*/
#include "trimseqscommand.h"
+#include "needlemanoverlap.hpp"
+
+//**********************************************************************************************************************
+
+vector<string> TrimSeqsCommand::getValidParameters(){
+ 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)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimSeqsCommand", "getValidParameters");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+TrimSeqsCommand::TrimSeqsCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["qual"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+vector<string> TrimSeqsCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"fasta"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimSeqsCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+vector<string> TrimSeqsCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimSeqsCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//***************************************************************************************************************
-TrimSeqsCommand::TrimSeqsCommand(string option){
+TrimSeqsCommand::TrimSeqsCommand(string option) {
try {
abort = false;
+ comboStarts = 0;
//allow user to run help
if(option == "help") { help(); abort = true; }
else {
//valid paramters for this command
- string AlignArray[] = {"fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength", "qfile", "qthreshold", "qaverage", "allfiles"};
+ 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)));
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
+ map<string,string>::iterator it;
//check to make sure all parameters are valid for command
- for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["qual"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("fasta");
+ //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["fasta"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("oligos");
+ //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["oligos"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("qfile");
+ //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["qfile"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("group");
+ //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; }
+ }
+ }
+
+
//check for required parameters
fastaFile = validParameter.validFile(parameters, "fasta", true);
- if (fastaFile == "not found") { mothurOut("fasta is a required parameter for the screen.seqs command."); mothurOutEndLine(); abort = 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 the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
+ outputDir = "";
+ outputDir += m->hasPath(fastaFile); //if user entered a file with a path then preserve it
+ }
-
+
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
string temp;
temp = validParameter.validFile(parameters, "flip", false);
if (temp == "not found"){ flip = 0; }
- else if(isTrue(temp)) { flip = 1; }
+ else if(m->isTrue(temp)) { flip = 1; }
temp = validParameter.validFile(parameters, "oligos", true);
if (temp == "not found"){ oligoFile = ""; }
else if(temp == "not open"){ abort = true; }
else { oligoFile = temp; }
+ 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);
temp = validParameter.validFile(parameters, "maxlength", false); if (temp == "not found") { temp = "0"; }
convert(temp, maxLength);
+ temp = validParameter.validFile(parameters, "bdiffs", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, bdiffs);
+
+ temp = validParameter.validFile(parameters, "pdiffs", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, pdiffs);
+
+ temp = validParameter.validFile(parameters, "tdiffs", false); if (temp == "not found") { int tempTotal = pdiffs + bdiffs; temp = toString(tempTotal); }
+ convert(temp, tdiffs);
+
+ if(tdiffs == 0){ tdiffs = bdiffs + pdiffs; }
+
temp = validParameter.validFile(parameters, "qfile", true);
if (temp == "not found") { qFileName = ""; }
- else if(temp == "not open") { abort = 0; }
+ else if(temp == "not open") { abort = true; }
else { qFileName = temp; }
temp = validParameter.validFile(parameters, "qthreshold", false); if (temp == "not found") { temp = "0"; }
convert(temp, qThreshold);
+
+ temp = validParameter.validFile(parameters, "qtrim", false); if (temp == "not found") { temp = "F"; }
+ qtrim = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "rollaverage", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, qRollAverage);
+
+ temp = validParameter.validFile(parameters, "qwindowaverage", false);if (temp == "not found") { temp = "0"; }
+ convert(temp, qWindowAverage);
+
+ temp = validParameter.validFile(parameters, "qwindowsize", false); if (temp == "not found") { temp = "50"; }
+ convert(temp, qWindowSize);
+
+ temp = validParameter.validFile(parameters, "qstepsize", false); if (temp == "not found") { temp = "1"; }
+ convert(temp, qWindowStep);
temp = validParameter.validFile(parameters, "qaverage", false); if (temp == "not found") { temp = "0"; }
convert(temp, qAverage);
+
+ temp = validParameter.validFile(parameters, "keepfirst", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, keepFirst);
+
+ temp = validParameter.validFile(parameters, "removelast", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, removeLast);
temp = validParameter.validFile(parameters, "allfiles", false); if (temp == "not found") { temp = "F"; }
- allFiles = isTrue(temp);
+ allFiles = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; }
+ convert(temp, processors);
- if(allFiles && oligoFile == ""){
- mothurOut("You selected allfiles, but didn't enter an oligos file. Ignoring the allfiles request."); mothurOutEndLine();
+ 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((qAverage != 0 && qThreshold != 0) && qFileName == ""){
- mothurOut("You didn't provide a quality file name, quality criteria will be ignored."); mothurOutEndLine();
+ m->mothurOut("You didn't provide a quality file name, quality criteria will be ignored."); m->mothurOutEndLine();
qAverage=0;
qThreshold=0;
}
if(!flip && oligoFile=="" && !maxLength && !minLength && (maxAmbig==-1) && !maxHomoP && qFileName == ""){
- mothurOut("You didn't set any options... quiting command."); mothurOutEndLine();
+ m->mothurOut("You didn't set any options... quiting command."); m->mothurOutEndLine();
abort = true;
}
}
}
catch(exception& e) {
- errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
+ m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
exit(1);
}
}
+
//**********************************************************************************************************************
void TrimSeqsCommand::help(){
try {
- mothurOut("The trim.seqs command reads a fastaFile and creates .....\n");
- mothurOut("The trim.seqs command parameters are fasta, flip, oligos, maxambig, maxhomop, minlength and maxlength.\n");
- mothurOut("The fasta parameter is required.\n");
- mothurOut("The flip parameter .... The default is 0.\n");
- mothurOut("The oligos parameter .... The default is "".\n");
- mothurOut("The maxambig parameter .... The default is -1.\n");
- mothurOut("The maxhomop parameter .... The default is 0.\n");
- mothurOut("The minlength parameter .... The default is 0.\n");
- mothurOut("The maxlength parameter .... The default is 0.\n");
- mothurOut("The trim.seqs command should be in the following format: \n");
- mothurOut("trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig, \n");
- mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength) \n");
- mothurOut("Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
- mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
+ m->mothurOut("The trim.seqs command reads a fastaFile and creates .....\n");
+ m->mothurOut("The trim.seqs command parameters are fasta, flip, oligos, group, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim 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 .... The default is "".\n");
+ m->mothurOut("The maxambig parameter .... The default is -1.\n");
+ m->mothurOut("The maxhomop parameter .... The default is 0.\n");
+ m->mothurOut("The minlength parameter .... The default is 0.\n");
+ m->mothurOut("The maxlength parameter .... The default is 0.\n");
+ m->mothurOut("The 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 .....\n");
+ m->mothurOut("The qthreshold parameter .... The default is 0.\n");
+ m->mothurOut("The qaverage parameter .... The default is 0.\n");
+ m->mothurOut("The allfiles parameter .... The default is F.\n");
+ m->mothurOut("The qtrim parameter .... The default is F.\n");
+ m->mothurOut("The trim.seqs command should be in the following format: \n");
+ m->mothurOut("trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig, \n");
+ m->mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength) \n");
+ m->mothurOut("Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n");
+ m->mothurOut("For more details please check out the wiki http://www.mothur.org/wiki/Trim.seqs .\n\n");
}
catch(exception& e) {
- errorOut(e, "TrimSeqsCommand", "help");
+ m->errorOut(e, "TrimSeqsCommand", "help");
exit(1);
}
}
try{
if (abort == true) { return 0; }
+
+ 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";
+ outputNames.push_back(trimSeqFile); outputTypes["fasta"].push_back(trimSeqFile);
+ string scrapSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.fasta";
+ outputNames.push_back(scrapSeqFile); outputTypes["fasta"].push_back(scrapSeqFile);
+ string trimQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.qual";
+ string scrapQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.qual";
+ if (qFileName != "") { outputNames.push_back(trimQualFile); outputNames.push_back(scrapQualFile); outputTypes["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(oligoFile != ""){
+ outputNames.push_back(groupFile); outputTypes["group"].push_back(groupFile);
+ getOligos(fastaFileNames, qualFileNames);
+ }
- ifstream inFASTA;
- openInputFile(fastaFile, inFASTA);
+ vector<unsigned long int> fastaFilePos;
+ vector<unsigned long int> qFilePos;
+
+ setLines(fastaFile, qFileName, fastaFilePos, qFilePos);
+
+ 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;
+ }
+ while (!inFASTA.eof()) { char c = inFASTA.get(); if (c == 10 || c == 13){ break; } }
+ }
+ outGroups.close();
+ inFASTA.close();
+ }
+ }
+
+ for (set<string>::iterator itBlanks = blanks.begin(); itBlanks != blanks.end(); itBlanks++) { remove((*(itBlanks)).c_str()); }
+
+ 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()); }
+ }
+ }
+
+ 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++) { remove(outputNames[i].c_str()); }
+ return 0;
+ }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimSeqsCommand", "execute");
+ exit(1);
+ }
+}
+
+/**************************************************************************************/
+
+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) {
+
+ try {
ofstream outFASTA;
- string trimSeqFile = getRootName(fastaFile) + "trim.fasta";
- openOutputFile(trimSeqFile, outFASTA);
+ int able = m->openOutputFile(trimFile, outFASTA);
+
+ ofstream scrapFASTA;
+ m->openOutputFile(scrapFile, scrapFASTA);
+
+ ofstream outQual;
+ ofstream scrapQual;
+ if(qFileName != ""){
+ m->openOutputFile(trimQFile, outQual);
+ m->openOutputFile(scrapQFile, scrapQual);
+ }
ofstream outGroups;
- vector<ofstream*> fastaFileNames;
- if(oligoFile != ""){
- string groupFile = getRootName(fastaFile) + "groups";
- openOutputFile(groupFile, outGroups);
- getOligos(fastaFileNames);
+
+ if (oligoFile != "") {
+ m->openOutputFile(groupFile, outGroups);
}
- ofstream scrapFASTA;
- string scrapSeqFile = getRootName(fastaFile) + "scrap.fasta";
- openOutputFile(scrapSeqFile, scrapFASTA);
+ ifstream inFASTA;
+ m->openInputFile(filename, inFASTA);
+ inFASTA.seekg(line->start);
ifstream qFile;
- if(qFileName != "") { openInputFile(qFileName, qFile); }
+ if(qFileName != "") { m->openInputFile(qFileName, qFile); qFile.seekg(qline->start); }
- bool success;
- while(!inFASTA.eof()){
- Sequence currSeq(inFASTA);
- string origSeq = currSeq.getUnaligned();
- int group;
- string trashCode = "";
+ 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 != ""){
- if(qThreshold != 0) { success = stripQualThreshold(currSeq, qFile); }
- else if(qAverage != 0) { success = cullQualAverage(currSeq, qFile); }
- if(!success) { trashCode += 'q'; }
- }
- if(barcodes.size() != 0){
- success = stripBarcode(currSeq, group);
- if(!success){ trashCode += 'b'; }
- }
- if(numFPrimers != 0){
- success = stripForward(currSeq);
- if(!success){ trashCode += 'f'; }
- }
- if(numRPrimers != 0){
- success = stripReverse(currSeq);
- if(!success){ trashCode += 'r'; }
- }
- if(minLength > 0 || maxLength > 0){
- success = cullLength(currSeq);
- if(!success){ trashCode += 'l'; }
- }
- if(maxHomoP > 0){
- success = cullHomoP(currSeq);
- if(!success){ trashCode += 'h'; }
- }
- if(maxAmbig != -1){
- success = cullAmbigs(currSeq);
- if(!success){ trashCode += 'n'; }
+ bool done = false;
+ int count = 0;
+
+ while (!done) {
+
+ 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(flip){ currSeq.reverseComplement(); } // should go last
+ int success = 1;
- if(trashCode.length() == 0){
- currSeq.printSequence(outFASTA);
+
+ Sequence currSeq(inFASTA); m->gobble(inFASTA);
+
+ QualityScores currQual;
+ if(qFileName != ""){
+ currQual = QualityScores(qFile, currSeq.getNumBases()); m->gobble(qFile);
+ }
+
+ string origSeq = currSeq.getUnaligned();
+ if (origSeq != "") {
+ int groupBar, groupPrime;
+ string trashCode = "";
+ int currentSeqsDiffs = 0;
+
if(barcodes.size() != 0){
- outGroups << currSeq.getName() << '\t' << groupVector[group] << endl;
+ success = stripBarcode(currSeq, currQual, groupBar);
+ if(success > bdiffs) { trashCode += 'b'; }
+ else{ currentSeqsDiffs += success; }
+ }
+
+ if(numFPrimers != 0){
+ success = stripForward(currSeq, currQual, groupPrime);
+ if(success > pdiffs) { trashCode += 'f'; }
+ else{ currentSeqsDiffs += success; }
+ }
+
+ if (currentSeqsDiffs > tdiffs) { trashCode += 't'; }
+
+ if(numRPrimers != 0){
+ success = stripReverse(currSeq, currQual);
+ if(!success) { trashCode += 'r'; }
+ }
+
+ if(keepFirst != 0){
+ success = keepFirstTrim(currSeq, currQual);
+ }
+
+ if(removeLast != 0){
+ success = removeLastTrim(currSeq, currQual);
+ if(!success) { trashCode += 'l'; }
+ }
+
+
+ if(qFileName != ""){
+
+ if(qThreshold != 0) { success = currQual.stripQualThreshold(currSeq, qThreshold); }
+ else if(qAverage != 0) { success = currQual.cullQualAverage(currSeq, qAverage); }
+ else if(qRollAverage != 0) { success = currQual.stripQualRollingAverage(currSeq, qRollAverage); }
+ else if(qWindowAverage != 0){ success = currQual.stripQualWindowAverage(currSeq, qWindowStep, qWindowSize, qWindowAverage); }
+ else { success = 1; }
+
+// if (qtrim == 1 && (origSeq.length() != currSeq.getUnaligned().length())) {
+// success = 0; //if you don't want to trim and the sequence does not meet quality requirements, move to scrap
+// }
+
+ if(!success) { trashCode += 'q'; }
+ }
+
+ if(minLength > 0 || maxLength > 0){
+ success = cullLength(currSeq);
+ if(!success) { trashCode += 'l'; }
+ }
+ if(maxHomoP > 0){
+ success = cullHomoP(currSeq);
+ if(!success) { trashCode += 'h'; }
+ }
+ if(maxAmbig != -1){
+ success = cullAmbigs(currSeq);
+ if(!success) { trashCode += 'n'; }
+ }
+
+ if(flip){ // should go last
+ currSeq.reverseComplement();
+ currQual.flipQScores();
+ }
+
+ 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];
+ }
+ }
+ 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(allFiles){
- currSeq.printSequence(*fastaFileNames[group]);
+ 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();
+ }
+ }
}
}
+ else{
+ currSeq.setName(currSeq.getName() + '|' + trashCode);
+ currSeq.setUnaligned(origSeq);
+ currSeq.setAligned(origSeq);
+ currSeq.printSequence(scrapFASTA);
+ currQual.printQScores(scrapQual);
+ }
+ count++;
}
- else{
- currSeq.setName(currSeq.getName() + '|' + trashCode);
- currSeq.setUnaligned(origSeq);
- currSeq.printSequence(scrapFASTA);
- }
- gobble(inFASTA);
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ unsigned long int pos = inFASTA.tellg();
+ if ((pos == -1) || (pos >= line->end)) { break; }
+ #else
+ if (inFASTA.eof()) { break; }
+ #endif
+
+ //report progress
+ if((count) % 1000 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
+
}
+ //report progress
+ if((count) % 1000 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
+
+
inFASTA.close();
outFASTA.close();
scrapFASTA.close();
- outGroups.close();
- if(qFileName != "") { qFile.close(); }
+ if (oligoFile != "") { outGroups.close(); }
+ if(qFileName != "") { qFile.close(); scrapQual.close(); outQual.close(); }
- for(int i=0;i<fastaFileNames.size();i++){
- fastaFileNames[i]->close();
- delete fastaFileNames[i];
- }
+ return count;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string trimQFile, string scrapQFile, string groupFile, vector<string> fastaNames, vector<string> qualNames) {
+ try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ int process = 1;
+ int exitCommand = 1;
+ processIDS.clear();
- for(int i=0;i<fastaFileNames.size();i++){
- string seqName;
- openInputFile(getRootName(fastaFile) + groupVector[i] + ".fasta", inFASTA);
- ofstream outGroups;
- openOutputFile(getRootName(fastaFile) + groupVector[i] + ".groups", outGroups);
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
- while(!inFASTA.eof()){
- if(inFASTA.get() == '>'){
- inFASTA >> seqName;
- outGroups << seqName << '\t' << groupVector[i] << endl;
+ if (pid > 0) {
+ 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
+ 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();
+ }
}
- while (!inFASTA.eof()) { char c = inFASTA.get(); if (c == 10 || c == 13){ break; } }
+
+ 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]);
+ exit(0);
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
}
- outGroups.close();
- inFASTA.close();
}
+ //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();
+ }
+ }
- return 0;
+ driverCreateTrim(filename, qFileName, trimFile, scrapFile, trimQFile, scrapQFile, groupFile, fastaNames, qualNames, 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
+ 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();
+
+ 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->mothurOut("Done with quality files"); m->mothurOutEndLine();
+ }
+
+ m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
+ remove((groupFile + toString(processIDS[i]) + ".temp").c_str());
+
+ 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(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 (allFiles) { m->mothurOut("Done with allfiles"); m->mothurOutEndLine(); }
+ }
+
+ return exitCommand;
+#endif
}
catch(exception& e) {
- errorOut(e, "TrimSeqsCommand", "execute");
+ m->errorOut(e, "TrimSeqsCommand", "createProcessesCreateTrim");
exit(1);
}
}
+/**************************************************************************************************/
+
+int TrimSeqsCommand::setLines(string filename, string qfilename, vector<unsigned long int>& fastaFilePos, vector<unsigned long int>& qfileFilePos) {
+ try {
+
+ //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++) {
+ ifstream in;
+ m->openInputFile(filename, in);
+ in.seekg(fastaFilePos[i]);
+
+ Sequence temp(in);
+ firstSeqNames[temp.getName()] = 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;
+
+ //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);
+
+ return processors;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimSeqsCommand", "setLines");
+ exit(1);
+ }
+}
//***************************************************************************************************************
-void TrimSeqsCommand::getOligos(vector<ofstream*>& outFASTAVec){
+void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec, vector<string>& outQualVec){
try {
ifstream inOligos;
- openInputFile(oligoFile, inOligos);
+ m->openInputFile(oligoFile, inOligos);
ofstream test;
string type, oligo, group;
int index=0;
+ //int indexPrimer = 0;
while(!inOligos.eof()){
- inOligos >> type;
-
+ inOligos >> type; m->gobble(inOligos);
+
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
}
else{
+ //make type case insensitive
+ for(int i=0;i<type.length();i++){ type[i] = toupper(type[i]); }
+
inOligos >> oligo;
for(int i=0;i<oligo.length();i++){
if(oligo[i] == 'U') { oligo[i] = 'T'; }
}
- if(type == "forward"){
- forPrimer.push_back(oligo);
+ if(type == "FORWARD"){
+ group = "";
+
+ // get rest of line in case there is a primer name
+ while (!inOligos.eof()) {
+ char c = inOligos.get();
+ if (c == 10 || c == 13){ break; }
+ else if (c == 32 || c == 9){;} //space or tab
+ else { group += c; }
+ }
+
+ //check for repeat barcodes
+ map<string, int>::iterator itPrime = primers.find(oligo);
+ if (itPrime != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine(); }
+
+ primers[oligo]=index; index++;
+ groupVector.push_back(group);
+
+ 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"));
+ }
+ }
+ }
+
}
- else if(type == "reverse"){
- revPrimer.push_back(oligo);
+ else if(type == "REVERSE"){
+ Sequence oligoRC("reverse", oligo);
+ oligoRC.reverseComplement();
+ revPrimer.push_back(oligoRC.getUnaligned());
}
- else if(type == "barcode"){
+ else if(type == "BARCODE"){
inOligos >> group;
- barcodes[oligo]=index++;
- groupVector.push_back(group);
- if(allFiles){
- outFASTAVec.push_back(new ofstream((getRootName(fastaFile) + group + ".fasta").c_str(), ios::ate));
- }
- }
+ //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(); }
}
+ m->gobble(inOligos);
}
inOligos.close();
- numFPrimers = forPrimer.size();
+ //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"));
+ }
+ }
+ }
+ }
+ }
+
+ numFPrimers = primers.size();
numRPrimers = revPrimer.size();
}
catch(exception& e) {
- errorOut(e, "TrimSeqsCommand", "getOligos");
+ m->errorOut(e, "TrimSeqsCommand", "getOligos");
exit(1);
}
-
}
-
//***************************************************************************************************************
-bool TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
+int TrimSeqsCommand::stripBarcode(Sequence& seq, QualityScores& qual, int& group){
try {
+
string rawSequence = seq.getUnaligned();
- bool success = 0; //guilty until proven innocent
+ 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 = 0;
- break;
+ 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()));
- success = 1;
+
+ if(qual.getName() != ""){
+ qual.trimQScores(oligo.length(), -1);
+ }
+
+ success = 0;
break;
}
}
+
+ //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 newStart=0;
+ 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; }
+
+ }
+// cout << success << endl;
+
return success;
}
catch(exception& e) {
- errorOut(e, "TrimSeqsCommand", "stripBarcode");
+ m->errorOut(e, "TrimSeqsCommand", "stripBarcode");
exit(1);
}
//***************************************************************************************************************
-bool TrimSeqsCommand::stripForward(Sequence& seq){
+int TrimSeqsCommand::stripForward(Sequence& seq, QualityScores& qual, int& group){
try {
string rawSequence = seq.getUnaligned();
- bool success = 0; //guilty until proven innocent
+ int success = pdiffs + 1; //guilty until proven innocent
- for(int i=0;i<numFPrimers;i++){
- string oligo = forPrimer[i];
-
- if(rawSequence.length() < oligo.length()){
- success = 0;
- break;
+ //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()));
- success = 1;
+ if(qual.getName() != ""){
+ qual.trimQScores(oligo.length(), -1);
+ }
+ success = 0;
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; }
- 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 newStart=0;
+ 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 > 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; }
+
+ }
+
+ return success;
+
}
catch(exception& e) {
- errorOut(e, "TrimSeqsCommand", "stripForward");
+ m->errorOut(e, "TrimSeqsCommand", "stripForward");
exit(1);
}
}
//***************************************************************************************************************
-bool TrimSeqsCommand::stripReverse(Sequence& seq){
+bool TrimSeqsCommand::stripReverse(Sequence& seq, QualityScores& qual){
try {
string rawSequence = seq.getUnaligned();
bool success = 0; //guilty until proven innocent
}
if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
- seq.setUnaligned(rawSequence.substr(rawSequence.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;
}
}
catch(exception& e) {
- errorOut(e, "TrimSeqsCommand", "stripReverse");
+ m->errorOut(e, "TrimSeqsCommand", "stripReverse");
exit(1);
}
}
//***************************************************************************************************************
+bool TrimSeqsCommand::keepFirstTrim(Sequence& sequence, QualityScores& qscores){
+ try {
+ bool success = 1;
+ if(qscores.getName() != ""){
+ qscores.trimQScores(-1, keepFirst);
+ }
+ sequence.trim(keepFirst);
+ return success;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "keepFirstTrim", "countDiffs");
+ exit(1);
+ }
+
+}
+
+//***************************************************************************************************************
+
+bool TrimSeqsCommand::removeLastTrim(Sequence& sequence, QualityScores& qscores){
+ try {
+ bool success = 0;
+
+ int length = sequence.getNumBases() - removeLast;
+
+ if(length > 0){
+ if(qscores.getName() != ""){
+ qscores.trimQScores(-1, length);
+ }
+ sequence.trim(length);
+ success = 1;
+ }
+ else{
+ success = 0;
+ }
+
+ return success;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "removeLastTrim", "countDiffs");
+ exit(1);
+ }
+
+}
+
+//***************************************************************************************************************
+
bool TrimSeqsCommand::cullLength(Sequence& seq){
try {
}
catch(exception& e) {
- errorOut(e, "TrimSeqsCommand", "cullLength");
+ m->errorOut(e, "TrimSeqsCommand", "cullLength");
exit(1);
}
return success;
}
catch(exception& e) {
- errorOut(e, "TrimSeqsCommand", "cullHomoP");
+ m->errorOut(e, "TrimSeqsCommand", "cullHomoP");
exit(1);
}
return success;
}
catch(exception& e) {
- errorOut(e, "TrimSeqsCommand", "cullAmbigs");
+ m->errorOut(e, "TrimSeqsCommand", "cullAmbigs");
exit(1);
}
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; }
+ 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] == '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; }
+ if(success == 0) { break; }
}
else{
success = 1;
return success;
}
catch(exception& e) {
- errorOut(e, "TrimSeqsCommand", "compareDNASeq");
+ m->errorOut(e, "TrimSeqsCommand", "compareDNASeq");
exit(1);
}
//***************************************************************************************************************
-bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){
+int TrimSeqsCommand::countDiffs(string oligo, string seq){
try {
- string rawSequence = seq.getUnaligned();
- int seqLength = rawSequence.length();
- string name;
-
- qFile >> name;
- if (name.length() != 0) { if(name.substr(1) != seq.getName()) { mothurOut("sequence name mismatch btwn fasta and qual file"); mothurOutEndLine(); } }
- while (!qFile.eof()) { char c = qFile.get(); if (c == 10 || c == 13){ break; } }
-
- int score;
- int end = seqLength;
+
+ int length = oligo.length();
+ int countDiffs = 0;
- for(int i=0;i<seqLength;i++){
- qFile >> score;
-
- if(score <= qThreshold){
- end = i;
- break;
+ 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++; }
}
+
}
- for(int i=end+1;i<seqLength;i++){
- qFile >> score;
- }
-
- seq.setUnaligned(rawSequence.substr(0,end));
- return 1;
+ return countDiffs;
}
catch(exception& e) {
- errorOut(e, "TrimSeqsCommand", "stripQualThreshold");
+ m->errorOut(e, "TrimSeqsCommand", "countDiffs");
exit(1);
}
-}
-//***************************************************************************************************************
-
-bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){
- try {
- string rawSequence = seq.getUnaligned();
- int seqLength = seq.getNumBases();
- bool success = 0; //guilty until proven innocent
- string name;
-
- qFile >> name;
- if (name[0] == '>') { if(name.substr(1) != seq.getName()) { mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); mothurOutEndLine(); } }
-
- while (!qFile.eof()) { char c = qFile.get(); if (c == 10 || c == 13){ break; } }
-
- float score;
- float average = 0;
-
- for(int i=0;i<seqLength;i++){
- qFile >> score;
- average += score;
- }
- average /= seqLength;
-
- if(average >= qAverage) { success = 1; }
- else { success = 0; }
-
- return success;
- }
- catch(exception& e) {
- errorOut(e, "TrimSeqsCommand", "cullQualAverage");
- exit(1);
- }
}
//***************************************************************************************************************
projects / mothur.git / blobdiff