//**********************************************************************************************************************
vector<string> ChimeraSlayerCommand::getValidParameters(){
try {
- string AlignArray[] = {"fasta", "processors","trim","trimera", "name","window", "include","template","numwanted", "ksize", "match","mismatch",
+ string AlignArray[] = {"fasta", "processors","trim","split", "name","window", "include","template","numwanted", "ksize", "match","mismatch",
"divergence", "minsim","mincov","minbs", "minsnp","parents", "iters","outputdir","inputdir", "search","realign" };
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
return myArray;
else {
//valid paramters for this command
- string Array[] = {"fasta", "processors","name", "include","trim", "trimera","window", "template","numwanted", "ksize", "match","mismatch",
+ string Array[] = {"fasta", "processors","name", "include","trim", "split","window", "template","numwanted", "ksize", "match","mismatch",
"divergence", "minsim","mincov","minbs", "minsnp","parents", "iters","outputdir","inputdir", "search","realign" };
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
temp = validParameter.validFile(parameters, "trim", false); if (temp == "not found") { temp = "f"; }
trim = m->isTrue(temp);
- temp = validParameter.validFile(parameters, "trimera", false); if (temp == "not found") { temp = "f"; }
+ temp = validParameter.validFile(parameters, "split", false); if (temp == "not found") { temp = "f"; }
trimera = m->isTrue(temp);
search = validParameter.validFile(parameters, "search", false); if (search == "not found") { search = "distance"; }
m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n");
#endif
m->mothurOut("The trim parameter allows you to output a new fasta file containing your sequences with the chimeric ones trimmed to include only their longest piece, default=F. \n");
- m->mothurOut("The trimera parameter allows you to check both peices of non-chimeric sequence for chimeras, thus looking for trimeras and quadmeras. default=F. \n");
+ m->mothurOut("The split parameter allows you to check both pieces of non-chimeric sequence for chimeras, thus looking for trimeras and quadmeras. default=F. \n");
m->mothurOut("The window parameter allows you to specify the window size for searching for chimeras, default=50. \n");
m->mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=5.\n");
m->mothurOut("The numwanted parameter allows you to specify how many sequences you would each query sequence compared with, default=15.\n");
chimera->getChimeras(candidateSeq);
if (m->control_pressed) { delete candidateSeq; return 1; }
-
- //do you want to check both pieces for chimeras
- if (trimera) {
- //if you are not chimeric, then check each half
- data_results wholeResults = chimera->getResults();
+ //if you are not chimeric, then check each half
+ data_results wholeResults = chimera->getResults();
+
+ //determine if we need to split
+ bool isChimeric = false;
+
+ if (wholeResults.flag == "yes") {
+ string chimeraFlag = "no";
+ if( (wholeResults.results[0].bsa >= minBS && wholeResults.results[0].divr_qla_qrb >= divR)
+ ||
+ (wholeResults.results[0].bsb >= minBS && wholeResults.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
- //determine if we need to split
- bool isChimeric = false;
- if (wholeResults.flag == "yes") {
- string chimeraFlag = "no";
- if( (wholeResults.results[0].bsa >= minBS && wholeResults.results[0].divr_qla_qrb >= divR)
- ||
- (wholeResults.results[0].bsb >= minBS && wholeResults.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
-
-
- if (chimeraFlag == "yes") {
- if ((wholeResults.results[0].bsa >= minBS) || (wholeResults.results[0].bsb >= minBS)) { isChimeric = true; }
- }
+ if (chimeraFlag == "yes") {
+ if ((wholeResults.results[0].bsa >= minBS) || (wholeResults.results[0].bsb >= minBS)) { isChimeric = true; }
}
+ }
+
+ if ((!isChimeric) && trimera) {
- if (!isChimeric) {
-
- //split sequence in half by bases
- string leftQuery, rightQuery;
- Sequence tempSeq(candidateSeq->getName(), candidateAligned);
- divideInHalf(tempSeq, leftQuery, rightQuery);
-
- //run chimeraSlayer on each piece
- Sequence* left = new Sequence(candidateSeq->getName(), leftQuery);
- Sequence* right = new Sequence(candidateSeq->getName(), rightQuery);
-
- //find chimeras
- chimera->getChimeras(left);
- data_results leftResults = chimera->getResults();
-
- chimera->getChimeras(right);
- data_results rightResults = chimera->getResults();
-
- //if either piece is chimeric then report
- Sequence* trimmed = chimera->print(out, out2, leftResults, rightResults);
- if (trim) { trimmed->printSequence(out3); delete trimmed; }
-
- delete left; delete right;
-
- }else { //already chimeric
- //print results
- Sequence* trimmed = chimera->print(out, out2);
- if (trim) { trimmed->printSequence(out3); delete trimmed; }
- }
- }else {
+ //split sequence in half by bases
+ string leftQuery, rightQuery;
+ Sequence tempSeq(candidateSeq->getName(), candidateAligned);
+ divideInHalf(tempSeq, leftQuery, rightQuery);
+
+ //run chimeraSlayer on each piece
+ Sequence* left = new Sequence(candidateSeq->getName(), leftQuery);
+ Sequence* right = new Sequence(candidateSeq->getName(), rightQuery);
+
+ //find chimeras
+ chimera->getChimeras(left);
+ data_results leftResults = chimera->getResults();
+
+ chimera->getChimeras(right);
+ data_results rightResults = chimera->getResults();
+
+ //if either piece is chimeric then report
+ Sequence* trimmed = chimera->print(out, out2, leftResults, rightResults);
+ if (trim) { trimmed->printSequence(out3); delete trimmed; }
+
+ delete left; delete right;
+
+ }else { //already chimeric
//print results
Sequence* trimmed = chimera->print(out, out2);
if (trim) { trimmed->printSequence(out3); delete trimmed; }
}
+
}
count++;
}
if (m->control_pressed) { delete candidateSeq; return 1; }
- //do you want to check both pieces for chimeras
- if (trimera) {
-
- //if you are not chimeric, then check each half
- data_results wholeResults = chimera->getResults();
+ //if you are not chimeric, then check each half
+ data_results wholeResults = chimera->getResults();
+
+ //determine if we need to split
+ bool isChimeric = false;
+
+ if (wholeResults.flag == "yes") {
+ string chimeraFlag = "no";
+ if( (wholeResults.results[0].bsa >= minBS && wholeResults.results[0].divr_qla_qrb >= divR)
+ ||
+ (wholeResults.results[0].bsb >= minBS && wholeResults.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
- //determine if we need to split
- bool isChimeric = false;
- if (wholeResults.flag == "yes") {
- string chimeraFlag = "no";
- if( (wholeResults.results[0].bsa >= minBS && wholeResults.results[0].divr_qla_qrb >= divR)
- ||
- (wholeResults.results[0].bsb >= minBS && wholeResults.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
-
-
- if (chimeraFlag == "yes") {
- if ((wholeResults.results[0].bsa >= minBS) || (wholeResults.results[0].bsb >= minBS)) { isChimeric = true; }
- }
+ if (chimeraFlag == "yes") {
+ if ((wholeResults.results[0].bsa >= minBS) || (wholeResults.results[0].bsb >= minBS)) { isChimeric = true; }
}
+ }
+
+ if ((!isChimeric) && trimera) {
+ //split sequence in half by bases
+ string leftQuery, rightQuery;
+ Sequence tempSeq(candidateSeq->getName(), candidateAligned);
+ divideInHalf(tempSeq, leftQuery, rightQuery);
- if (!isChimeric) {
- //split sequence in half by bases
- string leftQuery, rightQuery;
- Sequence tempSeq(candidateSeq->getName(), candidateAligned);
- divideInHalf(tempSeq, leftQuery, rightQuery);
-
- //run chimeraSlayer on each piece
- Sequence* left = new Sequence(candidateSeq->getName(), leftQuery);
- Sequence* right = new Sequence(candidateSeq->getName(), rightQuery);
-
- //find chimeras
- chimera->getChimeras(left);
- data_results leftResults = chimera->getResults();
-
- chimera->getChimeras(right);
- data_results rightResults = chimera->getResults();
-
- //if either piece is chimeric then report
- Sequence* trimmed = chimera->print(outMPI, outAccMPI, leftResults, rightResults);
- if (trim) {
- string outputString = ">" + trimmed->getName() + "\n" + trimmed->getAligned() + "\n";
- delete trimmed;
-
- //write to accnos file
- int length = outputString.length();
- char* buf2 = new char[length];
- memcpy(buf2, outputString.c_str(), length);
-
- MPI_File_write_shared(outFastaMPI, buf2, length, MPI_CHAR, &status);
- delete buf2;
- }
-
- delete left; delete right;
+ //run chimeraSlayer on each piece
+ Sequence* left = new Sequence(candidateSeq->getName(), leftQuery);
+ Sequence* right = new Sequence(candidateSeq->getName(), rightQuery);
+
+ //find chimeras
+ chimera->getChimeras(left);
+ data_results leftResults = chimera->getResults();
+
+ chimera->getChimeras(right);
+ data_results rightResults = chimera->getResults();
+
+ //if either piece is chimeric then report
+ Sequence* trimmed = chimera->print(outMPI, outAccMPI, leftResults, rightResults);
+ if (trim) {
+ string outputString = ">" + trimmed->getName() + "\n" + trimmed->getAligned() + "\n";
+ delete trimmed;
- }else { //already chimeric
- //print results
- Sequence* trimmed = chimera->print(outMPI, outAccMPI);
+ //write to accnos file
+ int length = outputString.length();
+ char* buf2 = new char[length];
+ memcpy(buf2, outputString.c_str(), length);
- if (trim) {
- string outputString = ">" + trimmed->getName() + "\n" + trimmed->getAligned() + "\n";
- delete trimmed;
-
- //write to accnos file
- int length = outputString.length();
- char* buf2 = new char[length];
- memcpy(buf2, outputString.c_str(), length);
-
- MPI_File_write_shared(outFastaMPI, buf2, length, MPI_CHAR, &status);
- delete buf2;
- }
+ MPI_File_write_shared(outFastaMPI, buf2, length, MPI_CHAR, &status);
+ delete buf2;
}
- }else {
+
+ delete left; delete right;
+
+ }else {
//print results
Sequence* trimmed = chimera->print(outMPI, outAccMPI);
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