#include "trimseqscommand.h"
#include "needlemanoverlap.hpp"
+#include "trimoligos.h"
-//**********************************************************************************************************************
-vector<string> TrimSeqsCommand::getValidParameters(){
+//**********************************************************************************************************************
+vector<string> TrimSeqsCommand::setParameters(){
try {
- string Array[] = {"fasta", "flip", "oligos", "maxambig", "maxhomop", "group","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","fasta",false,true,true); parameters.push_back(pfasta);
+ CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","group",false,false,true); parameters.push_back(poligos);
+ CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none","qfile",false,false,true); parameters.push_back(pqfile);
+ CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","name",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","count",false,false,true); parameters.push_back(pcount);
+ CommandParameter pflip("flip", "Boolean", "", "F", "", "", "","",false,false,true); parameters.push_back(pflip);
+ CommandParameter preorient("checkorient", "Boolean", "", "F", "", "", "","",false,false,true); parameters.push_back(preorient);
+ 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", "", "1", "", "", "","",false,false); parameters.push_back(pminlength);
+ CommandParameter pmaxlength("maxlength", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pmaxlength);
+ CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(ppdiffs);
+ CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false,true); 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,true); 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 plogtransform("logtransform", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(plogtransform);
+ 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;
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["fasta"] = tempOutNames;
- outputTypes["qual"] = 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, count, flip, checkorient, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim, keepfirst, removelast, logtransform 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 checkorient parameter will check the reverse compliment of the sequence if the barcodes and primers cannot be found in the forward. 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 count parameter allows you to provide a count 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 logtransform parameter allows you to indicate you want the averages for the qwindowaverage, rollaverage and qaverage to be calculated using a logtransform. Default=F.\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", "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);
- }
+string TrimSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "qfile") { pattern = "[filename],[tag],qual"; }
+ else if (type == "fasta") { pattern = "[filename],[tag],fasta"; }
+ else if (type == "group") { pattern = "[filename],groups"; }
+ else if (type == "name") { pattern = "[filename],[tag],names"; }
+ else if (type == "count") { pattern = "[filename],[tag],count_table-[filename],count_table"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimSeqsCommand", "getOutputPattern");
+ 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;
+ outputTypes["count"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "TrimSeqsCommand", "getRequiredFiles");
+ 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", "group","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();
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
- outputTypes["qual"] = tempOutNames;
+ outputTypes["qfile"] = tempOutNames;
outputTypes["group"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["count"] = 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("group");
+ 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["group"] = inputDir + it->second; }
+ if (path == "") { parameters["name"] = inputDir + it->second; }
}
+
+ it = parameters.find("count");
+ //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["count"] = 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; }
+ 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"){
// ...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(m->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, "group", true);
- if (temp == "not found"){ groupfile = ""; }
- else if(temp == "not open"){ abort = true; }
- else { groupfile = temp; }
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);
+ temp = validParameter.validFile(parameters, "minlength", false); if (temp == "not found") { temp = "1"; }
+ 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"; }
- convert(temp, bdiffs);
+ m->mothurConvert(temp, bdiffs);
temp = validParameter.validFile(parameters, "pdiffs", false); if (temp == "not found") { temp = "0"; }
- convert(temp, pdiffs);
+ 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, "tdiffs", false); if (temp == "not found") { int tempTotal = pdiffs + bdiffs; temp = toString(tempTotal); }
- convert(temp, tdiffs);
+ 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; }
+ 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); }
+
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { abort = true; countfile = ""; }
+ else if (countfile == "not found") { countfile = ""; }
+ else { m->setCountTableFile(countfile); }
+
+ if ((countfile != "") && (nameFile != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
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 = "t"; }
qtrim = m->isTrue(temp);
temp = validParameter.validFile(parameters, "allfiles", false); if (temp == "not found") { temp = "F"; }
allFiles = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "keepforward", false); if (temp == "not found") { temp = "F"; }
+ keepforward = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "logtransform", false); if (temp == "not found") { temp = "F"; }
+ logtransform = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "checkorient", false); if (temp == "not found") { temp = "F"; }
+ reorient = m->isTrue(temp);
- temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; }
- convert(temp, processors);
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ m->mothurConvert(temp, processors);
- if ((oligoFile != "") && (groupfile != "")) {
- m->mothurOut("You given both a oligos file and a groupfile, only one is allowed."); m->mothurOutEndLine(); abort = true;
- }
-
- if(allFiles && (oligoFile == "") && (groupfile == "")){
- m->mothurOut("You selected allfiles, but didn't enter an oligos or group 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 (countfile == "") {
+ 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 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, group, 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 group parameter allows you to enter a group file for your fasta file.\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(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+ pairedOligos = false;
numFPrimers = 0; //this needs to be initialized
numRPrimers = 0;
- vector<string> fastaFileNames;
- vector<string> qualFileNames;
-
- string trimSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.fasta";
+ numSpacers = 0;
+ numLinkers = 0;
+ createGroup = false;
+ vector<vector<string> > fastaFileNames;
+ vector<vector<string> > qualFileNames;
+ vector<vector<string> > nameFileNames;
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFile));
+ variables["[tag]"] = "trim";
+ string trimSeqFile = getOutputFileName("fasta",variables);
+ string trimQualFile = getOutputFileName("qfile",variables);
outputNames.push_back(trimSeqFile); outputTypes["fasta"].push_back(trimSeqFile);
- string scrapSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.fasta";
+
+ variables["[tag]"] = "scrap";
+ string scrapSeqFile = getOutputFileName("fasta",variables);
+ string scrapQualFile = getOutputFileName("qfile",variables);
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["qual"].push_back(trimQualFile); outputTypes["qual"].push_back(scrapQualFile); }
- string groupFile = "";
- if (groupfile == "") { groupFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "groups"; }
- else{
- groupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "trim.groups";
- outputNames.push_back(groupFile); outputTypes["group"].push_back(groupFile);
- groupMap = new GroupMap(groupfile);
- groupMap->readMap();
-
- if(allFiles){
- for (int i = 0; i < groupMap->namesOfGroups.size(); i++) {
- groupToIndex[groupMap->namesOfGroups[i]] = i;
- groupVector.push_back(groupMap->namesOfGroups[i]);
- fastaFileNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + groupMap->namesOfGroups[i] + ".fasta"));
-
- //we append later, so we want to clear file
- ofstream outRemove;
- m->openOutputFile(fastaFileNames[i], outRemove);
- outRemove.close();
- if(qFileName != ""){
- qualFileNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupMap->namesOfGroups[i] + ".qual"));
- ofstream outRemove2;
- m->openOutputFile(qualFileNames[i], outRemove2);
- outRemove2.close();
- }
- }
- }
- comboStarts = fastaFileNames.size()-1;
+
+ if (qFileName != "") {
+ outputNames.push_back(trimQualFile);
+ outputNames.push_back(scrapQualFile);
+ outputTypes["qfile"].push_back(trimQualFile);
+ outputTypes["qfile"].push_back(scrapQualFile);
}
- if(oligoFile != ""){
- outputNames.push_back(groupFile); outputTypes["group"].push_back(groupFile);
- getOligos(fastaFileNames, qualFileNames);
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(nameFile));
+ variables["[tag]"] = "trim";
+ string trimNameFile = getOutputFileName("name",variables);
+ variables["[tag]"] = "scrap";
+ string scrapNameFile = getOutputFileName("name",variables);
+
+ if (nameFile != "") {
+ m->readNames(nameFile, nameMap);
+ outputNames.push_back(trimNameFile);
+ outputNames.push_back(scrapNameFile);
+ outputTypes["name"].push_back(trimNameFile);
+ outputTypes["name"].push_back(scrapNameFile);
+ }
+
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[tag]"] = "trim";
+ string trimCountFile = getOutputFileName("count",variables);
+ variables["[tag]"] = "scrap";
+ string scrapCountFile = getOutputFileName("count",variables);
+
+ if (countfile != "") {
+ CountTable ct;
+ ct.readTable(countfile, true, false);
+ nameCount = ct.getNameMap();
+ outputNames.push_back(trimCountFile);
+ outputNames.push_back(scrapCountFile);
+ outputTypes["count"].push_back(trimCountFile);
+ outputTypes["count"].push_back(scrapCountFile);
}
- vector<unsigned long int> fastaFilePos;
- vector<unsigned long int> qFilePos;
- setLines(fastaFile, qFileName, fastaFilePos, qFilePos);
+ if (m->control_pressed) { return 0; }
+
+ string outputGroupFileName;
+ if(oligoFile != ""){
+ createGroup = getOligos(fastaFileNames, qualFileNames, nameFileNames);
+ if ((createGroup) && (countfile == "")){
+ map<string, string> myvariables;
+ myvariables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFile));
+ outputGroupFileName = getOutputFileName("group",myvariables);
+ outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
+ }
+ }
+
+ if (m->control_pressed) { return 0; }
+
+ //fills lines and qlines
+ setLines(fastaFile, qFileName);
+
+ if(processors == 1){
+ driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, trimNameFile, scrapNameFile, trimCountFile, scrapCountFile, outputGroupFileName, fastaFileNames, qualFileNames, nameFileNames, lines[0], qLines[0]);
+ }else{
+ createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, trimNameFile, scrapNameFile, trimCountFile, scrapCountFile, outputGroupFileName, fastaFileNames, qualFileNames, nameFileNames);
+ }
- for (int i = 0; i < (fastaFilePos.size()-1); i++) {
- lines.push_back(new linePair(fastaFilePos[i], fastaFilePos[(i+1)]));
- if (qFileName != "") { qLines.push_back(new linePair(qFilePos[i], qFilePos[(i+1)])); }
- }
- if(qFileName == "") { qLines = lines; } //files with duds
-
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- if(processors == 1){
- driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], qLines[0]);
- }else{
- createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames);
- }
- #else
- driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], qLines[0]);
- #endif
if (m->control_pressed) { return 0; }
-
- set<string> blanks;
- for(int i=0;i<fastaFileNames.size();i++){
- if (m->isBlank(fastaFileNames[i])) { blanks.insert(fastaFileNames[i]); }
- else if (filesToRemove.count(fastaFileNames[i]) > 0) { remove(fastaFileNames[i].c_str()); }
- else {
- ifstream inFASTA;
- string seqName;
- m->openInputFile(fastaFileNames[i], inFASTA);
- ofstream outGroups;
- string outGroupFilename = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "groups";
-
- //if the fastafile is on the blanks list then the groups file should be as well
- if (blanks.count(fastaFileNames[i]) != 0) { blanks.insert(outGroupFilename); }
-
- m->openOutputFile(outGroupFilename, outGroups);
- outputNames.push_back(outGroupFilename); outputTypes["group"].push_back(outGroupFilename);
-
- string thisGroup = "";
- if (i > comboStarts) {
- map<string, int>::iterator itCombo;
- for(itCombo=combos.begin();itCombo!=combos.end(); itCombo++){
- if(itCombo->second == i){ thisGroup = itCombo->first; combos.erase(itCombo); break; }
- }
- }else{ thisGroup = groupVector[i]; }
-
- while(!inFASTA.eof()){
- if(inFASTA.get() == '>'){
- inFASTA >> seqName;
- outGroups << seqName << '\t' << thisGroup << endl;
+
+ 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]);
+ }
+
+ 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];
+ }
+ }
+ }
}
- while (!inFASTA.eof()) { char c = inFASTA.get(); if (c == 10 || c == 13){ break; } }
}
- outGroups.close();
- inFASTA.close();
}
+
+ //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);
+
+ ofstream out;
+ map<string, string> myvariables;
+ myvariables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(it->first));
+ string thisGroupName = "";
+ if (countfile == "") { thisGroupName = getOutputFileName("group",myvariables); outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName); }
+ else { thisGroupName = getOutputFileName("count",myvariables); outputNames.push_back(thisGroupName); outputTypes["count"].push_back(thisGroupName); }
+ m->openOutputFile(thisGroupName, out);
+
+ if (countfile != "") { out << "Representative_Sequence\ttotal\t" << it->second << endl; }
+
+ while (!in.eof()){
+ if (m->control_pressed) { break; }
+
+ Sequence currSeq(in); m->gobble(in);
+ if (countfile == "") {
+ 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(); }
+ }
+ }else {
+ map<string, int>::iterator itTotalReps = nameCount.find(currSeq.getName());
+ if (itTotalReps != nameCount.end()) { out << currSeq.getName() << '\t' << itTotalReps->second << '\t' << itTotalReps->second << endl; }
+ else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your count file, please correct."); m->mothurOutEndLine(); }
+ }
+ }
+ in.close();
+ out.close();
+ }
+
+ if (countfile != "") { //create countfile with group info included
+ CountTable* ct = new CountTable();
+ ct->readTable(trimCountFile, true, false);
+ map<string, int> justTrimmedNames = ct->getNameMap();
+ delete ct;
+
+ CountTable newCt;
+ for (map<string, int>::iterator itCount = groupCounts.begin(); itCount != groupCounts.end(); itCount++) { newCt.addGroup(itCount->first); }
+ vector<int> tempCounts; tempCounts.resize(groupCounts.size(), 0);
+ for (map<string, int>::iterator itNames = justTrimmedNames.begin(); itNames != justTrimmedNames.end(); itNames++) {
+ newCt.push_back(itNames->first, tempCounts); //add it to the table with no abundance so we can set the groups abundance
+ map<string, string>::iterator it2 = groupMap.find(itNames->first);
+ if (it2 != groupMap.end()) { newCt.setAbund(itNames->first, it2->second, itNames->second); }
+ else { m->mothurOut("[ERROR]: missing group info for " + itNames->first + "."); m->mothurOutEndLine(); m->control_pressed = true; }
+ }
+ newCt.printTable(trimCountFile);
+ }
}
- for (set<string>::iterator itBlanks = blanks.begin(); itBlanks != blanks.end(); itBlanks++) { remove((*(itBlanks)).c_str()); }
+ 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(); }
- blanks.clear();
- if(qFileName != ""){
- for(int i=0;i<qualFileNames.size();i++){
- if (m->isBlank(qualFileNames[i])) { blanks.insert(qualFileNames[i]); }
- else if (filesToRemove.count(qualFileNames[i]) > 0) { remove(qualFileNames[i].c_str()); }
- }
+ 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); }
}
- for (set<string>::iterator itBlanks = blanks.begin(); itBlanks != blanks.end(); itBlanks++) { remove((*(itBlanks)).c_str()); }
+ itTypes = outputTypes.find("name");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
+ }
- if (m->control_pressed) {
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
- return 0;
+ 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); }
+ }
+
+ itTypes = outputTypes.find("count");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
}
m->mothurOutEndLine();
}
/**************************************************************************************/
-
-int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string trimQFile, string scrapQFile, string groupFile, vector<string> fastaNames, vector<string> qualNames, linePair* line, linePair* qline) {
+int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string trimFileName, string scrapFileName, string trimQFileName, string scrapQFileName, string trimNFileName, string scrapNFileName, string trimCFileName, string scrapCFileName, string groupFileName, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames, vector<vector<string> > nameFileNames, linePair line, linePair qline) {
try {
- ofstream outFASTA;
- m->openOutputFile(trimFile, outFASTA);
+ ofstream trimFASTAFile;
+ m->openOutputFile(trimFileName, trimFASTAFile);
- ofstream scrapFASTA;
- m->openOutputFile(scrapFile, scrapFASTA);
+ ofstream scrapFASTAFile;
+ m->openOutputFile(scrapFileName, scrapFASTAFile);
- ofstream outQual;
- ofstream scrapQual;
+ ofstream trimQualFile;
+ ofstream scrapQualFile;
if(qFileName != ""){
- m->openOutputFile(trimQFile, outQual);
- m->openOutputFile(scrapQFile, scrapQual);
+ m->openOutputFile(trimQFileName, trimQualFile);
+ m->openOutputFile(scrapQFileName, scrapQualFile);
}
- ofstream outGroups;
+ ofstream trimNameFile;
+ ofstream scrapNameFile;
+ if(nameFile != ""){
+ m->openOutputFile(trimNFileName, trimNameFile);
+ m->openOutputFile(scrapNFileName, scrapNameFile);
+ }
- if (oligoFile != "") {
- m->openOutputFile(groupFile, outGroups);
+ ofstream trimCountFile;
+ ofstream scrapCountFile;
+ if(countfile != ""){
+ m->openOutputFile(trimCFileName, trimCountFile);
+ m->openOutputFile(scrapCFileName, scrapCountFile);
+ if (line.start == 0) { trimCountFile << "Representative_Sequence\ttotal" << endl; scrapCountFile << "Representative_Sequence\ttotal" << endl; }
+ }
+
+ ofstream outGroupsFile;
+ if ((createGroup) && (countfile == "")){ 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;
m->openInputFile(filename, inFASTA);
- inFASTA.seekg(line->start);
+ inFASTA.seekg(line.start);
ifstream qFile;
- if(qFileName != "") { m->openInputFile(qFileName, qFile); qFile.seekg(qline->start); }
-
-
- for (int i = 0; i < fastaNames.size(); i++) { //clears old file
- ofstream temp;
- m->openOutputFile(fastaNames[i], temp);
- temp.close();
- }
- for (int i = 0; i < qualNames.size(); i++) { //clears old file
- ofstream temp;
- m->openOutputFile(qualNames[i], temp);
- temp.close();
+ if(qFileName != "") {
+ m->openInputFile(qFileName, qFile);
+ qFile.seekg(qline.start);
}
-
- bool done = false;
int count = 0;
-
- while (!done) {
+ bool moreSeqs = 1;
+ int numBarcodes = barcodes.size();
+ TrimOligos* trimOligos = NULL;
+ if (pairedOligos) { trimOligos = new TrimOligos(pdiffs, bdiffs, 0, 0, pairedPrimers, pairedBarcodes); numBarcodes = pairedBarcodes.size(); }
+ else { trimOligos = new TrimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimer, linker, spacer); }
+
+ TrimOligos* rtrimOligos = NULL;
+ if (reorient) {
+ //create reoriented primer and barcode pairs
+ map<int, oligosPair> rpairedPrimers, rpairedBarcodes;
+ for (map<int, oligosPair>::iterator it = pairedPrimers.begin(); it != pairedPrimers.end(); it++) {
+ oligosPair tempPair(reverseOligo((it->second).reverse), (reverseOligo((it->second).forward))); //reversePrimer, rc ForwardPrimer
+ rpairedPrimers[it->first] = tempPair;
+ //cout << reverseOligo((it->second).reverse) << '\t' << (reverseOligo((it->second).forward)) << '\t' << primerNameVector[it->first] << endl;
+ }
+ for (map<int, oligosPair>::iterator it = pairedBarcodes.begin(); it != pairedBarcodes.end(); it++) {
+ oligosPair tempPair(reverseOligo((it->second).reverse), (reverseOligo((it->second).forward))); //reverseBarcode, rc ForwardBarcode
+ rpairedBarcodes[it->first] = tempPair;
+ //cout << reverseOligo((it->second).reverse) << '\t' << (reverseOligo((it->second).forward)) << '\t' << barcodeNameVector[it->first] << endl;
+ }
+ int index = rpairedBarcodes.size();
+ for (map<string, int>::iterator it = barcodes.begin(); it != barcodes.end(); it++) {
+ oligosPair tempPair("", reverseOligo((it->first))); //reverseBarcode, rc ForwardBarcode
+ rpairedBarcodes[index] = tempPair; index++;
+ //cout << reverseOligo((it->second).reverse) << '\t' << (reverseOligo((it->second).forward)) << '\t' << barcodeNameVector[it->first] << endl;
+ }
+
+ index = rpairedPrimers.size();
+ for (map<string, int>::iterator it = primers.begin(); it != primers.end(); it++) {
+ oligosPair tempPair("", reverseOligo((it->first))); //reverseBarcode, rc ForwardBarcode
+ rpairedPrimers[index] = tempPair; index++;
+ //cout << reverseOligo((it->second).reverse) << '\t' << (reverseOligo((it->second).forward)) << '\t' << primerNameVector[it->first] << endl;
+ }
+
+ rtrimOligos = new TrimOligos(pdiffs, bdiffs, 0, 0, rpairedPrimers, rpairedBarcodes); numBarcodes = rpairedBarcodes.size();
+ }
+
+ 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 < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
-
- return 0;
+ if (m->control_pressed) {
+ delete trimOligos; if (reorient) { delete rtrimOligos; }
+ inFASTA.close(); trimFASTAFile.close(); scrapFASTAFile.close();
+ if ((createGroup) && (countfile == "")) { outGroupsFile.close(); }
+ if(qFileName != "") { qFile.close(); scrapQualFile.close(); trimQualFile.close(); }
+ if(nameFile != "") { scrapNameFile.close(); trimNameFile.close(); }
+ if(countfile != "") { scrapCountFile.close(); trimCountFile.close(); }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0;
}
int success = 1;
-
+ string trashCode = "";
+ int currentSeqsDiffs = 0;
Sequence currSeq(inFASTA); m->gobble(inFASTA);
-
- QualityScores currQual;
+ //cout << currSeq.getName() << '\t' << currSeq.getUnaligned() << endl;
+ Sequence savedSeq(currSeq.getName(), currSeq.getAligned());
+
+ QualityScores currQual; QualityScores savedQual;
if(qFileName != ""){
- currQual = QualityScores(qFile, currSeq.getNumBases()); m->gobble(qFile);
+ currQual = QualityScores(qFile); m->gobble(qFile);
+ savedQual.setName(currQual.getName()); savedQual.setScores(currQual.getScores());
+ //cout << currQual.getName() << endl;
}
-
+
string origSeq = currSeq.getUnaligned();
if (origSeq != "") {
- int groupBar, groupPrime;
- string trashCode = "";
- int currentSeqsDiffs = 0;
+
+ 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, currQual, groupBar);
- if(success > bdiffs) { trashCode += 'b'; }
+ }
+
+ if(numBarcodes != 0){
+ success = trimOligos->stripBarcode(currSeq, currQual, barcodeIndex);
+ if(success > bdiffs) {
+ trashCode += 'b';
+ }
else{ currentSeqsDiffs += success; }
}
-
+ //cout << currSeq.getName() << '\t' << currSeq.getUnaligned() << endl;
+ if(numSpacers != 0){
+ success = trimOligos->stripSpacer(currSeq, currQual);
+ if(success > sdiffs) { trashCode += 's'; }
+ else{ currentSeqsDiffs += success; }
+
+ }
+
if(numFPrimers != 0){
- success = stripForward(currSeq, currQual, groupPrime);
- if(success > pdiffs) { 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, currQual);
+ success = trimOligos->stripReverse(currSeq, currQual);
if(!success) { trashCode += 'r'; }
}
-
+
+ if (reorient && (trashCode != "")) { //if you failed and want to check the reverse
+ int thisSuccess = 0;
+ string thisTrashCode = "";
+ int thisCurrentSeqsDiffs = 0;
+
+ int thisBarcodeIndex = 0;
+ int thisPrimerIndex = 0;
+ //cout << currSeq.getName() << '\t' << savedSeq.getUnaligned() << endl;
+ if(numBarcodes != 0){
+ thisSuccess = rtrimOligos->stripBarcode(savedSeq, savedQual, thisBarcodeIndex);
+ if(thisSuccess > bdiffs) { thisTrashCode += "b"; }
+ else{ thisCurrentSeqsDiffs += thisSuccess; }
+ }
+ //cout << currSeq.getName() << '\t' << savedSeq.getUnaligned() << endl;
+ if(numFPrimers != 0){
+ thisSuccess = rtrimOligos->stripForward(savedSeq, savedQual, thisPrimerIndex, keepforward);
+ if(thisSuccess > pdiffs) { thisTrashCode += "f"; }
+ else{ thisCurrentSeqsDiffs += thisSuccess; }
+ }
+
+ if (thisCurrentSeqsDiffs > tdiffs) { thisTrashCode += 't'; }
+
+ if (thisTrashCode == "") {
+ trashCode = thisTrashCode;
+ success = thisSuccess;
+ currentSeqsDiffs = thisCurrentSeqsDiffs;
+ barcodeIndex = thisBarcodeIndex;
+ primerIndex = thisPrimerIndex;
+ savedSeq.reverseComplement();
+ currSeq.setAligned(savedSeq.getAligned());
+ if(qFileName != ""){
+ savedQual.flipQScores();
+ currQual.setScores(savedQual.getScores());
+ }
+ }else { trashCode += "(" + thisTrashCode + ")"; }
+ }
+
if(keepFirst != 0){
success = keepFirstTrim(currSeq, currQual);
}
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 if(qAverage != 0) { success = currQual.cullQualAverage(currSeq, qAverage, logtransform); }
+ else if(qRollAverage != 0) { success = currQual.stripQualRollingAverage(currSeq, qRollAverage, logtransform); }
+ else if(qWindowAverage != 0){ success = currQual.stripQualWindowAverage(currSeq, qWindowStep, qWindowSize, qWindowAverage, logtransform); }
else { success = 1; }
//you don't want to trim, if it fails above then scrap it
if(flip){ // should go last
currSeq.reverseComplement();
- currQual.flipQScores();
+ if(qFileName != ""){
+ currQual.flipQScores();
+ }
}
+ if (m->debug) { m->mothurOut("[DEBUG]: " + currSeq.getName() + ", trashcode= " + trashCode); if (trashCode.length() != 0) { m->mothurOutEndLine(); } }
+
if(trashCode.length() == 0){
- currSeq.setAligned(currSeq.getUnaligned());
- currSeq.printSequence(outFASTA);
- currQual.printQScores(outQual);
-
- if(barcodes.size() != 0){
- string thisGroup = groupVector[groupBar];
- int indexToFastaFile = groupBar;
- if (primers.size() != 0){
- //does this primer have a group
- if (groupVector[groupPrime] != "") {
- thisGroup += "." + groupVector[groupPrime];
- indexToFastaFile = combos[thisGroup];
+ string thisGroup = "";
+ if (createGroup) {
+ if(numBarcodes != 0){
+ thisGroup = barcodeNameVector[barcodeIndex];
+ if (numFPrimers != 0) {
+ if (primerNameVector[primerIndex] != "") {
+ if(thisGroup != "") {
+ thisGroup += "." + primerNameVector[primerIndex];
+ }else {
+ thisGroup = primerNameVector[primerIndex];
+ }
+ }
}
- }
- outGroups << currSeq.getName() << '\t' << thisGroup << endl;
- if(allFiles){
- ofstream outTemp;
- m->openOutputFileAppend(fastaNames[indexToFastaFile], outTemp);
- //currSeq.printSequence(*fastaFileNames[indexToFastaFile]);
- currSeq.printSequence(outTemp);
- outTemp.close();
-
- if(qFileName != ""){
- //currQual.printQScores(*qualFileNames[indexToFastaFile]);
- ofstream outTemp2;
- m->openOutputFileAppend(qualNames[indexToFastaFile], outTemp2);
- currQual.printQScores(outTemp2);
- outTemp2.close();
- }
- }
- }
-
- if (groupfile != "") {
- string thisGroup = groupMap->getGroup(currSeq.getName());
-
- if (thisGroup != "not found") {
- outGroups << currSeq.getName() << '\t' << thisGroup << endl;
- if (allFiles) {
- ofstream outTemp;
- m->openOutputFileAppend(fastaNames[groupToIndex[thisGroup]], outTemp);
- currSeq.printSequence(outTemp);
- outTemp.close();
- if(qFileName != ""){
- ofstream outTemp2;
- m->openOutputFileAppend(qualNames[groupToIndex[thisGroup]], outTemp2);
- currQual.printQScores(outTemp2);
- outTemp2.close();
- }
- }
- }else{
- m->mothurOut(currSeq.getName() + " is not in your groupfile, adding to group XXX."); m->mothurOutEndLine();
- outGroups << currSeq.getName() << '\t' << "XXX" << endl;
- if (allFiles) {
- m->mothurOut("[ERROR]: " + currSeq.getName() + " will not be added to any .group.fasta or .group.qual file."); m->mothurOutEndLine();
- }
- }
- }
+ }
+ }
+
+ int pos = thisGroup.find("ignore");
+ if (pos == string::npos) {
+ 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(); }
+ }
+
+ int numRedundants = 0;
+ if (countfile != "") {
+ map<string, int>::iterator itCount = nameCount.find(currSeq.getName());
+ if (itCount != nameCount.end()) {
+ trimCountFile << itCount->first << '\t' << itCount->second << endl;
+ numRedundants = itCount->second-1;
+ }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your count file, please correct."); m->mothurOutEndLine(); }
+ }
+
+ if (createGroup) {
+ if(numBarcodes != 0){
+
+ if (m->debug) { m->mothurOut(", group= " + thisGroup + "\n"); }
+
+ if (countfile == "") { outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl; }
+ else { groupMap[currSeq.getName()] = thisGroup; }
+
+ if (nameFile != "") {
+ map<string, string>::iterator itName = nameMap.find(currSeq.getName());
+ if (itName != nameMap.end()) {
+ vector<string> thisSeqsNames;
+ m->splitAtChar(itName->second, thisSeqsNames, ',');
+ numRedundants = thisSeqsNames.size()-1; //we already include ourselves below
+ 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 + numRedundants; }
+ else { groupCounts[it->first] += (1 + numRedundants); }
+
+ }
+ }
+
+ if(allFiles){
+ ofstream output;
+ m->openOutputFileAppend(fastaFileNames[barcodeIndex][primerIndex], output);
+ currSeq.printSequence(output);
+ output.close();
+
+ 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(); }
+ }
+ if (countfile != "") {
+ map<string, int>::iterator itCount = nameCount.find(currSeq.getName());
+ if (itCount != nameCount.end()) {
+ trimCountFile << itCount->first << '\t' << itCount->second << endl;
+ }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your count file, please correct."); m->mothurOutEndLine(); }
+ }
+
currSeq.setName(currSeq.getName() + '|' + trashCode);
currSeq.setUnaligned(origSeq);
currSeq.setAligned(origSeq);
- currSeq.printSequence(scrapFASTA);
- currQual.printQScores(scrapQual);
+ currSeq.printSequence(scrapFASTAFile);
+ if(qFileName != ""){
+ currQual.printQScores(scrapQualFile);
+ }
}
count++;
}
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- unsigned long int pos = inFASTA.tellg();
- if ((pos == -1) || (pos >= line->end)) { break; }
+ #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(); }
-
+ delete trimOligos;
+ if (reorient) { delete rtrimOligos; }
inFASTA.close();
- outFASTA.close();
- scrapFASTA.close();
- if (oligoFile != "") { outGroups.close(); }
- if(qFileName != "") { qFile.close(); scrapQual.close(); outQual.close(); }
+ trimFASTAFile.close();
+ scrapFASTAFile.close();
+ if (createGroup) { outGroupsFile.close(); }
+ if(qFileName != "") { qFile.close(); scrapQualFile.close(); trimQualFile.close(); }
+ if(nameFile != "") { scrapNameFile.close(); trimNameFile.close(); }
+ if(countfile != "") { scrapCountFile.close(); trimCountFile.close(); }
return count;
}
/**************************************************************************************************/
-int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string trimQFile, string scrapQFile, string groupFile, vector<string> fastaNames, vector<string> qualNames) {
+int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFASTAFileName, string scrapFASTAFileName, string trimQualFileName, string scrapQualFileName, string trimNameFileName, string scrapNameFileName, string trimCountFileName, string scrapCountFileName, string groupFile, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames, vector<vector<string> > nameFileNames) {
try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- int process = 1;
+
+ 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){
- for (int i = 0; i < fastaNames.size(); i++) {
- fastaNames[i] = (fastaNames[i] + toString(getpid()) + ".temp");
- //clear old file if it exists
+
+ vector<vector<string> > tempFASTAFileNames = fastaFileNames;
+ vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
+ vector<vector<string> > tempNameFileNames = nameFileNames;
+
+ if(allFiles){
ofstream temp;
- m->openOutputFile(fastaNames[i], temp);
- temp.close();
- if(qFileName != ""){
- qualNames[i] = (qualNames[i] + toString(getpid()) + ".temp");
- //clear old file if it exists
- ofstream temp2;
- m->openOutputFile(qualNames[i], temp2);
- temp2.close();
+
+ 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"),
+ (trimCountFileName + toString(getpid()) + ".temp"),
+ (scrapCountFileName + toString(getpid()) + ".temp"),
+ (groupFile + toString(getpid()) + ".temp"),
+ tempFASTAFileNames,
+ tempPrimerQualFileNames,
+ tempNameFileNames,
+ lines[process],
+ qLines[process]);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: " + toString(lines[process].start) + '\t' + toString(qLines[process].start) + '\t' + toString(getpid()) + '\n'); }
- driverCreateTrim(filename, qFileName, (trimFile + toString(getpid()) + ".temp"), (scrapFile + toString(getpid()) + ".temp"), (trimQFile + toString(getpid()) + ".temp"), (scrapQFile + toString(getpid()) + ".temp"), (groupFile + toString(getpid()) + ".temp"), fastaNames, qualNames, 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 << groupMap.size() << endl;
+ for (map<string, string>::iterator it = groupMap.begin(); it != groupMap.end(); it++) {
+ out << it->first << '\t' << it->second << endl;
+ }
+ out.close();
+ }
exit(0);
}else {
m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
}
//parent do my part
- for (int i = 0; i < fastaNames.size(); i++) {
- //clear old file if it exists
- ofstream temp;
- m->openOutputFile(fastaNames[i], temp);
- temp.close();
- if(qFileName != ""){
- //clear old file if it exists
- ofstream temp2;
- m->openOutputFile(qualNames[i], temp2);
- temp2.close();
- }
+ 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();
}
-
- driverCreateTrim(filename, qFileName, trimFile, scrapFile, trimQFile, scrapQFile, groupFile, fastaNames, qualNames, lines[0], qLines[0]);
-
+ if (nameFile != "") {
+ m->openOutputFile(trimNameFileName, temp); temp.close();
+ m->openOutputFile(scrapNameFileName, temp); temp.close();
+ }
+ if (countfile != "") {
+ m->openOutputFile(trimCountFileName, temp); temp.close();
+ m->openOutputFile(scrapCountFileName, temp); temp.close();
+ }
+
+ driverCreateTrim(filename, qFileName, trimFASTAFileName, scrapFASTAFileName, trimQualFileName, scrapQualFileName, trimNameFileName, scrapNameFileName, trimCountFileName, scrapCountFileName, 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++) {
int temp = processIDS[i];
wait(&temp);
}
-
- //append files
+#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 h=0; h<processors-1; h++){
+
+ string extension = "";
+ if (h != 0) { extension = toString(h) + ".temp"; processIDS.push_back(h); }
+ 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, countfile,
+ (trimFASTAFileName+extension),
+ (scrapFASTAFileName+extension),
+ (trimQualFileName+extension),
+ (scrapQualFileName+extension),
+ (trimNameFileName+extension),
+ (scrapNameFileName+extension),
+ (trimCountFileName+extension),
+ (scrapCountFileName+extension),
+ (groupFile+extension),
+ tempFASTAFileNames,
+ tempPrimerQualFileNames,
+ tempNameFileNames,
+ lines[h].start, lines[h].end, qLines[h].start, qLines[h].end, m,
+ pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, primers, barcodes, revPrimer, linker, spacer, pairedBarcodes, pairedPrimers, pairedOligos,
+ primerNameVector, barcodeNameVector, createGroup, allFiles, keepforward, keepFirst, removeLast,
+ qWindowStep, qWindowSize, qWindowAverage, qtrim, qThreshold, qAverage, qRollAverage, logtransform,
+ minLength, maxAmbig, maxHomoP, maxLength, flip, reorient, nameMap, nameCount);
+ pDataArray.push_back(tempTrim);
+
+ hThreadArray[h] = CreateThread(NULL, 0, MyTrimThreadFunction, pDataArray[h], 0, &dwThreadIdArray[h]);
+ }
+
+ //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();
+ }
+ vector<vector<string> > tempFASTAFileNames = fastaFileNames;
+ vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
+ vector<vector<string> > tempNameFileNames = nameFileNames;
+ if(allFiles){
+ ofstream temp;
+ string extension = toString(processors-1) + ".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();
+ }
+ }
+ }
+ }
+ }
+
+ 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"), (trimCountFileName + toString(processors-1) + ".temp"), (scrapCountFileName + toString(processors-1) + ".temp"), (groupFile + toString(processors-1) + ".temp"), tempFASTAFileNames, tempPrimerQualFileNames, tempNameFileNames, 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++){
+ if (pDataArray[i]->count != pDataArray[i]->lineEnd) {
+ m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->lineEnd) + " sequences assigned to it, quitting. \n"); m->control_pressed = true;
+ }
+ 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; }
+ }
+ for (map<string, string>::iterator it = pDataArray[i]->groupMap.begin(); it != pDataArray[i]->groupMap.end(); it++) {
+ map<string, string>::iterator it2 = groupMap.find(it->first);
+ if (it2 == groupMap.end()) { groupMap[it->first] = it->second; }
+ else { m->mothurOut("[ERROR]: " + it->first + " is in your fasta file more than once. Sequence names must be unique. please correct.\n"); }
+ }
+ 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((trimFile + toString(processIDS[i]) + ".temp"), trimFile);
- remove((trimFile + toString(processIDS[i]) + ".temp").c_str());
- m->appendFiles((scrapFile + toString(processIDS[i]) + ".temp"), scrapFile);
- remove((scrapFile + toString(processIDS[i]) + ".temp").c_str());
-
- m->mothurOut("Done with fasta files"); 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((trimQFile + toString(processIDS[i]) + ".temp"), trimQFile);
- remove((trimQFile + toString(processIDS[i]) + ".temp").c_str());
- m->appendFiles((scrapQFile + toString(processIDS[i]) + ".temp"), scrapQFile);
- remove((scrapQFile + toString(processIDS[i]) + ".temp").c_str());
+ 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"));
+ }
- m->mothurOut("Done with quality files"); m->mothurOutEndLine();
+ 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(countfile != ""){
+ m->appendFiles((trimCountFileName + toString(processIDS[i]) + ".temp"), trimCountFileName);
+ m->mothurRemove((trimCountFileName + toString(processIDS[i]) + ".temp"));
+ m->appendFiles((scrapCountFileName + toString(processIDS[i]) + ".temp"), scrapCountFileName);
+ m->mothurRemove((scrapCountFileName + toString(processIDS[i]) + ".temp"));
}
- m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
- remove((groupFile + toString(processIDS[i]) + ".temp").c_str());
+ if((createGroup)&&(countfile == "")){
+ m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
+ m->mothurRemove((groupFile + toString(processIDS[i]) + ".temp"));
+ }
- m->mothurOut("Done with group file"); m->mothurOutEndLine();
- for (int j = 0; j < fastaNames.size(); j++) {
- m->appendFiles((fastaNames[j] + toString(processIDS[i]) + ".temp"), fastaNames[j]);
- remove((fastaNames[j] + toString(processIDS[i]) + ".temp").c_str());
+ 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(qFileName != ""){
- for (int j = 0; j < qualNames.size(); j++) {
- m->appendFiles((qualNames[j] + toString(processIDS[i]) + ".temp"), qualNames[j]);
- remove((qualNames[j] + toString(processIDS[i]) + ".temp").c_str());
+ #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) {
+ for (int i = 0; i < tempNum; i++) {
+ int groupNum;
+ in >> group >> groupNum; m->gobble(in);
+
+ map<string, int>::iterator it = groupCounts.find(group);
+ if (it == groupCounts.end()) { groupCounts[group] = groupNum; }
+ else { groupCounts[it->first] += groupNum; }
+ }
+ }
+ in >> tempNum; m->gobble(in);
+ if (tempNum != 0) {
+ for (int i = 0; i < tempNum; i++) {
+ string group, seqName;
+ in >> seqName >> group; m->gobble(in);
+
+ map<string, string>::iterator it = groupMap.find(seqName);
+ if (it == groupMap.end()) { groupMap[seqName] = group; }
+ else { m->mothurOut("[ERROR]: " + seqName + " is in your fasta file more than once. Sequence names must be unique. please correct.\n"); }
+ }
}
+
+ in.close(); m->mothurRemove(tempFile);
}
-
- if (allFiles) { m->mothurOut("Done with allfiles"); m->mothurOutEndLine(); }
+ #endif
}
-
- return exitCommand;
-#endif
+
+ return exitCommand;
}
catch(exception& e) {
m->errorOut(e, "TrimSeqsCommand", "createProcessesCreateTrim");
/**************************************************************************************************/
-int TrimSeqsCommand::setLines(string filename, string qfilename, vector<unsigned long int>& fastaFilePos, vector<unsigned long int>& qfileFilePos) {
+int TrimSeqsCommand::setLines(string filename, string qfilename) {
try {
+
+ vector<unsigned long long> fastaFilePos;
+ vector<unsigned long long> qfileFilePos;
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//set file positions for fasta file
fastaFilePos = m->divideFile(filename, processors);
- if (qfilename == "") { return processors; }
-
//get name of first sequence in each chunk
map<string, int> firstSeqNames;
for (int i = 0; i < (fastaFilePos.size()-1); i++) {
in.close();
}
-
- //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 int 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 int size;
+ 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);
+
+ m->checkName(sname);
+
+ 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++) {
+ if (m->debug) { m->mothurOut("[DEBUG]: " + toString(i) +'\t' + toString(fastaFilePos[i]) + '\t' + toString(fastaFilePos[i+1]) + '\n'); }
+ 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
- //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);
- }
+ return processors;
- qfileFilePos.push_back(size);
+ #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));
+ if (qfilename != "") { qLines.push_back(linePair(qfileFilePos[startIndex], numSeqsPerProcessor)); }
+ }
+ }
+ if(qfilename == "") { qLines = lines; } //files with duds
+ return 1;
- return processors;
+ #endif
}
catch(exception& e) {
m->errorOut(e, "TrimSeqsCommand", "setLines");
//***************************************************************************************************************
-void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec, vector<string>& outQualVec){
+bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<vector<string> >& qualFileNames, vector<vector<string> >& nameFileNames){
try {
ifstream inOligos;
m->openInputFile(oligoFile, inOligos);
ofstream test;
- string type, oligo, group;
- int index=0;
- //int indexPrimer = 0;
+ string type, oligo, roligo, group;
+ bool hasPrimer = false; bool hasPairedBarcodes = false;
+
+ int indexPrimer = 0;
+ int indexBarcode = 0;
+ int indexPairedPrimer = 0;
+ int indexPairedBarcode = 0;
+ set<string> uniquePrimers;
+ set<string> uniqueBarcodes;
while(!inOligos.eof()){
- inOligos >> type; m->gobble(inOligos);
-
+
+ inOligos >> type;
+
+ if (m->debug) { m->mothurOut("[DEBUG]: reading type - " + type + ".\n"); }
+
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;
+
+ if (m->debug) { m->mothurOut("[DEBUG]: reading - " + oligo + ".\n"); }
for(int i=0;i<oligo.length();i++){
oligo[i] = toupper(oligo[i]);
// get rest of line in case there is a primer name
while (!inOligos.eof()) {
char c = inOligos.get();
- if (c == 10 || c == 13){ break; }
+ if (c == 10 || c == 13 || c == -1){ break; }
else if (c == 32 || c == 9){;} //space or tab
else { group += c; }
}
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]=index; index++;
- groupVector.push_back(group);
+ if (m->debug) { if (group != "") { m->mothurOut("[DEBUG]: reading group " + group + ".\n"); }else{ m->mothurOut("[DEBUG]: no group for primer " + oligo + ".\n"); } }
+
+ primers[oligo]=indexPrimer; indexPrimer++;
+ primerNameVector.push_back(group);
+ }
+ else if (type == "PRIMER"){
+ m->gobble(inOligos);
- if(allFiles){
- outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
- if(qFileName != ""){
- outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
- }
- if (group == "") { //if there is not a group for this primer, then this file will not get written to, but we add it to keep the indexes correct
- filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
- if(qFileName != ""){
- filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
- }
- }else {
- outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
- outputTypes["fasta"].push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
- if(qFileName != ""){
- outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
- outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
- }
- }
- }
+ inOligos >> roligo;
+
+ for(int i=0;i<roligo.length();i++){
+ roligo[i] = toupper(roligo[i]);
+ if(roligo[i] == 'U') { roligo[i] = 'T'; }
+ }
+ roligo = reverseOligo(roligo);
+
+ group = "";
+
+ // get rest of line in case there is a primer name
+ while (!inOligos.eof()) {
+ char c = inOligos.get();
+ if (c == 10 || c == 13 || c == -1){ break; }
+ else if (c == 32 || c == 9){;} //space or tab
+ else { group += c; }
+ }
+
+ oligosPair newPrimer(oligo, roligo);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: primer pair " + newPrimer.forward + " " + newPrimer.reverse + ", and group = " + group + ".\n"); }
- }
+ //check for repeat barcodes
+ string tempPair = oligo+roligo;
+ if (uniquePrimers.count(tempPair) != 0) { m->mothurOut("primer pair " + newPrimer.forward + " " + newPrimer.reverse + " is in your oligos file already."); m->mothurOutEndLine(); }
+ else { uniquePrimers.insert(tempPair); }
+
+ if (m->debug) { if (group != "") { m->mothurOut("[DEBUG]: reading group " + group + ".\n"); }else{ m->mothurOut("[DEBUG]: no group for primer pair " + newPrimer.forward + " " + newPrimer.reverse + ".\n"); } }
+
+ pairedPrimers[indexPairedPrimer]=newPrimer; indexPairedPrimer++;
+ primerNameVector.push_back(group);
+ hasPrimer = true;
+ }
else if(type == "REVERSE"){
- Sequence oligoRC("reverse", oligo);
- oligoRC.reverseComplement();
- revPrimer.push_back(oligoRC.getUnaligned());
+ //Sequence oligoRC("reverse", oligo);
+ //oligoRC.reverseComplement();
+ string oligoRC = reverseOligo(oligo);
+ revPrimer.push_back(oligoRC);
}
else if(type == "BARCODE"){
inOligos >> group;
+
+ //barcode lines can look like BARCODE atgcatgc groupName - for 454 seqs
+ //or BARCODE atgcatgc atgcatgc groupName - for illumina data that has forward and reverse info
+
+ string temp = "";
+ while (!inOligos.eof()) {
+ char c = inOligos.get();
+ if (c == 10 || c == 13 || c == -1){ break; }
+ else if (c == 32 || c == 9){;} //space or tab
+ else { temp += c; }
+ }
- //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]=index; index++;
- groupVector.push_back(group);
-
- if(allFiles){
- outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
- outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
- outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
- if(qFileName != ""){
- outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
- outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
- outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
- }
- }
-
- }else{ m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine(); }
+ //then this is illumina data with 4 columns
+ if (temp != "") {
+ hasPairedBarcodes = true;
+ string reverseBarcode = group; //reverseOligo(group); //reverse barcode
+ group = temp;
+
+ for(int i=0;i<reverseBarcode.length();i++){
+ reverseBarcode[i] = toupper(reverseBarcode[i]);
+ if(reverseBarcode[i] == 'U') { reverseBarcode[i] = 'T'; }
+ }
+
+ reverseBarcode = reverseOligo(reverseBarcode);
+ oligosPair newPair(oligo, reverseBarcode);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: barcode pair " + newPair.forward + " " + newPair.reverse + ", and group = " + group + ".\n"); }
+
+ //check for repeat barcodes
+ string tempPair = oligo+reverseBarcode;
+ if (uniqueBarcodes.count(tempPair) != 0) { m->mothurOut("barcode pair " + newPair.forward + " " + newPair.reverse + " is in your oligos file already, disregarding."); m->mothurOutEndLine(); }
+ else { uniqueBarcodes.insert(tempPair); }
+
+ pairedBarcodes[indexPairedBarcode]=newPair; indexPairedBarcode++;
+ barcodeNameVector.push_back(group);
+ }else {
+ //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("[WARNING]: " + type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine(); }
}
m->gobble(inOligos);
- }
-
+ }
inOligos.close();
+ if (hasPairedBarcodes || hasPrimer) {
+ pairedOligos = true;
+ if ((primers.size() != 0) || (barcodes.size() != 0) || (linker.size() != 0) || (spacer.size() != 0) || (revPrimer.size() != 0)) { m->control_pressed = true; m->mothurOut("[ERROR]: cannot mix paired primers and barcodes with non paired or linkers and spacers, quitting."); m->mothurOutEndLine(); return 0; }
+ }
+
+ if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0; }
+
//add in potential combos
- if(allFiles){
- comboStarts = outFASTAVec.size()-1;
- for (map<string, int>::iterator itBar = barcodes.begin(); itBar != barcodes.end(); itBar++) {
- for (map<string, int>::iterator itPrime = primers.begin(); itPrime != primers.end(); itPrime++) {
- if (groupVector[itPrime->second] != "") { //there is a group for this primer
- outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
- outputTypes["fasta"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
- outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
- combos[(groupVector[itBar->second] + "." + groupVector[itPrime->second])] = outFASTAVec.size()-1;
-
- if(qFileName != ""){
- outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
- outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
- outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
- }
- }
- }
- }
+ if(barcodeNameVector.size() == 0){
+ barcodes[""] = 0;
+ barcodeNameVector.push_back("");
}
- numFPrimers = primers.size();
- numRPrimers = revPrimer.size();
-
- }
- catch(exception& e) {
- m->errorOut(e, "TrimSeqsCommand", "getOligos");
- exit(1);
- }
-}
-//***************************************************************************************************************
-
-int TrimSeqsCommand::stripBarcode(Sequence& seq, QualityScores& qual, int& group){
- try {
-
- string rawSequence = seq.getUnaligned();
- int success = bdiffs + 1; //guilty until proven innocent
-
- //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 = bdiffs + 10; //if the sequence is shorter than the barcode then bail out
- break;
- }
-
- if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
- group = it->second;
- seq.setUnaligned(rawSequence.substr(oligo.length()));
-
- if(qual.getName() != ""){
- qual.trimQScores(oligo.length(), -1);
- }
-
- success = 0;
- break;
- }
+ if(primerNameVector.size() == 0){
+ primers[""] = 0;
+ primerNameVector.push_back("");
}
- //if you found the barcode or if you don't want to allow for diffs
-// cout << success;
- if ((bdiffs == 0) || (success == 0)) { return success; }
-
- else { //try aligning and see if you can find it
-// cout << endl;
-
- int maxLength = 0;
-
- Alignment* alignment;
- if (barcodes.size() > 0) {
- map<string,int>::iterator it=barcodes.begin();
-
- for(it;it!=barcodes.end();it++){
- if(it->first.length() > maxLength){
- maxLength = it->first.length();
- }
- }
- alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+bdiffs+1));
-
- }else{ alignment = NULL; }
-
- //can you find the barcode
- int minDiff = 1e6;
- int minCount = 1;
- int minGroup = -1;
- int minPos = 0;
-
- for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
- string oligo = it->first;
-// int length = oligo.length();
-
- if(rawSequence.length() < maxLength){ //let's just assume that the barcodes are the same length
- success = bdiffs + 10;
- break;
- }
-
- //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
- alignment->align(oligo, rawSequence.substr(0,oligo.length()+bdiffs));
- oligo = alignment->getSeqAAln();
- string temp = alignment->getSeqBAln();
-
- int alnLength = oligo.length();
-
- for(int i=oligo.length()-1;i>=0;i--){
- if(oligo[i] != '-'){ alnLength = i+1; break; }
- }
- oligo = oligo.substr(0,alnLength);
- temp = temp.substr(0,alnLength);
-
- int numDiff = countDiffs(oligo, temp);
-
-// cout << oligo << '\t' << temp << '\t' << numDiff << endl;
-
- if(numDiff < minDiff){
- minDiff = numDiff;
- minCount = 1;
- minGroup = it->second;
- minPos = 0;
- for(int i=0;i<alnLength;i++){
- if(temp[i] != '-'){
- minPos++;
- }
- }
- }
- else if(numDiff == minDiff){
- minCount++;
- }
-
- }
-
- if(minDiff > bdiffs) { success = minDiff; } //no good matches
- else if(minCount > 1) { success = bdiffs + 100; } //can't tell the difference between multiple barcodes
- else{ //use the best match
- group = minGroup;
- seq.setUnaligned(rawSequence.substr(minPos));
-
- if(qual.getName() != ""){
- qual.trimQScores(minPos, -1);
- }
- success = minDiff;
- }
-
- if (alignment != NULL) { delete alignment; }
-
+ fastaFileNames.resize(barcodeNameVector.size());
+ for(int i=0;i<fastaFileNames.size();i++){
+ fastaFileNames[i].assign(primerNameVector.size(), "");
}
-// cout << success << endl;
+ if(qFileName != "") { qualFileNames = fastaFileNames; }
+ if(nameFile != "") { nameFileNames = fastaFileNames; }
- return success;
+ if(allFiles){
+ set<string> uniqueNames; //used to cleanup outputFileNames
+ if (pairedOligos) {
+ for(map<int, oligosPair>::iterator itBar = pairedBarcodes.begin();itBar != pairedBarcodes.end();itBar++){
+ for(map<int, oligosPair>::iterator itPrimer = pairedPrimers.begin();itPrimer != pairedPrimers.end(); itPrimer++){
+
+ string primerName = primerNameVector[itPrimer->first];
+ string barcodeName = barcodeNameVector[itBar->first];
+
+ if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
+ else {
+ string comboGroupName = "";
+ string fastaFileName = "";
+ string qualFileName = "";
+ string nameFileName = "";
+ string countFileName = "";
+
+ if(primerName == ""){
+ comboGroupName = barcodeNameVector[itBar->first];
+ }
+ else{
+ if(barcodeName == ""){
+ comboGroupName = primerNameVector[itPrimer->first];
+ }
+ else{
+ comboGroupName = barcodeNameVector[itBar->first] + "." + primerNameVector[itPrimer->first];
+ }
+ }
+
+
+ ofstream temp;
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFile));
+ variables["[tag]"] = comboGroupName;
+ fastaFileName = getOutputFileName("fasta", variables);
+ if (uniqueNames.count(fastaFileName) == 0) {
+ outputNames.push_back(fastaFileName);
+ outputTypes["fasta"].push_back(fastaFileName);
+ uniqueNames.insert(fastaFileName);
+ }
+
+ fastaFileNames[itBar->first][itPrimer->first] = fastaFileName;
+ m->openOutputFile(fastaFileName, temp); temp.close();
+
+ if(qFileName != ""){
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(qFileName));
+ qualFileName = getOutputFileName("qfile", variables);
+ if (uniqueNames.count(qualFileName) == 0) {
+ outputNames.push_back(qualFileName);
+ outputTypes["qfile"].push_back(qualFileName);
+ }
+
+ qualFileNames[itBar->first][itPrimer->first] = qualFileName;
+ m->openOutputFile(qualFileName, temp); temp.close();
+ }
+
+ if(nameFile != ""){
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(nameFile));
+ nameFileName = getOutputFileName("name", variables);
+ if (uniqueNames.count(nameFileName) == 0) {
+ outputNames.push_back(nameFileName);
+ outputTypes["name"].push_back(nameFileName);
+ }
+
+ nameFileNames[itBar->first][itPrimer->first] = nameFileName;
+ m->openOutputFile(nameFileName, temp); temp.close();
+ }
+ }
+ }
+ }
+ }else {
+ 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];
+
+ if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
+ else {
+ string comboGroupName = "";
+ string fastaFileName = "";
+ string qualFileName = "";
+ string nameFileName = "";
+ string countFileName = "";
+
+ if(primerName == ""){
+ comboGroupName = barcodeNameVector[itBar->second];
+ }
+ else{
+ if(barcodeName == ""){
+ comboGroupName = primerNameVector[itPrimer->second];
+ }
+ else{
+ comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
+ }
+ }
+
+
+ ofstream temp;
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFile));
+ variables["[tag]"] = comboGroupName;
+ fastaFileName = getOutputFileName("fasta", variables);
+ 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 != ""){
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(qFileName));
+ qualFileName = getOutputFileName("qfile", variables);
+ 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 != ""){
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(nameFile));
+ nameFileName = getOutputFileName("name", variables);
+ 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();
+ if (pairedOligos) { numFPrimers = pairedPrimers.size(); }
+ numRPrimers = revPrimer.size();
+ numLinkers = linker.size();
+ numSpacers = spacer.size();
- }
- catch(exception& e) {
- m->errorOut(e, "TrimSeqsCommand", "stripBarcode");
- exit(1);
- }
-
-}
-
-//***************************************************************************************************************
-
-int TrimSeqsCommand::stripForward(Sequence& seq, QualityScores& qual, int& group){
- try {
- string rawSequence = seq.getUnaligned();
- int success = pdiffs + 1; //guilty until proven innocent
-
- //can you find the primer
- for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
- string oligo = it->first;
- if(rawSequence.length() < oligo.length()){ //let's just assume that the primers are the same length
- success = pdiffs + 10; //if the sequence is shorter than the barcode then bail out
- break;
- }
-
- if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
- group = it->second;
- seq.setUnaligned(rawSequence.substr(oligo.length()));
- if(qual.getName() != ""){
- qual.trimQScores(oligo.length(), -1);
- }
- success = 0;
+ bool allBlank = true;
+ for (int i = 0; i < barcodeNameVector.size(); i++) {
+ if (barcodeNameVector[i] != "") {
+ allBlank = false;
break;
}
}
-
- //if you found the barcode or if you don't want to allow for diffs
-// cout << success;
- if ((pdiffs == 0) || (success == 0)) { return success; }
-
- else { //try aligning and see if you can find it
-// cout << endl;
-
- int maxLength = 0;
-
- Alignment* alignment;
- if (primers.size() > 0) {
- map<string,int>::iterator it=primers.begin();
-
- for(it;it!=primers.end();it++){
- if(it->first.length() > maxLength){
- maxLength = it->first.length();
- }
- }
- alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+pdiffs+1));
-
- }else{ alignment = NULL; }
-
- //can you find the barcode
- int minDiff = 1e6;
- int minCount = 1;
- int minGroup = -1;
- int minPos = 0;
-
- for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
- string oligo = it->first;
-// int length = oligo.length();
-
- if(rawSequence.length() < maxLength){
- success = pdiffs + 100;
- break;
- }
-
- //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
- alignment->align(oligo, rawSequence.substr(0,oligo.length()+pdiffs));
- oligo = alignment->getSeqAAln();
- string temp = alignment->getSeqBAln();
-
- int alnLength = oligo.length();
-
- for(int i=oligo.length()-1;i>=0;i--){
- if(oligo[i] != '-'){ alnLength = i+1; break; }
- }
- oligo = oligo.substr(0,alnLength);
- temp = temp.substr(0,alnLength);
-
- int numDiff = countDiffs(oligo, temp);
-
-// cout << oligo << '\t' << temp << '\t' << numDiff << endl;
-
- if(numDiff < minDiff){
- minDiff = numDiff;
- minCount = 1;
- minGroup = it->second;
- minPos = 0;
- for(int i=0;i<alnLength;i++){
- if(temp[i] != '-'){
- minPos++;
- }
- }
- }
- else if(numDiff == minDiff){
- minCount++;
- }
-
+ for (int i = 0; i < primerNameVector.size(); i++) {
+ if (primerNameVector[i] != "") {
+ allBlank = false;
+ break;
}
+ }
- if(minDiff > pdiffs) { success = minDiff; } //no good matches
- else if(minCount > 1) { success = pdiffs + 10; } //can't tell the difference between multiple primers
- else{ //use the best match
- group = minGroup;
- seq.setUnaligned(rawSequence.substr(minPos));
- if(qual.getName() != ""){
- qual.trimQScores(minPos, -1);
- }
- success = minDiff;
- }
-
- 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;
-
- }
- catch(exception& e) {
- m->errorOut(e, "TrimSeqsCommand", "stripForward");
- exit(1);
- }
-}
-
-//***************************************************************************************************************
-
-bool TrimSeqsCommand::stripReverse(Sequence& seq, QualityScores& qual){
- try {
- string rawSequence = seq.getUnaligned();
- bool success = 0; //guilty until proven innocent
-
- 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()));
- if(qual.getName() != ""){
- qual.trimQScores(-1, rawSequence.length()-oligo.length());
- }
- success = 1;
- break;
- }
- }
- return success;
+ return true;
}
catch(exception& e) {
- m->errorOut(e, "TrimSeqsCommand", "stripReverse");
+ m->errorOut(e, "TrimSeqsCommand", "getOligos");
exit(1);
}
}
-
//***************************************************************************************************************
bool TrimSeqsCommand::keepFirstTrim(Sequence& sequence, QualityScores& qscores){
if(qscores.getName() != ""){
qscores.trimQScores(-1, keepFirst);
}
+
+// sequence.printSequence(cout);cout << endl;
+
sequence.trim(keepFirst);
+
+// sequence.printSequence(cout);cout << endl << endl;;
+
return success;
}
catch(exception& e) {
}
}
+//********************************************************************/
+string TrimSeqsCommand::reverseOligo(string oligo){
+ try {
+ 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", "reverseOligo");
+ 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);
- }
-
-}
-
-//***************************************************************************************************************
-
-int TrimSeqsCommand::countDiffs(string oligo, string seq){
- try {
-
- int length = oligo.length();
- int countDiffs = 0;
-
- 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' || 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++; }
- }
-
- }
-
- return countDiffs;
- }
- catch(exception& e) {
- m->errorOut(e, "TrimSeqsCommand", "countDiffs");
- exit(1);
- }
-
-}
-
//***************************************************************************************************************
projects / mothur.git / blobdiff