type == utility.getGlobalValue("terms.local")) {
codon_rate = alpha + "_" + class_from;
} else {
codon_rate = parameters.ApplyNameSpace(alpha + "_" + class_from, namespace);
}
(_GenerateRate.p[model_type])[alpha_term + ^"terms.model.MSS.syn_rate_within" + class_from] = codon_rate;
rate_entry += "*" + codon_rate;
}
(_GenerateRate.p[model_type])[^"terms.model.MSS.between"] = codon_rate;

} else {
if (class_from + class_to == nr) {
//console.log ("NEUTRAL");
codon_rate = 1;
} else {
if (class_from > class_to) {
codon_rate = class_to;
class_to = class_from;
class_from = codon_rate;
}
if (Abs (between_rate)) {
if (model_type == utility.getGlobalValue("terms.local")) {
codon_rate = alpha + "_" + class_from + "_" + class_to;
codon_rate = between_rate;
} else {
codon_rate = parameters.ApplyNameSpace(between_rate, namespace);
}
(_GenerateRate.p[model_type])[^"terms.model.MSS.between"] = codon_rate;

} else {
if (class_from + class_to == nr) {
//console.log ("NEUTRAL");
codon_rate = 1;
} else {
codon_rate = parameters.ApplyNameSpace(alpha + "_" + class_from + "_" + class_to, namespace);
if (model_type == utility.getGlobalValue("terms.local")) {
codon_rate = alpha + "_" + class_from + "_" + class_to;
} else {
codon_rate = parameters.ApplyNameSpace(alpha + "_" + class_from + "_" + class_to, namespace);
}
(_GenerateRate.p[model_type])[alpha_term + ^"terms.model.MSS.syn_rate_between" + class_from + " and " + class_to] = codon_rate;
}
(_GenerateRate.p[model_type])[alpha_term + ^"terms.model.MSS.syn_rate_between" + class_from + " and " + class_to] = codon_rate;
}
rate_entry += "*" + codon_rate;
}
rate_entry += "*" + codon_rate;
}
}

Expand All @@ -363,6 +408,27 @@ lfunction models.codon.MSS._GenerateRate (fromChar, toChar, namespace, model_typ

return _GenerateRate.p;
}

//----------------------------------------------------------------------------------------------------------------

lfunction models.codon.MSS.LoadEmpiricalRates (file) {

SetDialogPrompt ("A TSV file with three columns (Codon1, Codon2, Empirical Rate) which is used to define relative synonymous substitution rates");
classes = io.ReadDelimitedFile (file, "\t", TRUE);
headers = utility.Array1D(classes[^'terms.io.header']);
io.CheckAssertion("`&headers`>=3", "Expected a TSV file with at least 3 columns; 2nd column is the codon, 3rd is the class for this codon");
codon_pairs = {};
for (_record_; in; classes [^"terms.io.rows"]) {
if (_record_[0] < _record_[1]) {
key = _record_[0] + "|" + _record_[1];
} else {
key = _record_[1] + "|" + _record_[0];
}
codon_pairs [key] = Eval (_record_[2]);
}

return {^"terms.model.MSS.codon_classes" : codon_pairs, ^"terms.model.MSS.empirical" : TRUE};
}

//----------------------------------------------------------------------------------------------------------------

Expand Down Expand Up @@ -391,3 +457,37 @@ lfunction models.codon.MSS.LoadClasses (file) {

return {^"terms.model.MSS.codon_classes" : codons_by_class, ^"terms.model.MSS.neutral" : nr};
}

//----------------------------------------------------------------------------------------------------------------

lfunction models.codon.MSS.LoadClassesCodon (file) {

SetDialogPrompt ("A TSV file with three columns (Codon1, Codon2, Class) which is used to partition synonymous substitutions into groups");
classes = io.ReadDelimitedFile (file, "\t", TRUE);
headers = utility.Array1D(classes[^'terms.io.header']);
io.CheckAssertion("`&headers`>=3", "Expected a TSV file with at least 3 columns; 2nd column is the codon, 3rd is the class for this codon");
codon_pairs = {};
for (_record_; in; classes [^"terms.io.rows"]) {
if (_record_[0] < _record_[1]) {
key = _record_[0] + "|" + _record_[1];
} else {
key = _record_[1] + "|" + _record_[0];
}
codon_pairs [key] = _record_[2];
}

classes = utility.UniqueValues(codon_pairs);
class_count = utility.Array1D(classes);
io.CheckAssertion("`&class_count`>=2", "Expected at least 2 codon classes");

choices = {class_count,2};
for (i = 0; i < class_count; i += 1) {
choices[i][0] = classes[i];
choices[i][1] = "Codon class " + classes[i];
}

nr= io.SelectAnOption (choices, "Select the codon class which will serve as the neutral rate reference (relative rate = 1)");


return {^"terms.model.MSS.codon_classes" : codon_pairs, ^"terms.model.MSS.neutral" : nr, ^"terms.model.MSS.codon_pairs" : TRUE};
}
19 changes: 12 additions & 7 deletions res/TemplateBatchFiles/libv3/models/parameters.bf
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Expand Up @@ -853,18 +853,23 @@ lfunction parameters.helper.tree_lengths_to_initial_values(dict, type) {

for (i = 0; i < components; i += 1) {
this_component = {};
for (_branch_name_ , _branch_length_; in; (dict[i])[ utility.getGlobalValue("terms.branch_length")]) {
this_component [_branch_name_] = {
utility.getGlobalValue('terms.fit.MLE') :
factor*_branch_length_
};
}


utility.ForEachPair((dict[i])[ utility.getGlobalValue("terms.branch_length")], "_branch_name_", "_branch_length_",
"
`&this_component`[_branch_name_] = {utility.getGlobalValue('terms.fit.MLE') : `&factor`*_branch_length_}
");
result[i] = this_component;
if (Abs (this_component)) {
result[i] = this_component;
}

}

return { utility.getGlobalValue("terms.branch_length"): result
return {
utility.getGlobalValue("terms.branch_length"): result
};

}

/**
Expand Down
2 changes: 1 addition & 1 deletion src/core/global_things.cpp
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Expand Up @@ -122,7 +122,7 @@ namespace hy_global {
kErrorStringMatrixExportError ("Export matrix called with a non-polynomial matrix argument"),
kErrorStringNullOperand ("Attempting to operate on an undefined value; this is probably the result of an earlier 'soft' error condition"),
kErrorNumerical ("To treat numerical errors as warnings, please specify \"ENV=TOLERATE_NUMERICAL_ERRORS=1;\" as the command line argument. This often resolves the issue, which is indicative of numerical instability."),
kHyPhyVersion = _String ("2.5.64"),
kHyPhyVersion = _String ("2.5.65"),

kNoneToken = "None",
kNullToken = "null",
Expand Down
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