//**********************************************************************************************************************
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);
- CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pqfile);
- CommandParameter plarge("large", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(plarge);
- CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none","fasta",false,false); parameters.push_back(pfasta);
+ CommandParameter pflow("flow", "InputTypes", "", "", "none", "FNGLT", "none","flow",false,false); parameters.push_back(pflow);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none","name",false,false); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "FNGLT", "none","count",false,false); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "FNGLT", "none","group",false,false); parameters.push_back(pgroup);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none","taxonomy",false,false); parameters.push_back(ptaxonomy);
+ CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "FNGLT", "none","qfile",false,false); parameters.push_back(pqfile);
+ CommandParameter plarge("large", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(plarge);
+ CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
+ 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); }
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, flow or quality file.\n";
- helpString += "The sort.seqs command parameters are accnos, fasta, name, group, taxonomy, flow, 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, count, taxonomy, flow or quality file.\n";
+ helpString += "The sort.seqs command parameters are accnos, fasta, name, group, count, 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";
exit(1);
}
}
-
//**********************************************************************************************************************
-string SortSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string SortSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "fasta") { outputFileName = "sorted" + m->getExtension(inputName); }
- else if (type == "taxonomy") { outputFileName = "sorted" + m->getExtension(inputName); }
- else if (type == "name") { outputFileName = "sorted" + m->getExtension(inputName); }
- else if (type == "group") { outputFileName = "sorted" + m->getExtension(inputName); }
- else if (type == "flow") { outputFileName = "sorted" + m->getExtension(inputName); }
- else if (type == "qfile") { outputFileName = "sorted" + m->getExtension(inputName); }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "SortSeqsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],sorted,[extension]"; }
+ else if (type == "taxonomy") { pattern = "[filename],sorted,[extension]"; }
+ else if (type == "name") { pattern = "[filename],sorted,[extension]"; }
+ else if (type == "group") { pattern = "[filename],sorted,[extension]"; }
+ else if (type == "count") { pattern = "[filename],sorted,[extension]"; }
+ else if (type == "flow") { pattern = "[filename],sorted,[extension]"; }
+ else if (type == "qfile") { pattern = "[filename],sorted,[extension]"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SortSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
SortSeqsCommand::SortSeqsCommand(){
try {
outputTypes["fasta"] = tempOutNames;
outputTypes["taxonomy"] = tempOutNames;
outputTypes["name"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
outputTypes["group"] = tempOutNames;
outputTypes["qfile"] = tempOutNames;
outputTypes["flow"] = tempOutNames;
outputTypes["group"] = tempOutNames;
outputTypes["qfile"] = tempOutNames;
outputTypes["flow"] = tempOutNames;
+ outputTypes["count"] = 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["flow"] = 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; }
+ }
}
if (qualfile == "not open") { abort = true; }
else if (qualfile == "not found") { qualfile = ""; }
else { m->setQualFile(qualfile); }
+
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { countfile = ""; abort = true; }
+ else if (countfile == "not found") { countfile = ""; }
+ else { m->setCountTableFile(countfile); }
+
+ if ((namefile != "") && (countfile != "")) {
+ m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
+ }
+
+ if ((groupfile != "") && (countfile != "")) {
+ m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
+ }
string temp = validParameter.validFile(parameters, "large", false); if (temp == "not found") { temp = "f"; }
large = m->isTrue(temp);
- 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 == "") && (countfile == "") && (groupfile == "") && (taxfile == "") && (flowfile == "") && (qualfile == "")) { m->mothurOut("You must provide at least one of the following: fasta, name, group, count, taxonomy, flow or quality."); m->mothurOutEndLine(); abort = true; }
- if ((fastafile != "") && (namefile == "")) {
- vector<string> files; files.push_back(fastafile);
- parser.getNameFile(files);
- }
+ if (countfile == "") {
+ if ((fastafile != "") && (namefile == "")) {
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
+ }
}
}
if (qualfile != "") { readQual(); }
if (namefile != "") { readName(); }
if (groupfile != "") { readGroup(); }
+ if (countfile != "") { readCount(); }
if (taxfile != "") { readTax(); }
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
itTypes = outputTypes.find("flow");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFlowFile(current); }
- }
+ }
+
+ itTypes = outputTypes.find("count");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
+ }
}
return 0;
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
+ variables["[extension]"] = m->getExtension(fastafile);
+ string outputFileName = getOutputFileName("fasta", variables);
outputTypes["fasta"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(flowfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowfile)) + getOutputFileNameTag("flow", flowfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(flowfile));
+ variables["[extension]"] = m->getExtension(flowfile);
+ string outputFileName = getOutputFileName("flow", variables);
outputTypes["flow"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(qualfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(qualfile)) + getOutputFileNameTag("qfile", qualfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(qualfile));
+ variables["[extension]"] = m->getExtension(qualfile);
+ string outputFileName = getOutputFileName("qfile", variables);
outputTypes["qfile"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile));
+ variables["[extension]"] = m->getExtension(namefile);
+ string outputFileName = getOutputFileName("name", variables);
outputTypes["name"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;
exit(1);
}
}
-
+//**********************************************************************************************************************
+int SortSeqsCommand::readCount(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(countfile); }
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[extension]"] = m->getExtension(countfile);
+ string outputFileName = getOutputFileName("count", variables);
+ outputTypes["count"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(countfile, in);
+ string firstCol, rest;
+
+ 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(), "");
+
+ string headers = m->getline(in); m->gobble(in);
+
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ in >> firstCol; m->gobble(in);
+ rest = m->getline(in); m->gobble(in);
+
+ if (firstCol != "") {
+ map<string, int>::iterator it = names.find(firstCol);
+ if (it != names.end()) { //we found it, so put it in the vector in the right place.
+ seqs[it->second] = firstCol + '\t' + rest;
+ }else { //if we cant find it then add it to the end
+ names[firstCol] = seqs.size();
+ seqs.push_back((firstCol + '\t' + rest));
+ m->mothurOut(firstCol + " was not in the contained the file which determined the order, adding it to the end.\n");
+ }
+ }
+ }
+ in.close();
+
+ int count = 0;
+ out << headers << endl;
+ for (int i = 0; i < seqs.size(); i++) {
+ if (seqs[i] != "") { out << seqs[i] << endl; count++; }
+ }
+ out.close();
+
+ m->mothurOut("Ordered " + toString(count) + " sequences from " + countfile + ".\n");
+
+ }else { //read in file to fill names
+ int count = 0;
+
+ string headers = m->getline(in); m->gobble(in);
+ out << headers << endl;
+
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ in >> firstCol; m->gobble(in);
+ rest = m->getline(in); m->gobble(in);
+
+ if (firstCol != "") {
+ //if this name is in the accnos file
+ names[firstCol] = count;
+ count++;
+ out << firstCol << '\t' << rest << endl;
+ }
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ m->mothurOut("\nUsing " + countfile + " to determine the order. It contains " + toString(count) + " representative sequences.\n");
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SortSeqsCommand", "readCount");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
int SortSeqsCommand::readGroup(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
+ variables["[extension]"] = m->getExtension(groupfile);
+ string outputFileName = getOutputFileName("group", variables);
outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(taxfile));
+ variables["[extension]"] = m->getExtension(taxfile);
+ string outputFileName = getOutputFileName("taxonomy", variables);
+
outputTypes["taxonomy"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;
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