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Removes amino acid to dna code
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#788 #792
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@mothur-westcott
mothur-westcott committed Nov 16, 2021
1 parent ed1e71d commit 02a4cce
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Showing 3 changed files with 91 additions and 21 deletions.
4 changes: 2 additions & 2 deletions Mothur.xcodeproj/project.pbxproj
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Original file line number Diff line number Diff line change
Expand Up @@ -3984,7 +3984,7 @@
GCC_C_LANGUAGE_STANDARD = "compiler-default";
GCC_DYNAMIC_NO_PIC = NO;
GCC_MODEL_TUNING = G5;
GCC_OPTIMIZATION_LEVEL = 3;
GCC_OPTIMIZATION_LEVEL = 0;
GCC_PREPROCESSOR_DEFINITIONS = (
"MOTHUR_FILES=\"\\\"/Users/swestcott/Desktop/release/;/Users/swestcott/Desktop/mothurbugs/\\\"\"",
"VERSION=\"\\\"1.46.0\\\"\"",
Expand Down Expand Up @@ -4036,7 +4036,7 @@
"FRAMEWORK_SEARCH_PATHS[arch=*]" = "${SRCROOT}/mothur_resources_10.14/libs";
GCC_C_LANGUAGE_STANDARD = "compiler-default";
GCC_MODEL_TUNING = G5;
GCC_OPTIMIZATION_LEVEL = 3;
GCC_OPTIMIZATION_LEVEL = 0;
GCC_PREPROCESSOR_DEFINITIONS = (
"MOTHUR_FILES=\"\\\"/Users/swestcott/Desktop/release\\\"\"",
"VERSION=\"\\\"1.46.0\\\"\"",
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102 changes: 86 additions & 16 deletions source/commands/translateseqscommand.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ vector<string> TranslateSeqsCommand::setParameters(){
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
CommandParameter pframes("frames", "Multiple", "1-2-3--1--2--3", "1", "", "", "","",true,false,true); parameters.push_back(pframes);
CommandParameter pstop("stop", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pstop);
CommandParameter pdna("dna", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pdna);
//CommandParameter pdna("dna", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pdna);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
Expand All @@ -38,11 +38,11 @@ vector<string> TranslateSeqsCommand::setParameters(){
string TranslateSeqsCommand::getHelpString(){
try {
string helpString = "";
helpString += "The translate.seqs command reads a fastafile containing dna and translates it to amino acids, reads a fasta file containing amino acids and translates it to dna.\n";
helpString += "The translate.seqs command reads a fastafile containing dna and translates it to amino acids, .....\n";
helpString += "The translate.seqs command parameters are fasta, frames, stop, dna and processors.\n";
helpString += "The frames parameter is used to indicate the reading frames you want to use. Options are 1, 2, 3, -1, -2, -3. You can select multiple frames by separating them with '|' characters. For example: frames=1|-1|2.\n";
helpString += "The stop parameter is used to indicate when to stop the translation. If T, then if the translation hits a stop codon, it stops before that codon. If F, it returns the full translation with a * as the stop codon. Default=t.\n";
helpString += "The dna parameter is used to indicate which type of data is in your fasta file. Default=t, meaning the data is dna. dna=f, means the data in the fasta file is amino acids. \n";
//helpString += "The dna parameter is used to indicate which type of data is in your fasta file. Default=t, meaning the data is dna. dna=f, means the data in the fasta file is amino acids. \n";
helpString += "The translate.seqs command should be in the following format: \n";
helpString += "translate.seqs(fasta=yourFastaFile, processors=2) \n";

Expand All @@ -58,7 +58,7 @@ string TranslateSeqsCommand::getOutputPattern(string type) {
try {
string pattern = "";

if (type == "fasta") { pattern = "[filename],[tag],fasta"; }
if (type == "fasta") { pattern = "[filename],[tag2],fasta-[filename],[tag],align"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }

return pattern;
Expand Down Expand Up @@ -104,11 +104,11 @@ TranslateSeqsCommand::TranslateSeqsCommand(string option) : Command() {
temp = validParameter.valid(parameters, "stop"); if (temp == "not found") { temp = "T"; }
stop = util.isTrue(temp);

temp = validParameter.valid(parameters, "dna"); if (temp == "not found") { temp = "T"; }
dna = util.isTrue(temp);
//temp = validParameter.valid(parameters, "dna"); if (temp == "not found") { temp = "T"; }
//dna = util.isTrue(temp);

//force single frames for aa to dna translation
if (dna) { frames.clear(); frames.push_back(1); }
//if (dna) { frames.clear(); frames.push_back(1); }
}
}
catch(exception& e) {
Expand Down Expand Up @@ -152,12 +152,13 @@ int TranslateSeqsCommand::execute(){
for (int i = 0; i < frames.size(); i++) {
if (m->getControl_pressed()) { break; }

variables["[tag]"] = "dna";
if (!dna) { variables["[tag]"] = "aa" + toString(frames[i]); }
m->mothurOut("\nTranslating sequences to amino acids using frame " + toString(frames[i]) + ":\n");

variables["[tag2]"] = "aa"+toString(frames[i]);
string outputFileName = getOutputFileName("fasta", variables);
outputTypes["fasta"].push_back(outputFileName); outputNames.push_back(outputFileName);

numSeqs += createProcesses(outputFileName, lines, frames[i]);
numSeqs = createProcessesTranslateDNAtoAminoAcids(outputFileName, lines, frames[i]);
}

m->mothurOut("\nIt took " + toString(time(NULL) - start) + " seconds to translate " + toString(numSeqs) + " sequences.\n");
Expand All @@ -180,19 +181,88 @@ int TranslateSeqsCommand::execute(){
exit(1);
}
}
/**********************************************************************************************************************
void translateToDNADriver(translateSeqsStruct* params) {
try {
ifstream inFASTA; params->util.openInputFile(params->inputFilename, inFASTA);
inFASTA.seekg(params->filePos.start);
bool done = false;
long long count = 0;
while (!done) {
if (params->m->getControl_pressed()) { break; }
Protein seq(inFASTA); params->util.gobble(inFASTA);
if (seq.getName() != "") {
string translation; getDNA(seq.getAligned(), translation, params->m);
params->outputWriter->write('>' + seq.getName() + '\n' + translation + '\n');
}
#if defined NON_WINDOWS
unsigned long long pos = inFASTA.tellg();
if ((pos == -1) || (pos >= params->filePos.end)) { break; }
#else
if (count == params->filePos.end) { break; }
#endif
//report progress
if((count) % 1000 == 0){ params->m->mothurOutJustToScreen(toString(count) + "\n"); }
}
//report progress
if((count) % 1000 != 0){ params->m->mothurOutJustToScreen(toString(count) + "\n"); }
params->numSeqs = count; inFASTA.close();
}
catch(exception& e) {
params->m->errorOut(e, "TranslateSeqsCommand", "translateToDNADriver");
exit(1);
}
}*/
//**********************************************************************************************************************
void translateDriver(translateSeqsStruct* params) {
void translateToAminoAcidDriver(translateSeqsStruct* params) {
try {

ifstream inFASTA; params->util.openInputFile(params->inputFilename, inFASTA);
inFASTA.seekg(params->filePos.start);

bool done = false;
long long count = 0;
while (!done) {

if (params->m->getControl_pressed()) { break; }

Sequence seq(inFASTA); params->util.gobble(inFASTA);

if (seq.getName() != "") {
Protein prot = seq.getProtein(params->frame);
prot.printProtein(params->outputWriter);
count++;
}

#if defined NON_WINDOWS
unsigned long long pos = inFASTA.tellg();
if ((pos == -1) || (pos >= params->filePos.end)) { break; }
#else
if (count == params->filePos.end) { break; }
#endif

//report progress
if((count) % 1000 == 0){ params->m->mothurOutJustToScreen(toString(count) + "\n"); }

}
//report progress
if((count) % 1000 != 0){ params->m->mothurOutJustToScreen(toString(count) + "\n"); }
params->numSeqs = count; inFASTA.close();
}
catch(exception& e) {
params->m->errorOut(e, "TranslateSeqsCommand", "driver");
params->m->errorOut(e, "TranslateSeqsCommand", "translateToAminoAcidDriver");
exit(1);
}
}
//***************************************************************************************************************
// translateSeqsStruct (linePair fP, OutputWriter* oFName, string fname, bool st, bool dn, int frame) {
double TranslateSeqsCommand::createProcesses(string outputFileName, vector<linePair> lines, int frame) {
double TranslateSeqsCommand::createProcessesTranslateDNAtoAminoAcids(string outputFileName, vector<linePair> lines, int frame) {
try {
//create array of worker threads
vector<std::thread*> workerThreads;
Expand All @@ -207,13 +277,13 @@ double TranslateSeqsCommand::createProcesses(string outputFileName, vector<lineP
translateSeqsStruct* dataBundle = new translateSeqsStruct(lines[i+1], threadOutputWriter, fastafile, stop, dna, frame);
data.push_back(dataBundle);

workerThreads.push_back(new std::thread(translateDriver, dataBundle));
workerThreads.push_back(new std::thread(translateToAminoAcidDriver, dataBundle));
}

OutputWriter* threadOutputWriter = new OutputWriter(synchronizedOutputFile);
translateSeqsStruct* dataBundle = new translateSeqsStruct(lines[0], threadOutputWriter, fastafile, stop, dna, frame);

translateDriver(dataBundle);
translateToAminoAcidDriver(dataBundle);
double num = dataBundle->numSeqs;

for (int i = 0; i < processors-1; i++) {
Expand Down
6 changes: 3 additions & 3 deletions source/commands/translateseqscommand.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@

#include "command.hpp"
#include "sequence.hpp"
#include "protein.hpp"

/*
This command would take...
Expand Down Expand Up @@ -62,7 +63,7 @@ class TranslateSeqsCommand : public Command {
vector<string> outputNames;
vector<int> frames;

double createProcesses(string, vector<linePair>, int);
double createProcessesTranslateDNAtoAminoAcids(string, vector<linePair>, int);
};

//**********************************************************************************************************************
Expand All @@ -74,8 +75,7 @@ struct translateSeqsStruct {
double numSeqs;

linePair filePos;
MothurOut* m;
Utils util;
MothurOut* m; Utils util;

translateSeqsStruct (linePair fP, OutputWriter* oFName, string fname, bool st, bool dn, int f) {

Expand Down

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