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Merge pull request #1750 from veg/develop
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2.5.63
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@spond
spond authored Oct 22, 2024
2 parents afbcb6f + a88d72c commit cc6eee3
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Showing 12 changed files with 178 additions and 85 deletions.
4 changes: 3 additions & 1 deletion CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -236,7 +236,7 @@ if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX)
PCL_CHECK_FOR_NEON()
if(${HAVE_NEON_EXTENSIONS})
add_definitions (-D_SLKP_USE_ARM_NEON)

set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -mcpu=native -mtune=native ")
endif(${HAVE_NEON_EXTENSIONS})
endif(NOT NONEON)

Expand Down Expand Up @@ -284,6 +284,8 @@ if (CMAKE_CXX_COMPILER_ID MATCHES "Clang")
PCL_CHECK_FOR_NEON()
if(${HAVE_NEON_EXTENSIONS})
add_definitions (-D_SLKP_USE_ARM_NEON)
set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -mcpu=native -mtune=native ")

endif(${HAVE_NEON_EXTENSIONS})
endif(NOT NONEON)

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126 changes: 74 additions & 52 deletions res/TemplateBatchFiles/CleanStopCodons.bf
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Original file line number Diff line number Diff line change
Expand Up @@ -94,12 +94,13 @@ for (k=0; k<all64.species; k+= 1) {
sequenceNames [k] = newName;
}
else {
sequenceNames [k] = seqName;
sequenceNames [k] = seqName;
}

seqNamesListAll[testName] = 1;
}


GetInformation (sequenceData, all64);
GetDataInfo (duplicateMapper, all64);

Expand All @@ -118,78 +119,99 @@ all64.unique_sites = Rows (all64.site_freqs) * Columns (all64.site_freqs);

for (sequenceIndex = 0; sequenceIndex < all64.species; sequenceIndex += 1) {

stopCodonCount = 0;
sitesWithDeletions = {1,all64.unique_sites};

for (siteIndex = 0; siteIndex < all64.unique_sites; siteIndex += 1) {

GetDataInfo (siteInfo, all64, sequenceIndex, siteIndex);
siteInfo1 = stopCodonTemplate*siteInfo;
siteInfo2 = nonStopCodonTemplate*siteInfo;


if (siteInfo1[0]>0 && siteInfo2[0] == 0) {
sitesWithDeletions[siteIndex] = 1;
stopCodonCount += 1;
}
if (filteringOption % 2) {
if (haveInfoAtSites[siteIndex] == 0) {
if (siteInfo1[0]+siteInfo2[0] < +stopCodonTemplate) {
haveInfoAtSites[siteIndex] = 1;
stopCodonCount = 0;
sitesWithDeletions = {1,all64.unique_sites};

COUNT_GAPS_IN_FREQUENCIES = 0;

for (siteIndex = 0; siteIndex < all64.unique_sites; siteIndex += 1) {

GetDataInfo (siteInfo, all64, sequenceIndex, siteIndex);


siteInfo1 = stopCodonTemplate*siteInfo;
siteInfo2 = nonStopCodonTemplate*siteInfo;


if (siteInfo1[0]>0 && siteInfo2[0] == 0) {
sitesWithDeletions[siteIndex] = 1;
stopCodonCount += 1;
}

if (filteringOption % 2) {
if (haveInfoAtSites[siteIndex] == 0) {
if (siteInfo1[0]+siteInfo2[0] > 0) {
haveInfoAtSites[siteIndex] = 1;
}
}
}
}
}

if (stopCodonCount > 0) {
if (filterinOption == 4) {
continue;

if (stopCodonCount > 0) {
if (filterinOption == 4) {
continue;
}
fprintf (stdout, "\nSequence ", sequenceNames[sequenceIndex], ":");
fprintf (stdout, "\n\t", Format(stopCodonCount,8,0), " stop codons found.");

doSomething = 1;
cleanedString = "";
seqString = sequenceData[sequenceIndex];
cleanedString * (Abs(seqString)+1);

for (siteIndex = 0; siteIndex < all64.sites; siteIndex += 1) {
stopCodonCount = duplicateMapper[siteIndex];
if (sitesWithDeletions[stopCodonCount]) {
cleanedString * replacementString;
} else {
cleanedString * seqString[3*siteIndex][3*siteIndex+2];
}
}
cleanedString * 0;
sequenceData[sequenceIndex] = cleanedString;
}
fprintf (stdout, "\nSequence ", sequenceNames[sequenceIndex], ":");
fprintf (stdout, "\n\t", Format(stopCodonCount,8,0), " stop codons found.");

doSomething = 1;
cleanedString = "";
seqString = sequenceData[sequenceIndex];
cleanedString * (Abs(seqString)+1);

for (siteIndex = 0; siteIndex < all64.sites; siteIndex += 1) {
stopCodonCount = duplicateMapper[siteIndex];
if (sitesWithDeletions[stopCodonCount]) {
cleanedString * replacementString;



if (filteringOption >= 2) {
if (duplicateChecker[sequenceData[sequenceIndex]] == 0) {
duplicateChecker[sequenceData[sequenceIndex]] = 1;
notDuplicate[sequenceIndex] = 1;
} else {
cleanedString * seqString[3*siteIndex][3*siteIndex+2];
doSomething = 1;
}
}
cleanedString * 0;
sequenceData[sequenceIndex] = cleanedString;
}

if (filteringOption >= 2) {
if (duplicateChecker[sequenceData[sequenceIndex]] == 0) {
duplicateChecker[sequenceData[sequenceIndex]] = 1;
notDuplicate[sequenceIndex] = 1;
} else {
doSomething = 1;
notDuplicate[sequenceIndex] = 1;
}
} else {
notDuplicate[sequenceIndex] = 1; }
}

filterSites = 0;

if (filteringOption%2) {
doSomething = doSomething || (Abs(haveInfoAtSites)<all64.unique_sites);
filterSites = Abs(haveInfoAtSites)<all64.unique_sites;
doSomething = doSomething || filterSites;
}


if (!doSomething) {
fprintf (stdout, "\n\nNo stop codons found\n\n");
}

SetDialogPrompt ("Save cleaned data to:");
fprintf (PROMPT_FOR_FILE, CLEAR_FILE, KEEP_OPEN);
seqLen = Abs (sequenceData[0]);
for (sequenceIndex = 0; sequenceIndex < all64.species; sequenceIndex += 1) {
if (notDuplicate[sequenceIndex]) {
fprintf (LAST_FILE_PATH, ">", sequenceNames[sequenceIndex], "\n", sequenceData[sequenceIndex], "\n\n");
if (filterSites) {
fprintf (LAST_FILE_PATH, ">", sequenceNames[sequenceIndex], "\n");
for (s = 0; s < seqLen; s+=3) {
if (haveInfoAtSites[duplicateMapper[s$3]]) {
fprintf (LAST_FILE_PATH, (sequenceData[sequenceIndex])[s][s+2]);
}
}
fprintf (LAST_FILE_PATH, "\n\n");
} else {
fprintf (LAST_FILE_PATH, ">", sequenceNames[sequenceIndex], "\n", sequenceData[sequenceIndex], "\n\n");
}
}
}
fprintf (LAST_FILE_PATH, CLOSE_FILE);
Expand Down
3 changes: 1 addition & 2 deletions res/TemplateBatchFiles/SelectionAnalyses/MEME.bf
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Original file line number Diff line number Diff line change
Expand Up @@ -752,7 +752,6 @@ for (meme.partition_index = 0; meme.partition_index < meme.partition_count; meme
},
"meme.store_results");
}
pattern_count_all
'
);

Expand Down Expand Up @@ -1724,7 +1723,7 @@ lfunction meme.store_results (node, result, arguments) {
if (has_psi) {
result_row[has_psi] = estimators.GetGlobalMLE (result[utility.getGlobalValue("terms.alternative")],^"terms.meme.fg_param_prefix"+ ^"terms.parameters.triple_hit_rate");
if (None == result_row[has_psi]) {
result_row[has_delta] = ((scalers['BG'])[^"terms.parameters.triple_hit_rate"])["scaler"];
result_row[has_psi] = ((scalers['BG'])[^"terms.parameters.triple_hit_rate"])["scaler"];
}
^"meme.site_multihit_string" += "/" + Format (result_row[has_psi],0,2);
}
Expand Down
44 changes: 35 additions & 9 deletions res/TemplateBatchFiles/SelectionAnalyses/PRIME.bf
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Original file line number Diff line number Diff line change
Expand Up @@ -545,7 +545,10 @@ for (prime.partition_index = 0; prime.partition_index < prime.partition_count; p
/* run the main loop over all unique site pattern combinations */

prime.pattern_count = 1;


for (_pattern_, _pattern_info_; in; prime.site_patterns) {

io.ReportProgressBar("", "Working on site pattern " + (prime.pattern_count) + "/" + Abs (prime.site_patterns));
if (_pattern_info_[utility.getGlobalValue("terms.data.is_constant")]) {
prime.store_results (-1,None,{"0" : "prime.site_likelihood",
Expand All @@ -556,6 +559,7 @@ for (prime.partition_index = 0; prime.partition_index < prime.partition_count; p
"5" : prime.site_model_mapping
});
} else {

mpi.QueueJob (prime.queue, "prime.handle_a_site", {"0" : "prime.site_likelihood",
"1" : "prime.site_likelihood_property",
"2" : alignments.serialize_site_filter
Expand Down Expand Up @@ -703,6 +707,8 @@ lfunction prime.handle_a_site (lf_fel, lf_prop, filter_data, partition_index, pa
//Export (lfe, ^lf_prop);
// fprintf ("/tmp/PRIME-site." + (pattern_info["sites"])[0] + ".bf",CLEAR_FILE,lfe);

character_map = None;

if (^"prime.site_beta" > 0) {

// fit the universal alternative
Expand Down Expand Up @@ -781,8 +787,8 @@ lfunction prime.handle_a_site (lf_fel, lf_prop, filter_data, partition_index, pa
"OPTIMIZATION_PRECISION": 1e-3
});

// Export (lfe, ^lf_prop);
// fprintf ("/tmp/PRIME-site." + (pattern_info["sites"])[0] + ".bf",CLEAR_FILE,lfe);
//Export (lfe, ^lf_prop);
//fprintf ("/tmp/PRIME-site." + (pattern_info["sites"])[0] + ".bf",CLEAR_FILE,lfe);

//console.log ("\n" + ^"LF_INITIAL_GRID_MAXIMUM_VALUE" + "\nGrid best"+ ^"LF_INITIAL_GRID_MAXIMUM" + " / optimized " + results[1][0] + "\n");
Optimize (results, ^lf_prop);
Expand Down Expand Up @@ -878,25 +884,41 @@ lfunction prime.handle_a_site (lf_fel, lf_prop, filter_data, partition_index, pa
//console.log ("\nPRIME = " + altL);
//console.log ("alpha = " + ^"prime.site_alpha");
//console.log ("beta = " + ^"prime.site_beta");

character_map = None;

if (^"prime.impute_states") {
DataSet anc = ReconstructAncestors ( ^lf_prop, {{0}}, MARGINAL, DOLEAVES);
GetString (names, anc, -1);
GetDataInfo (codon_chars, ^((lfInfo["Datafilters"])[0]) , "CHARACTERS");
GetString (names_obs, ^((lfInfo["Datafilters"])[0]), -1);
names_obs = utility.MatrixToDict (names_obs);


character_map = {};
for (seq_id, seq_name; in; names) {
character_map [seq_name] = {};
GetDataInfo (site_map, ^((lfInfo["Datafilters"])[0]), names_obs[seq_name], 0);
character_map [seq_name] = {'observed' :{} , 'imputed' : {}, 'support' : 0};


for (char, char_support; in; site_map) {
if (char_support > 1e-6) {
(((character_map [seq_name]))['observed'])[codon_chars[char]] = char_support;
}
}

for (char, char_support; in; (anc.marginal_support_matrix)[seq_id][-1]) {
if (char_support > 1e-6) {
(character_map [seq_name])[codon_chars[char]] = char_support;
(((character_map [seq_name]))['imputed'])[codon_chars[char]] = char_support;
if ( (((character_map [seq_name]))['observed'])[codon_chars[char]]) {
(character_map [seq_name])['support'] += char_support;
}
}
}

}

}


utility.ToggleEnvVariable ("TOLERATE_CONSTRAINT_VIOLATION", None);

ancestral_info = ancestral.build (lf_prop,0,FALSE);
Expand Down Expand Up @@ -1138,7 +1160,9 @@ lfunction prime.store_results (node, result, arguments) {
//console.log (result_row);

utility.EnsureKey (^"prime.site_results", partition_index);
utility.EnsureKey (^"prime.imputed_leaf_states", partition_index);
if (^"prime.impute_states") {
utility.EnsureKey (^"prime.imputed_leaf_states", partition_index);
}
utility.EnsureKey (^"prime.sub_mapping", partition_index);

sites_mapping_to_pattern = pattern_info[utility.getGlobalValue("terms.data.sites")];
Expand All @@ -1148,7 +1172,9 @@ lfunction prime.store_results (node, result, arguments) {
site_index = sites_mapping_to_pattern[i];
((^"prime.site_results")[partition_index])[site_index] = result_row;
((^"prime.sub_mapping")[partition_index])[site_index] = sub_map;
((^"prime.imputed_leaf_states")[partition_index])[site_index] = result[^"terms.prime_imputed_states"];
if (^"prime.impute_states") {
((^"prime.imputed_leaf_states")[partition_index])[site_index] = result[^"terms.prime_imputed_states"];
}
prime.report.echo (site_index, partition_index, result_row);
}
}
11 changes: 9 additions & 2 deletions src/core/batchlan.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -507,11 +507,18 @@ hyBLFunctionType GetBFFunctionType (long idx) {
}

//____________________________________________________________________________________
_String const ExportBFFunction (long idx, bool recursive) {
_String const ExportBFFunction (long idx, bool recursive, _AVLList* tracker) {


_StringBuffer bf (8192UL);
if (IsBFFunctionIndexValid(idx)) {

if (tracker) {
if (tracker->FindLong (idx) >= 0) {
return bf;
}
tracker->InsertNumber(idx);
}

_String hbf_name = GetBFFunctionNameByIndex (idx);
_ExecutionList * body = &GetBFFunctionBody(idx);
Expand Down Expand Up @@ -567,7 +574,7 @@ _String const ExportBFFunction (long idx, bool recursive) {
bf << "\n/*----- Called function '"
<< *a_name
<< "' ------*/\n"
<< ExportBFFunction (FindBFFunctionName(*a_name), false)
<< ExportBFFunction (FindBFFunctionName(*a_name), tracker ? recursive : false, tracker)
<< "\n\n";
}
}
Expand Down
3 changes: 2 additions & 1 deletion src/core/batchlanruntime.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -887,7 +887,8 @@ bool _ElementaryCommand::HandleConstructCategoryMatrix (_ExecutionList& cur
_String ("WEIGHTS"),_hyphyLFConstructCategoryMatrixWeights,
_String ("SITE_LOG_LIKELIHOODS"), _hyphyLFConstructCategoryMatrixSiteProbabilities,
_String ("CLASSES"), _hyphyLFConstructCategoryMatrixClasses,
_String ("SHORT"), _hyphyLFConstructCategoryMatrixClasses
_String ("SHORT"), _hyphyLFConstructCategoryMatrixClasses,
_String ("PARTITIONS"), _hyphyLFConstructCategoryMatrixPartitions
);


Expand Down
18 changes: 15 additions & 3 deletions src/core/formula.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -289,16 +289,25 @@ _StringBuffer const _Formula::toRPN (_hyFormulaStringConversionMode mode, _List*
return r;
}
//__________________________________________________________________________________
BaseRef _Formula::toStr (_hyFormulaStringConversionMode mode, _List* matched_names, bool drop_tree) {
BaseRef _Formula::toStr (_hyFormulaStringConversionMode mode, _List* matched_names, bool drop_tree, _StringBuffer * hbl_dependencies) {
ConvertToTree(false);

_StringBuffer * result = new _StringBuffer (64UL);

long savepd = print_digit_specification;
print_digit_specification = 0L;



if (theTree) { // there is something to do
SubtreeToString (*result, theTree, -1, matched_names, nil, mode);
if (hbl_dependencies) {
_SimpleList _tracker;
_AVLList tracker (&_tracker);
SubtreeToString (*result, theTree, -1, matched_names, nil, mode, hbl_dependencies,&tracker);

} else {
SubtreeToString (*result, theTree, -1, matched_names, nil, mode);
}
} else {
if (theFormula.countitems()) {
(*result) << "RPN:" << toRPN (mode, matched_names);
Expand Down Expand Up @@ -990,7 +999,7 @@ bool _Formula::InternalSimplify (node<long>* top_node) {


//__________________________________________________________________________________
void _Formula::SubtreeToString (_StringBuffer & result, node<long>* top_node, int op_level, _List* match_names, _Operation* this_node_op, _hyFormulaStringConversionMode mode) {
void _Formula::SubtreeToString (_StringBuffer & result, node<long>* top_node, int op_level, _List* match_names, _Operation* this_node_op, _hyFormulaStringConversionMode mode, _StringBuffer * hbl_dependencies, _AVLList* hbl_tracker) {

if (!this_node_op) {
if (!top_node) {
Expand Down Expand Up @@ -1142,6 +1151,9 @@ void _Formula::SubtreeToString (_StringBuffer & result, node<long>* top_node, in
if (node_op_count < 0L) {
// a user-defined function
long func_id = this_node_op->UserFunctionID();
if (hbl_dependencies && hbl_tracker) {
(*hbl_dependencies) << ExportBFFunction(func_id, true, hbl_tracker);
}
result<< & GetBFFunctionNameByIndex(func_id);
if (top_node) {
result<<'(';
Expand Down
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