#include "needlemanoverlap.hpp"
//**********************************************************************************************************************
-
-vector<string> TrimSeqsCommand::getValidParameters(){
+vector<string> TrimSeqsCommand::setParameters(){
try {
- string Array[] = {"fasta", "flip", "oligos", "maxambig", "maxhomop","minlength", "maxlength", "qfile",
- "qthreshold", "qwindowaverage", "qstepsize", "qwindowsize", "qaverage", "rollaverage",
- "keepfirst", "removelast",
- "allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+ CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
+ CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pqfile);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+ CommandParameter pflip("flip", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflip);
+ CommandParameter pmaxambig("maxambig", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxambig);
+ CommandParameter pmaxhomop("maxhomop", "Number", "", "0", "", "", "",false,false); parameters.push_back(pmaxhomop);
+ CommandParameter pminlength("minlength", "Number", "", "0", "", "", "",false,false); parameters.push_back(pminlength);
+ CommandParameter pmaxlength("maxlength", "Number", "", "0", "", "", "",false,false); parameters.push_back(pmaxlength);
+ CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppdiffs);
+ CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pbdiffs);
+ CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ptdiffs);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+ CommandParameter pallfiles("allfiles", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pallfiles);
+ CommandParameter pqtrim("qtrim", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pqtrim);
+ CommandParameter pqthreshold("qthreshold", "Number", "", "0", "", "", "",false,false); parameters.push_back(pqthreshold);
+ CommandParameter pqaverage("qaverage", "Number", "", "0", "", "", "",false,false); parameters.push_back(pqaverage);
+ CommandParameter prollaverage("rollaverage", "Number", "", "0", "", "", "",false,false); parameters.push_back(prollaverage);
+ CommandParameter pqwindowaverage("qwindowaverage", "Number", "", "0", "", "", "",false,false); parameters.push_back(pqwindowaverage);
+ CommandParameter pqstepsize("qstepsize", "Number", "", "1", "", "", "",false,false); parameters.push_back(pqstepsize);
+ CommandParameter pqwindowsize("qwindowsize", "Number", "", "50", "", "", "",false,false); parameters.push_back(pqwindowsize);
+ CommandParameter pkeepfirst("keepfirst", "Number", "", "0", "", "", "",false,false); parameters.push_back(pkeepfirst);
+ CommandParameter premovelast("removelast", "Number", "", "0", "", "", "",false,false); parameters.push_back(premovelast);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "TrimSeqsCommand", "getValidParameters");
+ m->errorOut(e, "TrimSeqsCommand", "setParameters");
exit(1);
}
}
-
//**********************************************************************************************************************
-
-TrimSeqsCommand::TrimSeqsCommand(){
+string TrimSeqsCommand::getHelpString(){
try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["fasta"] = tempOutNames;
- outputTypes["qfile"] = tempOutNames;
- outputTypes["group"] = tempOutNames;
+ string helpString = "";
+ helpString += "The trim.seqs command reads a fastaFile and creates 2 new fasta files, .trim.fasta and scrap.fasta, as well as group files if you provide and oligos file.\n";
+ helpString += "The .trim.fasta contains sequences that meet your requirements, and the .scrap.fasta contains those which don't.\n";
+ helpString += "The trim.seqs command parameters are fasta, name, flip, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim, keepfirst, removelast and allfiles.\n";
+ helpString += "The fasta parameter is required.\n";
+ helpString += "The flip parameter will output the reverse compliment of your trimmed sequence. The default is false.\n";
+ helpString += "The oligos parameter allows you to provide an oligos file.\n";
+ helpString += "The name parameter allows you to provide a names file with your fasta file.\n";
+ helpString += "The maxambig parameter allows you to set the maximum number of ambigious bases allowed. The default is -1.\n";
+ helpString += "The maxhomop parameter allows you to set a maximum homopolymer length. \n";
+ helpString += "The minlength parameter allows you to set and minimum sequence length. \n";
+ helpString += "The maxlength parameter allows you to set and maximum sequence length. \n";
+ helpString += "The tdiffs parameter is used to specify the total number of differences allowed in the sequence. The default is pdiffs + bdiffs.\n";
+ helpString += "The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n";
+ helpString += "The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n";
+ helpString += "The qfile parameter allows you to provide a quality file.\n";
+ helpString += "The qthreshold parameter allows you to set a minimum quality score allowed. \n";
+ helpString += "The qaverage parameter allows you to set a minimum average quality score allowed. \n";
+ helpString += "The qwindowsize parameter allows you to set a number of bases in a window. Default=50.\n";
+ helpString += "The qwindowaverage parameter allows you to set a minimum average quality score allowed over a window. \n";
+ helpString += "The rollaverage parameter allows you to set a minimum rolling average quality score allowed over a window. \n";
+ helpString += "The qstepsize parameter allows you to set a number of bases to move the window over. Default=1.\n";
+ helpString += "The allfiles parameter will create separate group and fasta file for each grouping. The default is F.\n";
+ helpString += "The qtrim parameter will trim sequence from the point that they fall below the qthreshold and put it in the .trim file if set to true. The default is T.\n";
+ helpString += "The keepfirst parameter trims the sequence to the first keepfirst number of bases after the barcode or primers are removed, before the sequence is checked to see if it meets the other requirements. \n";
+ helpString += "The removelast removes the last removelast number of bases after the barcode or primers are removed, before the sequence is checked to see if it meets the other requirements.\n";
+ helpString += "The trim.seqs command should be in the following format: \n";
+ helpString += "trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig, \n";
+ helpString += "maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength) \n";
+ helpString += "Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
+ helpString += "For more details please check out the wiki http://www.mothur.org/wiki/Trim.seqs .\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
+ m->errorOut(e, "TrimSeqsCommand", "getHelpString");
exit(1);
}
}
-//**********************************************************************************************************************
-
-vector<string> TrimSeqsCommand::getRequiredParameters(){
- try {
- string Array[] = {"fasta"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "TrimSeqsCommand", "getRequiredParameters");
- exit(1);
- }
-}
//**********************************************************************************************************************
-vector<string> TrimSeqsCommand::getRequiredFiles(){
+TrimSeqsCommand::TrimSeqsCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["qfile"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "TrimSeqsCommand", "getRequiredFiles");
+ m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
exit(1);
}
}
-
//***************************************************************************************************************
TrimSeqsCommand::TrimSeqsCommand(string option) {
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string AlignArray[] = { "fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength", "qfile",
- "qthreshold", "qwindowaverage", "qstepsize", "qwindowsize", "qaverage", "rollaverage",
- "keepfirst", "removelast",
- "allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"};
-
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
outputTypes["fasta"] = tempOutNames;
outputTypes["qfile"] = tempOutNames;
outputTypes["group"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (path == "") { parameters["qfile"] = inputDir + it->second; }
}
+ it = parameters.find("name");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["name"] = inputDir + it->second; }
+ }
+
}
//check for required parameters
fastaFile = validParameter.validFile(parameters, "fasta", true);
- if (fastaFile == "not found") { m->mothurOut("fasta is a required parameter for the trim.seqs command."); m->mothurOutEndLine(); abort = true; }
- else if (fastaFile == "not open") { abort = true; }
+ if (fastaFile == "not found") {
+ fastaFile = m->getFastaFile();
+ if (fastaFile != "") { m->mothurOut("Using " + fastaFile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else if (fastaFile == "not open") { abort = true; }
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
else if(temp == "not open") { abort = true; }
else { qFileName = temp; }
+ temp = validParameter.validFile(parameters, "name", true);
+ if (temp == "not found") { nameFile = ""; }
+ else if(temp == "not open") { nameFile = ""; abort = true; }
+ else { nameFile = temp; }
+
temp = validParameter.validFile(parameters, "qthreshold", false); if (temp == "not found") { temp = "0"; }
convert(temp, qThreshold);
temp = validParameter.validFile(parameters, "allfiles", false); if (temp == "not found") { temp = "F"; }
allFiles = m->isTrue(temp);
- temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; }
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
convert(temp, processors);
exit(1);
}
}
-
-//**********************************************************************************************************************
-
-void TrimSeqsCommand::help(){
- try {
- m->mothurOut("The trim.seqs command reads a fastaFile and creates 2 new fasta files, .trim.fasta and scrap.fasta, as well as group files if you provide and oligos file.\n");
- m->mothurOut("The .trim.fasta contains sequences that meet your requirements, and the .scrap.fasta contains those which don't.\n");
- m->mothurOut("The trim.seqs command parameters are fasta, flip, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim, keepfirst, removelast and allfiles.\n");
- m->mothurOut("The fasta parameter is required.\n");
- m->mothurOut("The flip parameter will output the reverse compliment of your trimmed sequence. The default is false.\n");
- m->mothurOut("The oligos parameter allows you to provide an oligos file.\n");
- m->mothurOut("The maxambig parameter allows you to set the maximum number of ambigious bases allowed. The default is -1.\n");
- m->mothurOut("The maxhomop parameter allows you to set a maximum homopolymer length. \n");
- m->mothurOut("The minlength parameter allows you to set and minimum sequence length. \n");
- m->mothurOut("The maxlength parameter allows you to set and maximum sequence length. \n");
- m->mothurOut("The tdiffs parameter is used to specify the total number of differences allowed in the sequence. The default is pdiffs + bdiffs.\n");
- m->mothurOut("The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n");
- m->mothurOut("The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n");
- m->mothurOut("The qfile parameter allows you to provide a quality file.\n");
- m->mothurOut("The qthreshold parameter allows you to set a minimum quality score allowed. \n");
- m->mothurOut("The qaverage parameter allows you to set a minimum average quality score allowed. \n");
- m->mothurOut("The qwindowsize parameter allows you to set a number of bases in a window. Default=50.\n");
- m->mothurOut("The qwindowaverage parameter allows you to set a minimum average quality score allowed over a window. \n");
- m->mothurOut("The rollaverage parameter allows you to set a minimum rolling average quality score allowed over a window. \n");
- m->mothurOut("The qstepsize parameter allows you to set a number of bases to move the window over. Default=1.\n");
- m->mothurOut("The allfiles parameter will create separate group and fasta file for each grouping. The default is F.\n");
- m->mothurOut("The qtrim parameter will trim sequence from the point that they fall below the qthreshold and put it in the .trim file if set to true. The default is T.\n");
- m->mothurOut("The keepfirst parameter trims the sequence to the first keepfirst number of bases after the barcode or primers are removed, before the sequence is checked to see if it meets the other requirements. \n");
- m->mothurOut("The removelast removes the last removelast number of bases after the barcode or primers are removed, before the sequence is checked to see if it meets the other requirements.\n");
- m->mothurOut("The trim.seqs command should be in the following format: \n");
- m->mothurOut("trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig, \n");
- m->mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength) \n");
- m->mothurOut("Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n");
- m->mothurOut("For more details please check out the wiki http://www.mothur.org/wiki/Trim.seqs .\n\n");
-
- }
- catch(exception& e) {
- m->errorOut(e, "TrimSeqsCommand", "help");
- exit(1);
- }
-}
-
-
-//***************************************************************************************************************
-
-TrimSeqsCommand::~TrimSeqsCommand(){ /* do nothing */ }
-
//***************************************************************************************************************
int TrimSeqsCommand::execute(){
numRPrimers = 0;
vector<vector<string> > fastaFileNames;
vector<vector<string> > qualFileNames;
+ vector<vector<string> > nameFileNames;
string trimSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.fasta";
outputNames.push_back(trimSeqFile); outputTypes["fasta"].push_back(trimSeqFile);
string trimQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.qual";
string scrapQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.qual";
+
if (qFileName != "") {
outputNames.push_back(trimQualFile);
outputNames.push_back(scrapQualFile);
outputTypes["qfile"].push_back(scrapQualFile);
}
+ string trimNameFile = outputDir + m->getRootName(m->getSimpleName(nameFile)) + "trim.names";
+ string scrapNameFile = outputDir + m->getRootName(m->getSimpleName(nameFile)) + "scrap.names";
+
+ if (nameFile != "") {
+ m->readNames(nameFile, nameMap);
+ outputNames.push_back(trimNameFile);
+ outputNames.push_back(scrapNameFile);
+ outputTypes["name"].push_back(trimNameFile);
+ outputTypes["name"].push_back(scrapNameFile);
+ }
+
+ if (m->control_pressed) { return 0; }
+
string outputGroupFileName;
if(oligoFile != ""){
outputGroupFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "groups";
outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
- getOligos(fastaFileNames, qualFileNames);
+ getOligos(fastaFileNames, qualFileNames, nameFileNames);
}
-
+
vector<unsigned long int> fastaFilePos;
vector<unsigned long int> qFilePos;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
if(processors == 1){
- driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, outputGroupFileName, fastaFileNames, qualFileNames, lines[0], qLines[0]);
+ driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, trimNameFile, scrapNameFile, outputGroupFileName, fastaFileNames, qualFileNames, nameFileNames, lines[0], qLines[0]);
}else{
- createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, outputGroupFileName, fastaFileNames, qualFileNames);
+ createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, trimNameFile, scrapNameFile, outputGroupFileName, fastaFileNames, qualFileNames, nameFileNames);
}
#else
- driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, outputGroupFileName, fastaFileNames, qualFileNames, lines[0], qLines[0]);
+ driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, trimNameFile, scrapNameFile, outputGroupFileName, fastaFileNames, qualFileNames, nameFileNames, lines[0], qLines[0]);
#endif
if (m->control_pressed) { return 0; }
-
+
if(allFiles){
map<string, string> uniqueFastaNames;// so we don't add the same groupfile multiple times
map<string, string>::iterator it;
for(int i=0;i<fastaFileNames.size();i++){
for(int j=0;j<fastaFileNames[0].size();j++){
if (fastaFileNames[i][j] != "") {
- if(m->isBlank(fastaFileNames[i][j])){
- remove(fastaFileNames[i][j].c_str());
- namesToRemove.insert(fastaFileNames[i][j]);
+ if (namesToRemove.count(fastaFileNames[i][j]) == 0) {
+ if(m->isBlank(fastaFileNames[i][j])){
+ remove(fastaFileNames[i][j].c_str());
+ namesToRemove.insert(fastaFileNames[i][j]);
- if(qFileName != ""){
- remove(qualFileNames[i][j].c_str());
- namesToRemove.insert(qualFileNames[i][j]);
+ if(qFileName != ""){
+ remove(qualFileNames[i][j].c_str());
+ namesToRemove.insert(qualFileNames[i][j]);
+ }
+
+ if(nameFile != ""){
+ remove(nameFileNames[i][j].c_str());
+ namesToRemove.insert(nameFileNames[i][j]);
+ }
+ }else{
+ it = uniqueFastaNames.find(fastaFileNames[i][j]);
+ if (it == uniqueFastaNames.end()) {
+ uniqueFastaNames[fastaFileNames[i][j]] = barcodeNameVector[i];
+ }
}
- }else{
- it = uniqueFastaNames.find(fastaFileNames[i][j]);
- if (it == uniqueFastaNames.end()) {
- uniqueFastaNames[fastaFileNames[i][j]] = barcodeNameVector[i];
- }
}
}
}
//output group counts
m->mothurOutEndLine();
- //int total = 0;
-// for (int i = 0; i < barcodeNameVector.size(); i++) {
-// if ((barcodeNameVector[i] != "") && (groupCounts[i] != 0)) { total += groupCounts[i]; m->mothurOut("Group " + barcodeNameVector[i] + " contains " + toString(groupCounts[i]) + " sequences."); m->mothurOutEndLine(); }
-// }
-// if (total != 0) { m->mothurOut("Total of all groups is " + toString(total)); m->mothurOutEndLine(); }
+ int total = 0;
+ if (groupCounts.size() != 0) { m->mothurOut("Group count: \n"); }
+ for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
+ total += it->second; m->mothurOut(it->first + "\t" + toString(it->second)); m->mothurOutEndLine();
+ }
+ if (total != 0) { m->mothurOut("Total of all groups is " + toString(total)); m->mothurOutEndLine(); }
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
//set fasta file as new current fastafile
string current = "";
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
}
+ itTypes = outputTypes.find("name");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
+ }
+
itTypes = outputTypes.find("qfile");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
/**************************************************************************************/
-int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string trimFileName, string scrapFileName, string trimQFileName, string scrapQFileName, string groupFileName, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames, linePair* line, linePair* qline) {
+int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string trimFileName, string scrapFileName, string trimQFileName, string scrapQFileName, string trimNFileName, string scrapNFileName, string groupFileName, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames, vector<vector<string> > nameFileNames, linePair* line, linePair* qline) {
try {
m->openOutputFile(scrapQFileName, scrapQualFile);
}
+ ofstream trimNameFile;
+ ofstream scrapNameFile;
+ if(nameFile != ""){
+ m->openOutputFile(trimNFileName, trimNameFile);
+ m->openOutputFile(scrapNFileName, scrapNameFile);
+ }
+
+
ofstream outGroupsFile;
if (oligoFile != ""){ m->openOutputFile(groupFileName, outGroupsFile); }
if(allFiles){
if(qFileName != ""){
m->openOutputFile(qualFileNames[i][j], temp); temp.close();
}
+
+ if(nameFile != ""){
+ m->openOutputFile(nameFileNames[i][j], temp); temp.close();
+ }
}
}
}
int currentSeqsDiffs = 0;
Sequence currSeq(inFASTA); m->gobble(inFASTA);
-
+
QualityScores currQual;
if(qFileName != ""){
currQual = QualityScores(qFile); m->gobble(qFile);
else if(qRollAverage != 0) { success = currQual.stripQualRollingAverage(currSeq, qRollAverage); }
else if(qWindowAverage != 0){ success = currQual.stripQualWindowAverage(currSeq, qWindowStep, qWindowSize, qWindowAverage); }
else { success = 1; }
-
+
//you don't want to trim, if it fails above then scrap it
if ((!qtrim) && (origLength != currSeq.getNumBases())) { success = 0; }
currQual.printQScores(trimQualFile);
}
+ if(nameFile != ""){
+ map<string, string>::iterator itName = nameMap.find(currSeq.getName());
+ if (itName != nameMap.end()) { trimNameFile << itName->first << '\t' << itName->second << endl; }
+ else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
+ }
+
if(barcodes.size() != 0){
- outGroupsFile << currSeq.getName() << '\t' << barcodeNameVector[barcodeIndex] << endl;
- groupCounts[barcodeIndex]++;
+ string thisGroup = barcodeNameVector[barcodeIndex];
+ if (primers.size() != 0) { if (primerNameVector[primerIndex] != "") { thisGroup += "." + primerNameVector[primerIndex]; } }
+
+ outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl;
+
+ if (nameFile != "") {
+ map<string, string>::iterator itName = nameMap.find(currSeq.getName());
+ if (itName != nameMap.end()) {
+ vector<string> thisSeqsNames;
+ m->splitAtChar(itName->second, thisSeqsNames, ',');
+ for (int k = 1; k < thisSeqsNames.size(); k++) { //start at 1 to skip self
+ outGroupsFile << thisSeqsNames[k] << '\t' << thisGroup << endl;
+ }
+ }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
+ }
+
+ map<string, int>::iterator it = groupCounts.find(thisGroup);
+ if (it == groupCounts.end()) { groupCounts[thisGroup] = 1; }
+ else { groupCounts[it->first]++; }
+
}
currQual.printQScores(output);
output.close();
}
+
+ if(nameFile != ""){
+ map<string, string>::iterator itName = nameMap.find(currSeq.getName());
+ if (itName != nameMap.end()) {
+ m->openOutputFileAppend(nameFileNames[barcodeIndex][primerIndex], output);
+ output << itName->first << '\t' << itName->second << endl;
+ output.close();
+ }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
+ }
}
}
else{
+ if(nameFile != ""){ //needs to be before the currSeq name is changed
+ map<string, string>::iterator itName = nameMap.find(currSeq.getName());
+ if (itName != nameMap.end()) { scrapNameFile << itName->first << '\t' << itName->second << endl; }
+ else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
+ }
currSeq.setName(currSeq.getName() + '|' + trashCode);
currSeq.setUnaligned(origSeq);
currSeq.setAligned(origSeq);
scrapFASTAFile.close();
if (oligoFile != "") { outGroupsFile.close(); }
if(qFileName != "") { qFile.close(); scrapQualFile.close(); trimQualFile.close(); }
+ if(nameFile != "") { scrapNameFile.close(); trimNameFile.close(); }
return count;
}
/**************************************************************************************************/
-int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFASTAFileName, string scrapFASTAFileName, string trimQualFileName, string scrapQualFileName, string groupFile, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames) {
+int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFASTAFileName, string scrapFASTAFileName, string trimQualFileName, string scrapQualFileName, string trimNameFileName, string scrapNameFileName, string groupFile, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames, vector<vector<string> > nameFileNames) {
try {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
int process = 1;
vector<vector<string> > tempFASTAFileNames = fastaFileNames;
vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
+ vector<vector<string> > tempNameFileNames = nameFileNames;
if(allFiles){
ofstream temp;
tempPrimerQualFileNames[i][j] += toString(getpid()) + ".temp";
m->openOutputFile(tempPrimerQualFileNames[i][j], temp); temp.close();
}
+ if(nameFile != ""){
+ tempNameFileNames[i][j] += toString(getpid()) + ".temp";
+ m->openOutputFile(tempNameFileNames[i][j], temp); temp.close();
+ }
}
}
}
(scrapFASTAFileName + toString(getpid()) + ".temp"),
(trimQualFileName + toString(getpid()) + ".temp"),
(scrapQualFileName + toString(getpid()) + ".temp"),
+ (trimNameFileName + toString(getpid()) + ".temp"),
+ (scrapNameFileName + toString(getpid()) + ".temp"),
(groupFile + toString(getpid()) + ".temp"),
tempFASTAFileNames,
tempPrimerQualFileNames,
+ tempNameFileNames,
lines[process],
qLines[process]);
ofstream out;
string tempFile = filename + toString(getpid()) + ".num.temp";
m->openOutputFile(tempFile, out);
- for(int i = 0; i < groupCounts.size(); i++) {
- out << groupCounts[i] << endl;
+ for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
+ out << it->first << '\t' << it->second << endl;
}
out.close();
ofstream temp;
m->openOutputFile(trimFASTAFileName, temp); temp.close();
m->openOutputFile(scrapFASTAFileName, temp); temp.close();
- m->openOutputFile(trimQualFileName, temp); temp.close();
- m->openOutputFile(scrapQualFileName, temp); temp.close();
+ if(qFileName != ""){
+ m->openOutputFile(trimQualFileName, temp); temp.close();
+ m->openOutputFile(scrapQualFileName, temp); temp.close();
+ }
+ if (nameFile != "") {
+ m->openOutputFile(trimNameFileName, temp); temp.close();
+ m->openOutputFile(scrapNameFileName, temp); temp.close();
+ }
- driverCreateTrim(filename, qFileName, trimFASTAFileName, scrapFASTAFileName, trimQualFileName, scrapQualFileName, groupFile, fastaFileNames, qualFileNames, lines[0], qLines[0]);
+ driverCreateTrim(filename, qFileName, trimFASTAFileName, scrapFASTAFileName, trimQualFileName, scrapQualFileName, trimNameFileName, scrapNameFileName, groupFile, fastaFileNames, qualFileNames, nameFileNames, lines[0], qLines[0]);
//force parent to wait until all the processes are done
for (int i=0;i<processIDS.size();i++) {
remove((scrapQualFileName + toString(processIDS[i]) + ".temp").c_str());
}
+ if(nameFile != ""){
+ m->appendFiles((trimNameFileName + toString(processIDS[i]) + ".temp"), trimNameFileName);
+ remove((trimNameFileName + toString(processIDS[i]) + ".temp").c_str());
+ m->appendFiles((scrapNameFileName + toString(processIDS[i]) + ".temp"), scrapNameFileName);
+ remove((scrapNameFileName + toString(processIDS[i]) + ".temp").c_str());
+ }
+
m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
remove((groupFile + toString(processIDS[i]) + ".temp").c_str());
m->appendFiles((qualFileNames[j][k] + toString(processIDS[i]) + ".temp"), qualFileNames[j][k]);
remove((qualFileNames[j][k] + toString(processIDS[i]) + ".temp").c_str());
}
+
+ if(nameFile != ""){
+ m->appendFiles((nameFileNames[j][k] + toString(processIDS[i]) + ".temp"), nameFileNames[j][k]);
+ remove((nameFileNames[j][k] + toString(processIDS[i]) + ".temp").c_str());
+ }
}
}
}
ifstream in;
string tempFile = filename + toString(processIDS[i]) + ".num.temp";
m->openInputFile(tempFile, in);
- int count = 0;
int tempNum;
+ string group;
while (!in.eof()) {
- in >> tempNum; m->gobble(in);
- groupCounts[count] += tempNum;
- count++;
+ in >> group >> tempNum; m->gobble(in);
+
+ map<string, int>::iterator it = groupCounts.find(group);
+ if (it == groupCounts.end()) { groupCounts[group] = tempNum; }
+ else { groupCounts[it->first] += tempNum; }
}
in.close(); remove(tempFile.c_str());
int TrimSeqsCommand::setLines(string filename, string qfilename, vector<unsigned long int>& fastaFilePos, vector<unsigned long int>& qfileFilePos) {
try {
-
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
//set file positions for fasta file
fastaFilePos = m->divideFile(filename, processors);
qfileFilePos.push_back(size);
return processors;
+
+ #else
+
+ fastaFilePos.push_back(0); qfileFilePos.push_back(0);
+ //get last file position of fastafile
+ FILE * pFile;
+ unsigned long int size;
+
+ //get num bytes in file
+ pFile = fopen (filename.c_str(),"rb");
+ if (pFile==NULL) perror ("Error opening file");
+ else{
+ fseek (pFile, 0, SEEK_END);
+ size=ftell (pFile);
+ fclose (pFile);
+ }
+ fastaFilePos.push_back(size);
+
+ //get last file position of fastafile
+ FILE * qFile;
+
+ //get num bytes in file
+ qFile = fopen (qfilename.c_str(),"rb");
+ if (qFile==NULL) perror ("Error opening file");
+ else{
+ fseek (qFile, 0, SEEK_END);
+ size=ftell (qFile);
+ fclose (qFile);
+ }
+ qfileFilePos.push_back(size);
+
+ return 1;
+
+ #endif
}
catch(exception& e) {
m->errorOut(e, "TrimSeqsCommand", "setLines");
//***************************************************************************************************************
-void TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<vector<string> >& qualFileNames){
+void TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<vector<string> >& qualFileNames, vector<vector<string> >& nameFileNames){
try {
ifstream inOligos;
m->openInputFile(oligoFile, inOligos);
while(!inOligos.eof()){
- inOligos >> type; m->gobble(inOligos);
+ inOligos >> type;
if(type[0] == '#'){
- while (!inOligos.eof()) { char c = inOligos.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
+ while (!inOligos.eof()) { char c = inOligos.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
+ m->gobble(inOligos);
}
else{
+ m->gobble(inOligos);
//make type case insensitive
for(int i=0;i<type.length();i++){ type[i] = toupper(type[i]); }
for(int i=0;i<fastaFileNames.size();i++){
fastaFileNames[i].assign(primerNameVector.size(), "");
}
- if(qFileName != ""){ qualFileNames = fastaFileNames; }
+ if(qFileName != "") { qualFileNames = fastaFileNames; }
+ if(nameFile != "") { nameFileNames = fastaFileNames; }
if(allFiles){
set<string> uniqueNames; //used to cleanup outputFileNames
string comboGroupName = "";
string fastaFileName = "";
string qualFileName = "";
+ string nameFileName = "";
if(primerName == ""){
comboGroupName = barcodeNameVector[itBar->second];
comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
}
}
-
+
+
ofstream temp;
fastaFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + comboGroupName + ".fasta";
if (uniqueNames.count(fastaFileName) == 0) {
fastaFileNames[itBar->second][itPrimer->second] = fastaFileName;
m->openOutputFile(fastaFileName, temp); temp.close();
-
+
if(qFileName != ""){
qualFileName = outputDir + m->getRootName(m->getSimpleName(qFileName)) + comboGroupName + ".qual";
- if (uniqueNames.count(fastaFileName) == 0) {
+ if (uniqueNames.count(qualFileName) == 0) {
outputNames.push_back(qualFileName);
outputTypes["qfile"].push_back(qualFileName);
}
qualFileNames[itBar->second][itPrimer->second] = qualFileName;
m->openOutputFile(qualFileName, temp); temp.close();
}
+
+ if(nameFile != ""){
+ nameFileName = outputDir + m->getRootName(m->getSimpleName(nameFile)) + comboGroupName + ".names";
+ if (uniqueNames.count(nameFileName) == 0) {
+ outputNames.push_back(nameFileName);
+ outputTypes["name"].push_back(nameFileName);
+ }
+
+ nameFileNames[itBar->second][itPrimer->second] = nameFileName;
+ m->openOutputFile(nameFileName, temp); temp.close();
+ }
+
}
}
}
numFPrimers = primers.size();
numRPrimers = revPrimer.size();
- groupCounts.resize(barcodeNameVector.size(), 0);
}
catch(exception& e) {