#include "trimseqscommand.h"
#include "needlemanoverlap.hpp"
+#include "trimoligos.h"
+//**********************************************************************************************************************
+vector<string> TrimSeqsCommand::setParameters(){
+ try {
+ 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 pldiffs("ldiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pldiffs);
+ CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(psdiffs);
+ 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 pkeepforward("keepforward", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pkeepforward);
+ 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", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string TrimSeqsCommand::getHelpString(){
+ try {
+ 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 + sdiffs + ldiffs.\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 ldiffs parameter is used to specify the number of differences allowed in the linker. The default is 0.\n";
+ helpString += "The sdiffs parameter is used to specify the number of differences allowed in the spacer. 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 keepforward parameter allows you to indicate whether you want the forward primer removed or not. The default is F, meaning remove the forward primer.\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", "getHelpString");
+ exit(1);
+ }
+}
+
+
+//**********************************************************************************************************************
+
+TrimSeqsCommand::TrimSeqsCommand(){
+ try {
+ 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", "TrimSeqsCommand");
+ exit(1);
+ }
+}
//***************************************************************************************************************
TrimSeqsCommand::TrimSeqsCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
+ comboStarts = 0;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ 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", "qaverage", "allfiles", "qtrim","diffs", "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();
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ 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 (inputDir == "not found"){ inputDir = ""; }
it = parameters.find("fasta");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["fasta"] = inputDir + it->second; }
}
it = parameters.find("oligos");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["oligos"] = inputDir + it->second; }
}
it = parameters.find("qfile");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
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 screen.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; }
+ else { m->setFastaFile(fastaFile); }
//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"){
outputDir = "";
- outputDir += hasPath(fastaFile); //if user entered a file with a path then preserve it
+ outputDir += m->hasPath(fastaFile); //if user entered a file with a path then preserve it
}
+
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
string temp;
temp = validParameter.validFile(parameters, "flip", false);
- if (temp == "not found"){ flip = 0; }
- else if(isTrue(temp)) { flip = 1; }
+ if (temp == "not found") { flip = 0; }
+ else { flip = m->isTrue(temp); }
temp = validParameter.validFile(parameters, "oligos", true);
if (temp == "not found"){ oligoFile = ""; }
else if(temp == "not open"){ abort = true; }
- else { oligoFile = temp; }
+ else { oligoFile = temp; m->setOligosFile(oligoFile); }
+
temp = validParameter.validFile(parameters, "maxambig", false); if (temp == "not found") { temp = "-1"; }
- convert(temp, maxAmbig);
+ m->mothurConvert(temp, maxAmbig);
temp = validParameter.validFile(parameters, "maxhomop", false); if (temp == "not found") { temp = "0"; }
- convert(temp, maxHomoP);
+ m->mothurConvert(temp, maxHomoP);
temp = validParameter.validFile(parameters, "minlength", false); if (temp == "not found") { temp = "0"; }
- convert(temp, minLength);
+ m->mothurConvert(temp, minLength);
temp = validParameter.validFile(parameters, "maxlength", false); if (temp == "not found") { temp = "0"; }
- convert(temp, maxLength);
+ m->mothurConvert(temp, maxLength);
+
+ temp = validParameter.validFile(parameters, "bdiffs", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, bdiffs);
+
+ temp = validParameter.validFile(parameters, "pdiffs", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, pdiffs);
+
+ temp = validParameter.validFile(parameters, "ldiffs", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, ldiffs);
+
+ temp = validParameter.validFile(parameters, "sdiffs", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, sdiffs);
- temp = validParameter.validFile(parameters, "diffs", false); if (temp == "not found") { temp = "0"; }
- convert(temp, diffs);
+ temp = validParameter.validFile(parameters, "tdiffs", false); if (temp == "not found") { int tempTotal = pdiffs + bdiffs + ldiffs + sdiffs; temp = toString(tempTotal); }
+ m->mothurConvert(temp, tdiffs);
+
+ if(tdiffs == 0){ tdiffs = bdiffs + pdiffs + ldiffs + sdiffs; }
temp = validParameter.validFile(parameters, "qfile", true);
if (temp == "not found") { qFileName = ""; }
else if(temp == "not open") { abort = true; }
- else { qFileName = temp; }
+ else { qFileName = temp; m->setQualFile(qFileName); }
+
+ temp = validParameter.validFile(parameters, "name", true);
+ if (temp == "not found") { nameFile = ""; }
+ else if(temp == "not open") { nameFile = ""; abort = true; }
+ else { nameFile = temp; m->setNameFile(nameFile); }
temp = validParameter.validFile(parameters, "qthreshold", false); if (temp == "not found") { temp = "0"; }
- convert(temp, qThreshold);
+ m->mothurConvert(temp, qThreshold);
- temp = validParameter.validFile(parameters, "qtrim", false); if (temp == "not found") { temp = "F"; }
- qtrim = isTrue(temp);
+ temp = validParameter.validFile(parameters, "qtrim", false); if (temp == "not found") { temp = "t"; }
+ qtrim = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "rollaverage", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, qRollAverage);
+
+ temp = validParameter.validFile(parameters, "qwindowaverage", false);if (temp == "not found") { temp = "0"; }
+ convert(temp, qWindowAverage);
+
+ temp = validParameter.validFile(parameters, "qwindowsize", false); if (temp == "not found") { temp = "50"; }
+ convert(temp, qWindowSize);
+
+ temp = validParameter.validFile(parameters, "qstepsize", false); if (temp == "not found") { temp = "1"; }
+ convert(temp, qWindowStep);
temp = validParameter.validFile(parameters, "qaverage", false); if (temp == "not found") { temp = "0"; }
convert(temp, qAverage);
+
+ temp = validParameter.validFile(parameters, "keepfirst", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, keepFirst);
+
+ temp = validParameter.validFile(parameters, "removelast", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, removeLast);
temp = validParameter.validFile(parameters, "allfiles", false); if (temp == "not found") { temp = "F"; }
- allFiles = isTrue(temp);
+ allFiles = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "keepforward", false); if (temp == "not found") { temp = "F"; }
+ keepforward = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ m->mothurConvert(temp, processors);
- temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; }
- convert(temp, processors);
- if(allFiles && oligoFile == ""){
- m->mothurOut("You selected allfiles, but didn't enter an oligos file. Ignoring the allfiles request."); m->mothurOutEndLine();
+ if(allFiles && (oligoFile == "")){
+ m->mothurOut("You selected allfiles, but didn't enter an oligos. Ignoring the allfiles request."); m->mothurOutEndLine();
}
if((qAverage != 0 && qThreshold != 0) && qFileName == ""){
m->mothurOut("You didn't provide a quality file name, quality criteria will be ignored."); m->mothurOutEndLine();
m->mothurOut("You didn't set any options... quiting command."); m->mothurOutEndLine();
abort = true;
}
+
+ if (nameFile == "") {
+ vector<string> files; files.push_back(fastaFile);
+ parser.getNameFile(files);
+ }
}
}
exit(1);
}
}
-//**********************************************************************************************************************
-
-void TrimSeqsCommand::help(){
- try {
- m->mothurOut("The trim.seqs command reads a fastaFile and creates .....\n");
- m->mothurOut("The trim.seqs command parameters are fasta, flip, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim and allfiles.\n");
- m->mothurOut("The fasta parameter is required.\n");
- m->mothurOut("The flip parameter .... The default is 0.\n");
- m->mothurOut("The oligos parameter .... The default is "".\n");
- m->mothurOut("The maxambig parameter .... The default is -1.\n");
- m->mothurOut("The maxhomop parameter .... The default is 0.\n");
- m->mothurOut("The minlength parameter .... The default is 0.\n");
- m->mothurOut("The maxlength parameter .... The default is 0.\n");
- m->mothurOut("The diffs parameter .... The default is 0.\n");
- m->mothurOut("The qfile parameter .....\n");
- m->mothurOut("The qthreshold parameter .... The default is 0.\n");
- m->mothurOut("The qaverage parameter .... The default is 0.\n");
- m->mothurOut("The allfiles parameter .... The default is F.\n");
- m->mothurOut("The qtrim parameter .... The default is F.\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(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
numFPrimers = 0; //this needs to be initialized
numRPrimers = 0;
+ numSpacers = 0;
+ numLinkers = 0;
+ createGroup = false;
+ 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 scrapSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.fasta";
+ outputNames.push_back(scrapSeqFile); outputTypes["fasta"].push_back(scrapSeqFile);
+
+ 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(trimQualFile);
+ outputTypes["qfile"].push_back(scrapQualFile);
+ }
- string trimSeqFile = outputDir + getRootName(getSimpleName(fastaFile)) + "trim.fasta";
- outputNames.push_back(trimSeqFile);
- string scrapSeqFile = outputDir + getRootName(getSimpleName(fastaFile)) + "scrap.fasta";
- outputNames.push_back(scrapSeqFile);
- string groupFile = outputDir + getRootName(getSimpleName(fastaFile)) + "groups";
+ string trimNameFile = outputDir + m->getRootName(m->getSimpleName(nameFile)) + "trim.names";
+ string scrapNameFile = outputDir + m->getRootName(m->getSimpleName(nameFile)) + "scrap.names";
- vector<string> fastaFileNames;
- if(oligoFile != ""){
- outputNames.push_back(groupFile);
- getOligos(fastaFileNames);
+ 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(qFileName != "") { setLines(qFileName, qLines); }
-
+ if (m->control_pressed) { return 0; }
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- if(processors == 1){
- ifstream inFASTA;
- openInputFile(fastaFile, inFASTA);
- int numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
- inFASTA.close();
-
- lines.push_back(new linePair(0, numSeqs));
-
- driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames, lines[0], lines[0]);
-
- for (int j = 0; j < fastaFileNames.size(); j++) {
- rename((fastaFileNames[j] + toString(getpid()) + ".temp").c_str(), fastaFileNames[j].c_str());
- }
-
- }else{
- setLines(fastaFile, lines);
- if(qFileName == "") { qLines = lines; }
+ string outputGroupFileName;
+ if(oligoFile != ""){
+ createGroup = getOligos(fastaFileNames, qualFileNames, nameFileNames);
+ if (createGroup) {
+ outputGroupFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "groups";
+ outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
+ }
+ }
+
+ //fills lines and qlines
+ setLines(fastaFile, qFileName);
+
+ if(processors == 1){
+ 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, trimNameFile, scrapNameFile, outputGroupFileName, fastaFileNames, qualFileNames, nameFileNames);
+ }
+
+
+ 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;
+ set<string> namesToRemove;
+ for(int i=0;i<fastaFileNames.size();i++){
+ for(int j=0;j<fastaFileNames[0].size();j++){
+ if (fastaFileNames[i][j] != "") {
+ if (namesToRemove.count(fastaFileNames[i][j]) == 0) {
+ if(m->isBlank(fastaFileNames[i][j])){
+ m->mothurRemove(fastaFileNames[i][j]);
+ namesToRemove.insert(fastaFileNames[i][j]);
+
+ if(qFileName != ""){
+ m->mothurRemove(qualFileNames[i][j]);
+ namesToRemove.insert(qualFileNames[i][j]);
+ }
- createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames);
-
- rename((trimSeqFile + toString(processIDS[0]) + ".temp").c_str(), trimSeqFile.c_str());
- rename((scrapSeqFile + toString(processIDS[0]) + ".temp").c_str(), scrapSeqFile.c_str());
- rename((groupFile + toString(processIDS[0]) + ".temp").c_str(), groupFile.c_str());
- for (int j = 0; j < fastaFileNames.size(); j++) {
- rename((fastaFileNames[j] + toString(processIDS[0]) + ".temp").c_str(), fastaFileNames[j].c_str());
- }
- //append files
- for(int i=1;i<processors;i++){
- appendFiles((trimSeqFile + toString(processIDS[i]) + ".temp"), trimSeqFile);
- remove((trimSeqFile + toString(processIDS[i]) + ".temp").c_str());
- appendFiles((scrapSeqFile + toString(processIDS[i]) + ".temp"), scrapSeqFile);
- remove((scrapSeqFile + toString(processIDS[i]) + ".temp").c_str());
- appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
- remove((groupFile + toString(processIDS[i]) + ".temp").c_str());
- for (int j = 0; j < fastaFileNames.size(); j++) {
- appendFiles((fastaFileNames[j] + toString(processIDS[i]) + ".temp"), fastaFileNames[j]);
- remove((fastaFileNames[j] + toString(processIDS[i]) + ".temp").c_str());
+ if(nameFile != ""){
+ m->mothurRemove(nameFileNames[i][j]);
+ namesToRemove.insert(nameFileNames[i][j]);
+ }
+ }else{
+ it = uniqueFastaNames.find(fastaFileNames[i][j]);
+ if (it == uniqueFastaNames.end()) {
+ uniqueFastaNames[fastaFileNames[i][j]] = barcodeNameVector[i];
+ }
+ }
}
}
}
+ }
+
+ //remove names for outputFileNames, just cleans up the output
+ vector<string> outputNames2;
+ for(int i = 0; i < outputNames.size(); i++) { if (namesToRemove.count(outputNames[i]) == 0) { outputNames2.push_back(outputNames[i]); } }
+ outputNames = outputNames2;
+
+ for (it = uniqueFastaNames.begin(); it != uniqueFastaNames.end(); it++) {
+ ifstream in;
+ m->openInputFile(it->first, in);
- if (m->control_pressed) { return 0; }
- #else
- ifstream inFASTA;
- openInputFile(fastafileNames[s], inFASTA);
- numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
- inFASTA.close();
-
- lines.push_back(new linePair(0, numSeqs));
-
- driverCreateSummary(fastafile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames, lines[0], lines[0]);
+ ofstream out;
+ string thisGroupName = outputDir + m->getRootName(m->getSimpleName(it->first)) + "groups";
+ outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName);
+ m->openOutputFile(thisGroupName, out);
- if (m->control_pressed) { return 0; }
- #endif
-
-
- for(int i=0;i<fastaFileNames.size();i++){
- ifstream inFASTA;
- string seqName;
- openInputFile(getRootName(fastaFile) + groupVector[i] + ".fasta", inFASTA);
- ofstream outGroups;
- openOutputFile(outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[i] + ".groups", outGroups);
- outputNames.push_back(outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[i] + ".groups");
-
- while(!inFASTA.eof()){
- if(inFASTA.get() == '>'){
- inFASTA >> seqName;
- outGroups << seqName << '\t' << groupVector[i] << endl;
+ while (!in.eof()){
+ if (m->control_pressed) { break; }
+
+ Sequence currSeq(in); m->gobble(in);
+ out << currSeq.getName() << '\t' << it->second << 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
+ out << thisSeqsNames[k] << '\t' << it->second << endl;
+ }
+ }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
+ }
}
- while (!inFASTA.eof()) { char c = inFASTA.get(); if (c == 10 || c == 13){ break; } }
+ in.close();
+ out.close();
}
- outGroups.close();
- inFASTA.close();
}
- 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++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ //output group counts
+ 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++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ //set fasta file as new current fastafile
+ string current = "";
+ itTypes = outputTypes.find("fasta");
+ if (itTypes != outputTypes.end()) {
+ 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); }
+ }
+
+ itTypes = outputTypes.find("group");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
}
m->mothurOutEndLine();
}
/**************************************************************************************/
-int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string groupFile, vector<string> fastaNames, 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 {
- ofstream outFASTA;
- int able = openOutputFile(trimFile, outFASTA);
+ ofstream trimFASTAFile;
+ m->openOutputFile(trimFileName, trimFASTAFile);
+
+ ofstream scrapFASTAFile;
+ m->openOutputFile(scrapFileName, scrapFASTAFile);
- ofstream scrapFASTA;
- openOutputFile(scrapFile, scrapFASTA);
+ ofstream trimQualFile;
+ ofstream scrapQualFile;
+ if(qFileName != ""){
+ m->openOutputFile(trimQFileName, trimQualFile);
+ m->openOutputFile(scrapQFileName, scrapQualFile);
+ }
- ofstream outGroups;
- vector<ofstream*> fastaFileNames;
- if (oligoFile != "") {
- openOutputFile(groupFile, outGroups);
- for (int i = 0; i < fastaNames.size(); i++) {
- fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate));
+ ofstream trimNameFile;
+ ofstream scrapNameFile;
+ if(nameFile != ""){
+ m->openOutputFile(trimNFileName, trimNameFile);
+ m->openOutputFile(scrapNFileName, scrapNameFile);
+ }
+
+
+ ofstream outGroupsFile;
+ if (createGroup){ m->openOutputFile(groupFileName, outGroupsFile); }
+ if(allFiles){
+ for (int i = 0; i < fastaFileNames.size(); i++) { //clears old file
+ for (int j = 0; j < fastaFileNames[i].size(); j++) { //clears old file
+ if (fastaFileNames[i][j] != "") {
+ ofstream temp;
+ m->openOutputFile(fastaFileNames[i][j], temp); temp.close();
+ if(qFileName != ""){
+ m->openOutputFile(qualFileNames[i][j], temp); temp.close();
+ }
+
+ if(nameFile != ""){
+ m->openOutputFile(nameFileNames[i][j], temp); temp.close();
+ }
+ }
+ }
}
}
ifstream inFASTA;
- openInputFile(filename, inFASTA);
+ m->openInputFile(filename, inFASTA);
+ inFASTA.seekg(line.start);
ifstream qFile;
- if(qFileName != "") { openInputFile(qFileName, qFile); }
-
- qFile.seekg(qline->start);
- inFASTA.seekg(line->start);
+ if(qFileName != "") {
+ m->openInputFile(qFileName, qFile);
+ qFile.seekg(qline.start);
+ }
- for(int i=0;i<line->num;i++){
+ int count = 0;
+ bool moreSeqs = 1;
+ TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimer, linker, spacer);
+
+ while (moreSeqs) {
if (m->control_pressed) {
- inFASTA.close();
- outFASTA.close();
- scrapFASTA.close();
- if (oligoFile != "") { outGroups.close(); }
- if(qFileName != "") { qFile.close(); }
- for(int i=0;i<fastaFileNames.size();i++){
- fastaFileNames[i]->close();
- delete fastaFileNames[i];
- }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ inFASTA.close(); trimFASTAFile.close(); scrapFASTAFile.close();
+ if (createGroup) { outGroupsFile.close(); }
+
+ if(qFileName != ""){
+ qFile.close();
+ }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
+
return 0;
}
- bool success = 1;
-
- Sequence currSeq(inFASTA);
+ int success = 1;
+ string trashCode = "";
+ int currentSeqsDiffs = 0;
+ Sequence currSeq(inFASTA); m->gobble(inFASTA);
+ //cout << currSeq.getName() << '\t' << currSeq.getUnaligned().length() << endl;
+ QualityScores currQual;
+ if(qFileName != ""){
+ currQual = QualityScores(qFile); m->gobble(qFile);
+ }
+
string origSeq = currSeq.getUnaligned();
if (origSeq != "") {
- int group;
- string trashCode = "";
- if(qFileName != ""){
- if(qThreshold != 0) { success = stripQualThreshold(currSeq, qFile); }
- else if(qAverage != 0) { success = cullQualAverage(currSeq, qFile); }
- if ((!qtrim) && (origSeq.length() != currSeq.getUnaligned().length())) {
- success = 0; //if you don't want to trim and the sequence does not meet quality requirements, move to scrap
- }
- if(!success) { trashCode += 'q'; }
+ int barcodeIndex = 0;
+ int primerIndex = 0;
+
+ if(numLinkers != 0){
+ success = trimOligos.stripLinker(currSeq, currQual);
+ if(success > ldiffs) { trashCode += 'k'; }
+ else{ currentSeqsDiffs += success; }
+
}
-
+
if(barcodes.size() != 0){
- success = stripBarcode(currSeq, group);
- if(!success){ trashCode += 'b'; }
+ success = trimOligos.stripBarcode(currSeq, currQual, barcodeIndex);
+ if(success > bdiffs) { trashCode += 'b'; }
+ else{ currentSeqsDiffs += success; }
}
-
+
+ if(numSpacers != 0){
+ success = trimOligos.stripSpacer(currSeq, currQual);
+ if(success > sdiffs) { trashCode += 's'; }
+ else{ currentSeqsDiffs += success; }
+
+ }
+
if(numFPrimers != 0){
- success = stripForward(currSeq);
- if(!success){ trashCode += 'f'; }
+ success = trimOligos.stripForward(currSeq, currQual, primerIndex, keepforward);
+ if(success > pdiffs) { trashCode += 'f'; }
+ else{ currentSeqsDiffs += success; }
}
-
+
+ if (currentSeqsDiffs > tdiffs) { trashCode += 't'; }
+
if(numRPrimers != 0){
- success = stripReverse(currSeq);
- if(!success){ trashCode += 'r'; }
+ success = trimOligos.stripReverse(currSeq, currQual);
+ if(!success) { trashCode += 'r'; }
}
+
+ if(keepFirst != 0){
+ success = keepFirstTrim(currSeq, currQual);
+ }
+
+ if(removeLast != 0){
+ success = removeLastTrim(currSeq, currQual);
+ if(!success) { trashCode += 'l'; }
+ }
+
+
+ if(qFileName != ""){
+ int origLength = currSeq.getNumBases();
+
+ if(qThreshold != 0) { success = currQual.stripQualThreshold(currSeq, qThreshold); }
+ else if(qAverage != 0) { success = currQual.cullQualAverage(currSeq, qAverage); }
+ 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; }
+
+ if(!success) { trashCode += 'q'; }
+ }
if(minLength > 0 || maxLength > 0){
success = cullLength(currSeq);
- if(!success){ trashCode += 'l'; }
+ if(!success) { trashCode += 'l'; }
}
if(maxHomoP > 0){
success = cullHomoP(currSeq);
- if(!success){ trashCode += 'h'; }
+ if(!success) { trashCode += 'h'; }
}
if(maxAmbig != -1){
success = cullAmbigs(currSeq);
- if(!success){ trashCode += 'n'; }
+ if(!success) { trashCode += 'n'; }
}
- if(flip){ currSeq.reverseComplement(); } // should go last
+ if(flip){ // should go last
+ currSeq.reverseComplement();
+ if(qFileName != ""){
+ currQual.flipQScores();
+ }
+ }
if(trashCode.length() == 0){
- currSeq.setAligned(currSeq.getUnaligned()); //this is because of a modification we made to the sequence class to fix a bug. all seqs have an aligned version, which is the version that gets printed.
- currSeq.printSequence(outFASTA);
- if(barcodes.size() != 0){
- outGroups << currSeq.getName() << '\t' << groupVector[group] << endl;
+ currSeq.setAligned(currSeq.getUnaligned());
+ currSeq.printSequence(trimFASTAFile);
+
+ if(qFileName != ""){
+ 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 (createGroup) {
+ if(barcodes.size() != 0){
+ string thisGroup = barcodeNameVector[barcodeIndex];
+ if (primers.size() != 0) {
+ if (primerNameVector[primerIndex] != "") {
+ if(thisGroup != "") {
+ thisGroup += "." + primerNameVector[primerIndex];
+ }else {
+ 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]++; }
+
+ }
+ }
+
+ if(allFiles){
+ ofstream output;
+ m->openOutputFileAppend(fastaFileNames[barcodeIndex][primerIndex], output);
+ currSeq.printSequence(output);
+ output.close();
- if(allFiles){
- currSeq.printSequence(*fastaFileNames[group]);
+ if(qFileName != ""){
+ m->openOutputFileAppend(qualFileNames[barcodeIndex][primerIndex], output);
+ 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.printSequence(scrapFASTA);
+ currSeq.setAligned(origSeq);
+ currSeq.printSequence(scrapFASTAFile);
+ if(qFileName != ""){
+ currQual.printQScores(scrapQualFile);
+ }
}
+ count++;
}
- gobble(inFASTA);
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ unsigned long long pos = inFASTA.tellg();
+ if ((pos == -1) || (pos >= line.end)) { break; }
+
+ #else
+ if (inFASTA.eof()) { break; }
+ #endif
+
+ //report progress
+ if((count) % 1000 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
+
}
+ //report progress
+ if((count) % 1000 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
- inFASTA.close();
- outFASTA.close();
- scrapFASTA.close();
- if (oligoFile != "") { outGroups.close(); }
- if(qFileName != "") { qFile.close(); }
- for(int i=0;i<fastaFileNames.size();i++){
- fastaFileNames[i]->close();
- delete fastaFileNames[i];
- }
+ inFASTA.close();
+ trimFASTAFile.close();
+ scrapFASTAFile.close();
+ if (createGroup) { outGroupsFile.close(); }
+ if(qFileName != "") { qFile.close(); scrapQualFile.close(); trimQualFile.close(); }
+ if(nameFile != "") { scrapNameFile.close(); trimNameFile.close(); }
- return 0;
+ return count;
}
catch(exception& e) {
m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
exit(1);
}
}
+
/**************************************************************************************************/
-int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string groupFile, vector<string> fastaNames) {
+
+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 = 0;
+
+ int process = 1;
int exitCommand = 1;
processIDS.clear();
- //loop through and create all the processes you want
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ //loop through and create all the processes you want
while (process != processors) {
int pid = fork();
processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
process++;
}else if (pid == 0){
- driverCreateTrim(filename, qFileName, (trimFile + toString(getpid()) + ".temp"), (scrapFile + toString(getpid()) + ".temp"), (groupFile + toString(getpid()) + ".temp"), fastaNames, lines[process], qLines[process]);
+
+ vector<vector<string> > tempFASTAFileNames = fastaFileNames;
+ vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
+ vector<vector<string> > tempNameFileNames = nameFileNames;
+
+ if(allFiles){
+ ofstream temp;
+
+ for(int i=0;i<tempFASTAFileNames.size();i++){
+ for(int j=0;j<tempFASTAFileNames[i].size();j++){
+ if (tempFASTAFileNames[i][j] != "") {
+ tempFASTAFileNames[i][j] += toString(getpid()) + ".temp";
+ m->openOutputFile(tempFASTAFileNames[i][j], temp); temp.close();
+
+ if(qFileName != ""){
+ 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();
+ }
+ }
+ }
+ }
+ }
+
+ driverCreateTrim(filename,
+ qFileName,
+ (trimFASTAFileName + toString(getpid()) + ".temp"),
+ (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]);
+
+ //pass groupCounts to parent
+ if(createGroup){
+ ofstream out;
+ string tempFile = filename + toString(getpid()) + ".num.temp";
+ m->openOutputFile(tempFile, out);
+
+ out << groupCounts.size() << endl;
+
+ for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
+ out << it->first << '\t' << it->second << endl;
+ }
+ out.close();
+ }
exit(0);
- }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
}
+ //parent do my part
+ ofstream temp;
+ m->openOutputFile(trimFASTAFileName, temp); temp.close();
+ m->openOutputFile(scrapFASTAFileName, 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, 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<processors;i++) {
+ for (int i=0;i<processIDS.size();i++) {
int temp = processIDS[i];
wait(&temp);
}
-
- return exitCommand;
+#else
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //Windows version shared memory, so be careful when passing variables through the trimData struct.
+ //Above fork() will clone, so memory is separate, but that's not the case with windows,
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+
+ vector<trimData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+
+ //Create processor worker threads.
+ for( int i=0; i<processors-1; i++){
+
+ string extension = "";
+ if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
+ vector<vector<string> > tempFASTAFileNames = fastaFileNames;
+ vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
+ vector<vector<string> > tempNameFileNames = nameFileNames;
+
+ if(allFiles){
+ ofstream temp;
+
+ for(int i=0;i<tempFASTAFileNames.size();i++){
+ for(int j=0;j<tempFASTAFileNames[i].size();j++){
+ if (tempFASTAFileNames[i][j] != "") {
+ tempFASTAFileNames[i][j] += extension;
+ m->openOutputFile(tempFASTAFileNames[i][j], temp); temp.close();
+
+ if(qFileName != ""){
+ tempPrimerQualFileNames[i][j] += extension;
+ m->openOutputFile(tempPrimerQualFileNames[i][j], temp); temp.close();
+ }
+ if(nameFile != ""){
+ tempNameFileNames[i][j] += extension;
+ m->openOutputFile(tempNameFileNames[i][j], temp); temp.close();
+ }
+ }
+ }
+ }
+ }
+
+
+ trimData* tempTrim = new trimData(filename,
+ qFileName, nameFile,
+ (trimFASTAFileName+extension),
+ (scrapFASTAFileName+extension),
+ (trimQualFileName+extension),
+ (scrapQualFileName+extension),
+ (trimNameFileName+extension),
+ (scrapNameFileName+extension),
+ (groupFile+extension),
+ tempFASTAFileNames,
+ tempPrimerQualFileNames,
+ tempNameFileNames,
+ lines[i].start, lines[i].end, qLines[i].start, qLines[i].end, m,
+ pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, primers, barcodes, revPrimer, linker, spacer,
+ primerNameVector, barcodeNameVector, createGroup, allFiles, keepforward, keepFirst, removeLast,
+ qWindowStep, qWindowSize, qWindowAverage, qtrim, qThreshold, qAverage, qRollAverage,
+ minLength, maxAmbig, maxHomoP, maxLength, flip, nameMap);
+ pDataArray.push_back(tempTrim);
+
+ hThreadArray[i] = CreateThread(NULL, 0, MyTrimThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
+ }
+
+ //parent do my part
+ ofstream temp;
+ m->openOutputFile(trimFASTAFileName, temp); temp.close();
+ m->openOutputFile(scrapFASTAFileName, 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 + toString(processors-1) + ".temp"), (scrapFASTAFileName + toString(processors-1) + ".temp"), (trimQualFileName + toString(processors-1) + ".temp"), (scrapQualFileName + toString(processors-1) + ".temp"), (trimNameFileName + toString(processors-1) + ".temp"), (scrapNameFileName + toString(processors-1) + ".temp"), (groupFile + toString(processors-1) + ".temp"), fastaFileNames, qualFileNames, nameFileNames, lines[processors-1], qLines[processors-1]);
+ processIDS.push_back(processors-1);
+
+
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
+
+ //Close all thread handles and free memory allocations.
+ for(int i=0; i < pDataArray.size(); i++){
+ for (map<string, int>::iterator it = pDataArray[i]->groupCounts.begin(); it != pDataArray[i]->groupCounts.end(); it++) {
+ map<string, int>::iterator it2 = groupCounts.find(it->first);
+ if (it2 == groupCounts.end()) { groupCounts[it->first] = it->second; }
+ else { groupCounts[it->first] += it->second; }
+ }
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+
#endif
+
+
+ //append files
+ for(int i=0;i<processIDS.size();i++){
+
+ m->mothurOut("Appending files from process " + toString(processIDS[i])); m->mothurOutEndLine();
+
+ m->appendFiles((trimFASTAFileName + toString(processIDS[i]) + ".temp"), trimFASTAFileName);
+ m->mothurRemove((trimFASTAFileName + toString(processIDS[i]) + ".temp"));
+ m->appendFiles((scrapFASTAFileName + toString(processIDS[i]) + ".temp"), scrapFASTAFileName);
+ m->mothurRemove((scrapFASTAFileName + toString(processIDS[i]) + ".temp"));
+
+ if(qFileName != ""){
+ m->appendFiles((trimQualFileName + toString(processIDS[i]) + ".temp"), trimQualFileName);
+ m->mothurRemove((trimQualFileName + toString(processIDS[i]) + ".temp"));
+ m->appendFiles((scrapQualFileName + toString(processIDS[i]) + ".temp"), scrapQualFileName);
+ m->mothurRemove((scrapQualFileName + toString(processIDS[i]) + ".temp"));
+ }
+
+ if(nameFile != ""){
+ m->appendFiles((trimNameFileName + toString(processIDS[i]) + ".temp"), trimNameFileName);
+ m->mothurRemove((trimNameFileName + toString(processIDS[i]) + ".temp"));
+ m->appendFiles((scrapNameFileName + toString(processIDS[i]) + ".temp"), scrapNameFileName);
+ m->mothurRemove((scrapNameFileName + toString(processIDS[i]) + ".temp"));
+ }
+
+ if(createGroup){
+ m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
+ m->mothurRemove((groupFile + toString(processIDS[i]) + ".temp"));
+ }
+
+
+ if(allFiles){
+ for(int j=0;j<fastaFileNames.size();j++){
+ for(int k=0;k<fastaFileNames[j].size();k++){
+ if (fastaFileNames[j][k] != "") {
+ m->appendFiles((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"), fastaFileNames[j][k]);
+ m->mothurRemove((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"));
+
+ if(qFileName != ""){
+ m->appendFiles((qualFileNames[j][k] + toString(processIDS[i]) + ".temp"), qualFileNames[j][k]);
+ m->mothurRemove((qualFileNames[j][k] + toString(processIDS[i]) + ".temp"));
+ }
+
+ if(nameFile != ""){
+ m->appendFiles((nameFileNames[j][k] + toString(processIDS[i]) + ".temp"), nameFileNames[j][k]);
+ m->mothurRemove((nameFileNames[j][k] + toString(processIDS[i]) + ".temp"));
+ }
+ }
+ }
+ }
+ }
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ if(createGroup){
+ ifstream in;
+ string tempFile = filename + toString(processIDS[i]) + ".num.temp";
+ m->openInputFile(tempFile, in);
+ int tempNum;
+ string group;
+
+ in >> tempNum; m->gobble(in);
+
+ if (tempNum != 0) {
+ while (!in.eof()) {
+ 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(); m->mothurRemove(tempFile);
+ }
+ #endif
+ }
+
+ return exitCommand;
}
catch(exception& e) {
m->errorOut(e, "TrimSeqsCommand", "createProcessesCreateTrim");
exit(1);
}
}
+
/**************************************************************************************************/
-int TrimSeqsCommand::setLines(string filename, vector<linePair*>& lines) {
+int TrimSeqsCommand::setLines(string filename, string qfilename) {
try {
+
+ vector<unsigned long long> fastaFilePos;
+ vector<unsigned long long> qfileFilePos;
- lines.clear();
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ //set file positions for fasta file
+ fastaFilePos = m->divideFile(filename, processors);
- vector<long int> positions;
-
- ifstream inFASTA;
- openInputFile(filename, inFASTA);
-
- string input;
- while(!inFASTA.eof()){
- input = getline(inFASTA);
-
- if (input.length() != 0) {
- if(input[0] == '>'){ long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
- }
- }
- inFASTA.close();
+ //get name of first sequence in each chunk
+ map<string, int> firstSeqNames;
+ for (int i = 0; i < (fastaFilePos.size()-1); i++) {
+ ifstream in;
+ m->openInputFile(filename, in);
+ in.seekg(fastaFilePos[i]);
- int numFastaSeqs = positions.size();
-
- FILE * pFile;
- long size;
+ Sequence temp(in);
+ firstSeqNames[temp.getName()] = i;
- //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);
+ in.close();
}
- int numSeqsPerProcessor = numFastaSeqs / processors;
+ if(qfilename != "") {
+ //seach for filePos of each first name in the qfile and save in qfileFilePos
+ ifstream inQual;
+ m->openInputFile(qfilename, inQual);
+
+ string input;
+ while(!inQual.eof()){
+ input = m->getline(inQual);
+
+ if (input.length() != 0) {
+ if(input[0] == '>'){ //this is a sequence name line
+ istringstream nameStream(input);
+
+ string sname = ""; nameStream >> sname;
+ sname = sname.substr(1);
+
+ map<string, int>::iterator it = firstSeqNames.find(sname);
+
+ if(it != firstSeqNames.end()) { //this is the start of a new chunk
+ unsigned long long pos = inQual.tellg();
+ qfileFilePos.push_back(pos - input.length() - 1);
+ firstSeqNames.erase(it);
+ }
+ }
+ }
+
+ if (firstSeqNames.size() == 0) { break; }
+ }
+ inQual.close();
+
+
+ if (firstSeqNames.size() != 0) {
+ for (map<string, int>::iterator it = firstSeqNames.begin(); it != firstSeqNames.end(); it++) {
+ m->mothurOut(it->first + " is in your fasta file and not in your quality file, not using quality file."); m->mothurOutEndLine();
+ }
+ qFileName = "";
+ return processors;
+ }
+
+ //get last file position of qfile
+ FILE * pFile;
+ unsigned long long size;
+
+ //get num bytes in file
+ pFile = fopen (qfilename.c_str(),"rb");
+ if (pFile==NULL) perror ("Error opening file");
+ else{
+ fseek (pFile, 0, SEEK_END);
+ size=ftell (pFile);
+ fclose (pFile);
+ }
+
+ qfileFilePos.push_back(size);
+ }
+
+ for (int i = 0; i < (fastaFilePos.size()-1); i++) {
+ lines.push_back(linePair(fastaFilePos[i], fastaFilePos[(i+1)]));
+ if (qfilename != "") { qLines.push_back(linePair(qfileFilePos[i], qfileFilePos[(i+1)])); }
+ }
+ if(qfilename == "") { qLines = lines; } //files with duds
- for (int i = 0; i < processors; i++) {
-
- long int startPos = positions[ i * numSeqsPerProcessor ];
- if(i == processors - 1){
- numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
- }else{
- long int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
- }
- lines.push_back(new linePair(startPos, numSeqsPerProcessor));
- }
+ return processors;
+
+ #else
+
+ if (processors == 1) { //save time
+ //fastaFilePos.push_back(0); qfileFilePos.push_back(0);
+ //fastaFilePos.push_back(1000); qfileFilePos.push_back(1000);
+ lines.push_back(linePair(0, 1000));
+ if (qfilename != "") { qLines.push_back(linePair(0, 1000)); }
+ }else{
+ int numFastaSeqs = 0;
+ fastaFilePos = m->setFilePosFasta(filename, numFastaSeqs);
+ if (fastaFilePos.size() < processors) { processors = fastaFilePos.size(); }
+
+ if (qfilename != "") {
+ int numQualSeqs = 0;
+ qfileFilePos = m->setFilePosFasta(qfilename, numQualSeqs);
+
+ if (numFastaSeqs != numQualSeqs) {
+ m->mothurOut("[ERROR]: You have " + toString(numFastaSeqs) + " sequences in your fasta file, but " + toString(numQualSeqs) + " sequences in your quality file."); m->mothurOutEndLine(); m->control_pressed = true;
+ }
+ }
+
+ //figure out how many sequences you have to process
+ int numSeqsPerProcessor = numFastaSeqs / processors;
+ for (int i = 0; i < processors; i++) {
+ int startIndex = i * numSeqsPerProcessor;
+ if(i == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; }
+ lines.push_back(linePair(fastaFilePos[startIndex], numSeqsPerProcessor));
+ cout << fastaFilePos[startIndex] << '\t' << numSeqsPerProcessor << endl;
+ if (qfilename != "") { qLines.push_back(linePair(qfileFilePos[startIndex], numSeqsPerProcessor)); }
+ }
+ }
+ if(qfilename == "") { qLines = lines; } //files with duds
+ return 1;
- return numFastaSeqs;
+ #endif
}
catch(exception& e) {
m->errorOut(e, "TrimSeqsCommand", "setLines");
exit(1);
}
}
+
//***************************************************************************************************************
-void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec){ //vector<ofstream*>& outFASTAVec
+bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<vector<string> >& qualFileNames, vector<vector<string> >& nameFileNames){
try {
ifstream inOligos;
- openInputFile(oligoFile, inOligos);
+ m->openInputFile(oligoFile, inOligos);
ofstream test;
string type, oligo, group;
- int index=0;
+
+ int indexPrimer = 0;
+ int indexBarcode = 0;
while(!inOligos.eof()){
- inOligos >> type;
-
+
+ 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]); }
+
inOligos >> oligo;
for(int i=0;i<oligo.length();i++){
if(oligo[i] == 'U') { oligo[i] = 'T'; }
}
- if(type == "forward"){
- forPrimer.push_back(oligo);
+ if(type == "FORWARD"){
+ group = "";
+
+ // get rest of line in case there is a primer name
+ while (!inOligos.eof()) {
+ char c = inOligos.get();
+ if (c == 10 || c == 13){ break; }
+ else if (c == 32 || c == 9){;} //space or tab
+ else { group += c; }
+ }
+
+ //check for repeat barcodes
+ map<string, int>::iterator itPrime = primers.find(oligo);
+ if (itPrime != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine(); }
+
+ primers[oligo]=indexPrimer; indexPrimer++;
+ primerNameVector.push_back(group);
}
- else if(type == "reverse"){
- Sequence oligoRC("reverse", oligo);
- oligoRC.reverseComplement();
- revPrimer.push_back(oligoRC.getUnaligned());
+ else if(type == "REVERSE"){
+ //Sequence oligoRC("reverse", oligo);
+ //oligoRC.reverseComplement();
+ string oligoRC = reverseOligo(oligo);
+ revPrimer.push_back(oligoRC);
}
- else if(type == "barcode"){
+ else if(type == "BARCODE"){
inOligos >> group;
- barcodes[oligo]=index++;
- groupVector.push_back(group);
- if(allFiles){
- //outFASTAVec.push_back(new ofstream((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta").c_str(), ios::ate));
- outputNames.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
- outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
- }
+ //check for repeat barcodes
+ map<string, int>::iterator itBar = barcodes.find(oligo);
+ if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine(); }
+
+ barcodes[oligo]=indexBarcode; indexBarcode++;
+ barcodeNameVector.push_back(group);
+ }else if(type == "LINKER"){
+ linker.push_back(oligo);
+ }else if(type == "SPACER"){
+ spacer.push_back(oligo);
}
+ else{ m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine(); }
}
+ m->gobble(inOligos);
+ }
+ inOligos.close();
+
+ if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0; }
+
+ //add in potential combos
+ if(barcodeNameVector.size() == 0){
+ barcodes[""] = 0;
+ barcodeNameVector.push_back("");
}
- inOligos.close();
+ if(primerNameVector.size() == 0){
+ primers[""] = 0;
+ primerNameVector.push_back("");
+ }
- numFPrimers = forPrimer.size();
- numRPrimers = revPrimer.size();
+ fastaFileNames.resize(barcodeNameVector.size());
+ for(int i=0;i<fastaFileNames.size();i++){
+ fastaFileNames[i].assign(primerNameVector.size(), "");
+ }
+ if(qFileName != "") { qualFileNames = fastaFileNames; }
+ if(nameFile != "") { nameFileNames = fastaFileNames; }
- }
- catch(exception& e) {
- m->errorOut(e, "TrimSeqsCommand", "getOligos");
- exit(1);
- }
-}
-//***************************************************************************************************************
-
-bool TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
- try {
- string rawSequence = seq.getUnaligned();
- bool success = 0; //guilty until proven innocent
+ if(allFiles){
+ set<string> uniqueNames; //used to cleanup outputFileNames
+ for(map<string, int>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
+ for(map<string, int>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
+
+ string primerName = primerNameVector[itPrimer->second];
+ string barcodeName = barcodeNameVector[itBar->second];
+
+ string comboGroupName = "";
+ string fastaFileName = "";
+ string qualFileName = "";
+ string nameFileName = "";
+
+ if(primerName == ""){
+ comboGroupName = barcodeNameVector[itBar->second];
+ }
+ else{
+ if(barcodeName == ""){
+ comboGroupName = primerNameVector[itPrimer->second];
+ }
+ else{
+ comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
+ }
+ }
+
+
+ ofstream temp;
+ fastaFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + comboGroupName + ".fasta";
+ if (uniqueNames.count(fastaFileName) == 0) {
+ outputNames.push_back(fastaFileName);
+ outputTypes["fasta"].push_back(fastaFileName);
+ uniqueNames.insert(fastaFileName);
+ }
+
+ 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(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();
+ numLinkers = linker.size();
+ numSpacers = spacer.size();
- //can you find the barcode
- for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
- string oligo = it->first;
- if(rawSequence.length() < oligo.length()){ //let's just assume that the barcodes are the same length
- success = 0;
+ bool allBlank = true;
+ for (int i = 0; i < barcodeNameVector.size(); i++) {
+ if (barcodeNameVector[i] != "") {
+ allBlank = false;
break;
}
-
- if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
- group = it->second;
- seq.setUnaligned(rawSequence.substr(oligo.length()));
- success = 1;
+ }
+ for (int i = 0; i < primerNameVector.size(); i++) {
+ if (primerNameVector[i] != "") {
+ allBlank = false;
break;
}
}
- //if you found the barcode or if you don't want to allow for diffs
- if ((diffs == 0) || (success == 1)) { return success; }
-
- else { //try aligning and see if you can find it
-
- Alignment* alignment;
- if (barcodes.size() > 0) { //assumes barcodes are all the same length
- map<string,int>::iterator it=barcodes.begin();
- string temp = it->first;
-
- alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, (temp.length()+diffs+1));
- }else{ alignment = NULL; }
-
-
- //can you find the barcode
- for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
- string oligo = it->first;
- int length = oligo.length();
-
- if(rawSequence.length() < oligo.length()){ //let's just assume that the barcodes are the same length
- success = 0;
- break;
- }
-
- //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
- alignment->align(oligo, rawSequence.substr(0,length+diffs));
- oligo = alignment->getSeqAAln();
- string temp = alignment->getSeqBAln();
- cout << "barcode = " << oligo << " raw = " << rawSequence.substr(0,oligo.length()) << " raw aligned = " << temp << endl;
-
- int newStart=0;
- if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()), length, newStart)){
- cout << "found match" << endl;
- group = it->second;
- seq.setUnaligned(rawSequence.substr(newStart));
- success = 1;
- break;
- }
- }
-
- if (alignment != NULL) { delete alignment; }
+ if (allBlank) {
+ m->mothurOut("[WARNING]: your oligos file does not contain any group names. mothur will not create a groupfile."); m->mothurOutEndLine();
+ allFiles = false;
+ return false;
}
- return success;
+
+ return true;
}
catch(exception& e) {
- m->errorOut(e, "TrimSeqsCommand", "stripBarcode");
+ m->errorOut(e, "TrimSeqsCommand", "getOligos");
exit(1);
}
-
}
-
//***************************************************************************************************************
-bool TrimSeqsCommand::stripForward(Sequence& seq){
+bool TrimSeqsCommand::keepFirstTrim(Sequence& sequence, QualityScores& qscores){
try {
- string rawSequence = seq.getUnaligned();
- bool success = 0; //guilty until proven innocent
-
- for(int i=0;i<numFPrimers;i++){
- string oligo = forPrimer[i];
-
- if(rawSequence.length() < oligo.length()){
- success = 0;
- break;
- }
-
- if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
- seq.setUnaligned(rawSequence.substr(oligo.length()));
- success = 1;
- break;
- }
- }
-
- //if you found the primer or if you don't want to allow for diffs
- if ((diffs == 0) || (success == 1)) { return success; }
-
- else { //try aligning and see if you can find it
-
-
- Alignment* alignment;
- if (numFPrimers > 0) { alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, (forPrimer[0].length()+diffs+1)); } //assumes primers are all the same length
- else{ alignment = NULL; }
-
- //can you find the primer
- for(int i=0;i<numFPrimers;i++){
- string oligo = forPrimer[i];
- int length = oligo.length();
-
- if(rawSequence.length() < oligo.length()){
- success = 0;
- break;
- }
-
- //use needleman to align first primer.length()+numdiffs of sequence to each primer
- alignment->align(oligo, rawSequence.substr(0,length+diffs));
- oligo = alignment->getSeqAAln();
-
- int newStart = 0;
- if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()), length, newStart)){
- seq.setUnaligned(rawSequence.substr(newStart));
- success = 1;
- break;
- }
- }
-
- if (alignment != NULL) { delete alignment; }
+ bool success = 1;
+ if(qscores.getName() != ""){
+ qscores.trimQScores(-1, keepFirst);
}
-
+ sequence.trim(keepFirst);
return success;
-
}
catch(exception& e) {
- m->errorOut(e, "TrimSeqsCommand", "stripForward");
+ m->errorOut(e, "keepFirstTrim", "countDiffs");
exit(1);
}
-}
+
+}
//***************************************************************************************************************
-bool TrimSeqsCommand::stripReverse(Sequence& seq){
+bool TrimSeqsCommand::removeLastTrim(Sequence& sequence, QualityScores& qscores){
try {
- string rawSequence = seq.getUnaligned();
- bool success = 0; //guilty until proven innocent
+ bool success = 0;
- for(int i=0;i<numRPrimers;i++){
- string oligo = revPrimer[i];
-
- if(rawSequence.length() < oligo.length()){
- success = 0;
- break;
- }
-
- if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
- seq.setUnaligned(rawSequence.substr(0,rawSequence.length()-oligo.length()));
- success = 1;
- break;
+ int length = sequence.getNumBases() - removeLast;
+
+ if(length > 0){
+ if(qscores.getName() != ""){
+ qscores.trimQScores(-1, length);
}
- }
+ sequence.trim(length);
+ success = 1;
+ }
+ else{
+ success = 0;
+ }
+
return success;
-
}
catch(exception& e) {
- m->errorOut(e, "TrimSeqsCommand", "stripReverse");
+ m->errorOut(e, "removeLastTrim", "countDiffs");
exit(1);
}
-}
+
+}
//***************************************************************************************************************
}
}
-
-//***************************************************************************************************************
-
-bool TrimSeqsCommand::cullAmbigs(Sequence& seq){
- try {
- int numNs = seq.getAmbigBases();
- bool success = 0; //guilty until proven innocent
-
- if(numNs <= maxAmbig) { success = 1; }
- else { success = 0; }
-
- return success;
- }
- catch(exception& e) {
- m->errorOut(e, "TrimSeqsCommand", "cullAmbigs");
- exit(1);
- }
-
-}
-
-//***************************************************************************************************************
-
-bool TrimSeqsCommand::compareDNASeq(string oligo, string seq){
- try {
- bool success = 1;
- int length = oligo.length();
-
- for(int i=0;i<length;i++){
-
- if(oligo[i] != seq[i]){
- if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C') { success = 0; }
- else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N')) { success = 0; }
- else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G')) { success = 0; }
- else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T')) { success = 0; }
- else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A')) { success = 0; }
- else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G')) { success = 0; }
- else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A')) { success = 0; }
- else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G')) { success = 0; }
- else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G')) { success = 0; }
- else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G')) { success = 0; }
- else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C')) { success = 0; }
- else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G')) { success = 0; }
-
- if(success == 0) { break; }
- }
- else{
- success = 1;
- }
- }
-
- return success;
- }
- catch(exception& e) {
- m->errorOut(e, "TrimSeqsCommand", "compareDNASeq");
- exit(1);
- }
-
-}
-//***************************************************************************************************************
-
-bool TrimSeqsCommand::compareDNASeq(string oligo, string seq, int numBases, int& end){
- try {
- bool success = 1;
- int length = oligo.length();
- end = length;
- int countBases = 0;
- int countDiffs = 0;
-
- if (length != 0) {
- if ((oligo[0] == '-') || (oligo[0] == '.')) { success = 0; return success; } //no gaps allowed at beginning
- }
-
- for(int i=0;i<length;i++){
-
- if ((oligo[i] != '-') && (oligo[i] != '.')) { countBases++; }
-
- //cout << oligo[i] << " " << seq[i] << " diffs = " << countDiffs << " countBases = " << countBases << endl;
-
- if(oligo[i] != seq[i]){
- if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C' || oligo[i] == '-' || oligo[i] == '.') { countDiffs++; }
- else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N')) { countDiffs++; }
- else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G')) { countDiffs++; }
- else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T')) { countDiffs++; }
- else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A')) { countDiffs++; }
- else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G')) { countDiffs++; }
- else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A')) { countDiffs++; }
- else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G')) { countDiffs++; }
- else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G')) { countDiffs++; }
- else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G')) { countDiffs++; }
- else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C')) { countDiffs++; }
- else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G')) { countDiffs++; }
-
- if(countDiffs > diffs) { success = 0; break; }
- }
- else{
- success = 1;
- }
-
- if (countBases >= numBases) { end = i; break; } //stop checking after end of barcode or primer
- }
-
- return success;
- }
- catch(exception& e) {
- m->errorOut(e, "TrimSeqsCommand", "compareDNASeq");
- exit(1);
- }
-
-}
-//***************************************************************************************************************
-
-bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){
+//********************************************************************/
+string TrimSeqsCommand::reverseOligo(string oligo){
try {
- string rawSequence = seq.getUnaligned();
- int seqLength; // = rawSequence.length();
- string name, temp, temp2;
-
- qFile >> name >> temp;
-
- splitAtEquals(temp2, temp); //separates length=242, temp=length, temp2=242
- convert(temp, seqLength); //converts string to int
-
- if (name.length() != 0) { if(name.substr(1) != seq.getName()) { m->mothurOut("sequence name mismatch btwn fasta and qual file"); m->mothurOutEndLine(); } }
- while (!qFile.eof()) { char c = qFile.get(); if (c == 10 || c == 13){ break; } }
-
- int score;
- int end = seqLength;
-
- for(int i=0;i<seqLength;i++){
- qFile >> score;
-
- if(score <= qThreshold){
- end = i;
- break;
- }
- }
- for(int i=end+1;i<seqLength;i++){
- qFile >> score;
- }
-
- seq.setUnaligned(rawSequence.substr(0,end));
-
- return 1;
- }
+ string reverse = "";
+
+ for(int i=oligo.length()-1;i>=0;i--){
+
+ if(oligo[i] == 'A') { reverse += 'T'; }
+ else if(oligo[i] == 'T'){ reverse += 'A'; }
+ else if(oligo[i] == 'U'){ reverse += 'A'; }
+
+ else if(oligo[i] == 'G'){ reverse += 'C'; }
+ else if(oligo[i] == 'C'){ reverse += 'G'; }
+
+ else if(oligo[i] == 'R'){ reverse += 'Y'; }
+ else if(oligo[i] == 'Y'){ reverse += 'R'; }
+
+ else if(oligo[i] == 'M'){ reverse += 'K'; }
+ else if(oligo[i] == 'K'){ reverse += 'M'; }
+
+ else if(oligo[i] == 'W'){ reverse += 'W'; }
+ else if(oligo[i] == 'S'){ reverse += 'S'; }
+
+ else if(oligo[i] == 'B'){ reverse += 'V'; }
+ else if(oligo[i] == 'V'){ reverse += 'B'; }
+
+ else if(oligo[i] == 'D'){ reverse += 'H'; }
+ else if(oligo[i] == 'H'){ reverse += 'D'; }
+
+ else { reverse += 'N'; }
+ }
+
+
+ return reverse;
+ }
catch(exception& e) {
- m->errorOut(e, "TrimSeqsCommand", "stripQualThreshold");
+ m->errorOut(e, "TrimSeqsCommand", "reverseOligo");
exit(1);
}
}
//***************************************************************************************************************
-bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){
+bool TrimSeqsCommand::cullAmbigs(Sequence& seq){
try {
- string rawSequence = seq.getUnaligned();
- int seqLength = seq.getNumBases();
+ int numNs = seq.getAmbigBases();
bool success = 0; //guilty until proven innocent
- string name;
-
- qFile >> name;
- if (name[0] == '>') { if(name.substr(1) != seq.getName()) { m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine(); } }
-
- while (!qFile.eof()) { char c = qFile.get(); if (c == 10 || c == 13){ break; } }
-
- float score;
- float average = 0;
- for(int i=0;i<seqLength;i++){
- qFile >> score;
- average += score;
- }
- average /= seqLength;
-
- if(average >= qAverage) { success = 1; }
+ if(numNs <= maxAmbig) { success = 1; }
else { success = 0; }
return success;
}
catch(exception& e) {
- m->errorOut(e, "TrimSeqsCommand", "cullQualAverage");
+ m->errorOut(e, "TrimSeqsCommand", "cullAmbigs");
exit(1);
}
+
}
-
//***************************************************************************************************************
projects / mothur.git / blobdiff