vector<string> SortSeqsCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
+ CommandParameter pflow("flow", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pflow);
CommandParameter pname("name", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pname);
CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pgroup);
CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy);
string SortSeqsCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The sort.seqs command puts the sequences in the same order for the following file types: accnos fasta, name, group, taxonomy or quality file.\n";
- helpString += "The sort.seqs command parameters are accnos, fasta, name, group, taxonomy, qfile and large.\n";
+ helpString += "The sort.seqs command puts the sequences in the same order for the following file types: accnos fasta, name, group, taxonomy, flow or quality file.\n";
+ helpString += "The sort.seqs command parameters are accnos, fasta, name, group, taxonomy, flow, qfile and large.\n";
helpString += "The accnos file allows you to specify the order you want the files in. If none is provided, mothur will use the order of the first file it reads.\n";
helpString += "The large parameters is used to indicate your files are too large to fit in RAM.\n";
helpString += "The sort.seqs command should be in the following format: sort.seqs(fasta=yourFasta).\n";
outputTypes["name"] = tempOutNames;
outputTypes["group"] = tempOutNames;
outputTypes["qfile"] = tempOutNames;
+ outputTypes["flow"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "SortSeqsCommand", "SortSeqsCommand");
outputTypes["name"] = tempOutNames;
outputTypes["group"] = tempOutNames;
outputTypes["qfile"] = tempOutNames;
+ outputTypes["flow"] = tempOutNames;
//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 = ""; }
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["accnos"] = inputDir + it->second; }
}
+
+ it = parameters.find("flow");
+ //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["flow"] = inputDir + it->second; }
+ }
}
else if (fastafile == "not found") { fastafile = ""; }
else { m->setFastaFile(fastafile); }
+ flowfile = validParameter.validFile(parameters, "flow", true);
+ if (flowfile == "not open") { flowfile = ""; abort = true; }
+ else if (flowfile == "not found") { flowfile = ""; }
+ else { m->setFlowFile(flowfile); }
+
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { namefile = ""; abort = true; }
else if (namefile == "not found") { namefile = ""; }
string temp = validParameter.validFile(parameters, "large", false); if (temp == "not found") { temp = "f"; }
large = m->isTrue(temp);
- if ((fastafile == "") && (namefile == "") && (groupfile == "") && (taxfile == "") && (qualfile == "")) { m->mothurOut("You must provide at least one of the following: fasta, name, group, taxonomy or quality."); m->mothurOutEndLine(); abort = true; }
+ if ((fastafile == "") && (namefile == "") && (groupfile == "") && (taxfile == "") && (flowfile == "") && (qualfile == "")) { m->mothurOut("You must provide at least one of the following: fasta, name, group, taxonomy, flow or quality."); m->mothurOutEndLine(); abort = true; }
if ((fastafile != "") && (namefile == "")) {
vector<string> files; files.push_back(fastafile);
//read through the correct file and output lines you want to keep
if (accnosfile != "") { readAccnos(); }
if (fastafile != "") { readFasta(); }
+ if (flowfile != "") { readFlow(); }
if (qualfile != "") { readQual(); }
if (namefile != "") { readName(); }
if (groupfile != "") { readGroup(); }
itTypes = outputTypes.find("qfile");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
- }
+ }
+
+ itTypes = outputTypes.find("flow");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFlowFile(current); }
+ }
}
return 0;
int times = 0;
vector<Sequence> seqs; seqs.resize(size);
+ for (int i = 0; i < seqs.size(); i++) { seqs[i].setName(""); } //this is so if some of the seqs are missing we dont print out garbage
while (numLeft > 0) {
if (numLeft < seqs.size()) { output = numLeft; }
for (int i = 0; i < output; i++) {
- seqs[i].printSequence(out2);
+ if (seqs[i].getName() != "") { seqs[i].printSequence(out2); }
}
out2.close();
}else {
vector<Sequence> seqs; seqs.resize(names.size());
+ for (int i = 0; i < seqs.size(); i++) { seqs[i].setName(""); } //this is so if some of the seqs are missing we dont print out garbage
while(!in.eof()){
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
}
in.close();
+ int count = 0;
for (int i = 0; i < seqs.size(); i++) {
- seqs[i].printSequence(out);
+ if (seqs[i].getName() != "") {
+ seqs[i].printSequence(out); count++;
+ }
}
out.close();
- m->mothurOut("Ordered " + toString(seqs.size()) + " sequences from " + fastafile + ".\n");
+ m->mothurOut("Ordered " + toString(count) + " sequences from " + fastafile + ".\n");
}
}else { //read in file to fill names
exit(1);
}
}
+//**********************************************************************************************************************
+int SortSeqsCommand::readFlow(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(flowfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowfile)) + "sorted" + m->getExtension(flowfile);
+ outputTypes["flow"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(flowfile, in);
+ int numFlows;
+ string name;
+
+ in >> numFlows; m->gobble(in);
+
+ if (names.size() != 0) {//this is not the first file we are reading so we need to use the order we already have
+
+ if (large) { //if the file is too large to fit in memory we can still process it, but the io will be very time consuming.
+ //read through the file looking for 1000 seqs at a time. Once we find them output them and start looking for the next 1000.
+ //this way we only store 1000 seqs in memory at a time.
+
+ int numNames = names.size();
+ int numNamesInFile = 0;
+
+ //to make sure we dont miss any seqs, add any seqs that are not in names but in the file to the end of names
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ in >> name;
+ string rest = m->getline(in);
+
+ if (name != "") {
+ numNamesInFile++;
+ map<string, int>::iterator it = names.find(name);
+ if (it == names.end()) {
+ names[name] = numNames; numNames++;
+ m->mothurOut(name + " was not in the contained the file which determined the order, adding it to the end.\n");
+ }
+ }
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ int numLeft = names.size();
+ if (numNamesInFile < numLeft) { numLeft = numNamesInFile; }
+
+ int size = 1000; //assume that user can hold 1000 seqs in memory
+ if (numLeft < size) { size = numLeft; }
+ int times = 0;
+
+ vector<string> seqs; seqs.resize(size, "");
+
+ while (numLeft > 0) {
+
+ ifstream in2;
+ m->openInputFile(flowfile, in2); in2 >> numFlows; m->gobble(in2);
+
+ if (m->control_pressed) { in2.close(); m->mothurRemove(outputFileName); return 0; }
+
+ int found = 0;
+ int needToFind = size;
+ if (numLeft < size) { needToFind = numLeft; }
+
+ while(!in2.eof()){
+ if (m->control_pressed) { in2.close(); m->mothurRemove(outputFileName); return 0; }
+
+ //stop reading if we already found the seqs we are looking for
+ if (found >= needToFind) { break; }
+
+ in2 >> name;
+ string rest = m->getline(in2);
+
+ if (name != "") {
+ map<string, int>::iterator it = names.find(name);
+ if (it != names.end()) { //we found it, so put it in the vector in the right place.
+ //is it in the set of seqs we are looking for this time around
+ int thisSeqsPlace = it->second;
+ thisSeqsPlace -= (times * size);
+ if ((thisSeqsPlace < size) && (thisSeqsPlace >= 0)) {
+ seqs[thisSeqsPlace] = (name +'\t' + rest);
+ found++;
+ }
+ }else { m->mothurOut("[ERROR]: in logic of readFlow function.\n"); m->control_pressed = true; }
+ }
+ m->gobble(in2);
+ }
+ in2.close();
+
+ ofstream out2;
+ m->openOutputFileAppend(outputFileName, out2);
+
+ int output = seqs.size();
+ if (numLeft < seqs.size()) { output = numLeft; }
+
+ for (int i = 0; i < output; i++) {
+ if (seqs[i] != "") {
+ out2 << seqs[i] << endl;
+ }
+ }
+ out2.close();
+
+ times++;
+ numLeft -= output;
+ }
+
+ m->mothurOut("Ordered " + toString(numNamesInFile) + " flows from " + flowfile + ".\n");
+ }else {
+
+ vector<string> seqs; seqs.resize(names.size(), "");
+
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ in >> name;
+ string rest = m->getline(in);
+
+ if (name != "") {
+ map<string, int>::iterator it = names.find(name);
+ if (it != names.end()) { //we found it, so put it in the vector in the right place.
+ seqs[it->second] = (name + '\t' + rest);
+ }else { //if we cant find it then add it to the end
+ names[name] = seqs.size();
+ seqs.push_back((name + '\t' + rest));
+ m->mothurOut(name + " was not in the contained the file which determined the order, adding it to the end.\n");
+ }
+ }
+ m->gobble(in);
+ }
+ in.close();
+
+ int count = 0;
+ for (int i = 0; i < seqs.size(); i++) {
+ if (seqs[i] != "") {
+ out << seqs[i] << endl;
+ count++;
+ }
+ }
+ out.close();
+
+ m->mothurOut("Ordered " + toString(count) + " flows from " + flowfile + ".\n");
+ }
+
+ }else { //read in file to fill names
+ int count = 0;
+
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ in >> name;
+ string rest = m->getline(in);
+
+ if (name != "") {
+ //if this name is in the accnos file
+ names[name] = count;
+ count++;
+ out << name << '\t' << rest << endl;
+ }
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ m->mothurOut("\nUsing " + flowfile + " to determine the order. It contains " + toString(count) + " flows.\n");
+ }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SortSeqsCommand", "readFlow");
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
int SortSeqsCommand::readQual(){
try {
vector<QualityScores> seqs; seqs.resize(size);
+ for (int i = 0; i < seqs.size(); i++) { seqs[i].setName(""); } //this is so if some of the seqs are missing we dont print out garbage
while (numLeft > 0) {
if (numLeft < seqs.size()) { output = numLeft; }
for (int i = 0; i < output; i++) {
- seqs[i].printQScores(out2);
+ if (seqs[i].getName() != "") {
+ seqs[i].printQScores(out2);
+ }
}
out2.close();
}else {
vector<QualityScores> seqs; seqs.resize(names.size());
+ for (int i = 0; i < seqs.size(); i++) { seqs[i].setName(""); } //this is so if some of the seqs are missing we dont print out garbage
while(!in.eof()){
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
}
in.close();
+ int count = 0;
for (int i = 0; i < seqs.size(); i++) {
- seqs[i].printQScores(out);
+ if (seqs[i].getName() != "") { seqs[i].printQScores(out); count++; }
}
out.close();
- m->mothurOut("Ordered " + toString(seqs.size()) + " sequences from " + qualfile + ".\n");
+ m->mothurOut("Ordered " + toString(count) + " sequences from " + qualfile + ".\n");
}
}else { //read in file to fill names
if (names.size() != 0) {//this is not the first file we are reading so we need to use the order we already have
- vector<string> seqs; seqs.resize(names.size());
+ vector<string> seqs; seqs.resize(names.size(), "");
while(!in.eof()){
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
}
in.close();
+ int count = 0;
for (int i = 0; i < seqs.size(); i++) {
- out << seqs[i] << endl;
+ if (seqs[i] != "") { out << seqs[i] << endl; count++; }
}
out.close();
- m->mothurOut("Ordered " + toString(seqs.size()) + " sequences from " + namefile + ".\n");
+ m->mothurOut("Ordered " + toString(count) + " sequences from " + namefile + ".\n");
}else { //read in file to fill names
int count = 0;
if (names.size() != 0) {//this is not the first file we are reading so we need to use the order we already have
- vector<string> seqs; seqs.resize(names.size());
+ vector<string> seqs; seqs.resize(names.size(), "");
while(!in.eof()){
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
}
in.close();
+ int count = 0;
for (int i = 0; i < seqs.size(); i++) {
- out << seqs[i] << endl;
+ if (seqs[i] != "") { out << seqs[i] << endl; count++; }
}
out.close();
- m->mothurOut("Ordered " + toString(seqs.size()) + " sequences from " + groupfile + ".\n");
+ m->mothurOut("Ordered " + toString(count) + " sequences from " + groupfile + ".\n");
}else { //read in file to fill names
int count = 0;
if (names.size() != 0) {//this is not the first file we are reading so we need to use the order we already have
- vector<string> seqs; seqs.resize(names.size());
+ vector<string> seqs; seqs.resize(names.size(), "");
while(!in.eof()){
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
}
in.close();
+ int count = 0;
for (int i = 0; i < seqs.size(); i++) {
- out << seqs[i] << endl;
+ if (seqs[i] != "") { out << seqs[i] << endl; count++; }
}
out.close();
- m->mothurOut("Ordered " + toString(seqs.size()) + " sequences from " + taxfile + ".\n");
+ m->mothurOut("Ordered " + toString(count) + " sequences from " + taxfile + ".\n");
}else { //read in file to fill names
int count = 0;
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