GCC_ENABLE_SSE42_EXTENSIONS = NO;
GCC_OPTIMIZATION_LEVEL = 3;
GCC_PREPROCESSOR_DEFINITIONS = (
- "MOTHUR_FILES=\"\\\"../../release\\\"\"",
- "VERSION=\"\\\"1.32.0\\\"\"",
- "RELEASE_DATE=\"\\\"10/31/2013\\\"\"",
+ "MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
+ "VERSION=\"\\\"1.33.0\\\"\"",
+ "RELEASE_DATE=\"\\\"2/7/2014\\\"\"",
);
GCC_VERSION = "";
"GCC_VERSION[arch=*]" = "";
}
/**************************************************************************************************/
+
/**************************************************************************************************/
#endif
+
+
try {
string pattern = "";
- if (type == "fit") { pattern = "[filename],[distance],mix.fit"; }
- else if (type == "relabund") { pattern = "[filename],[distance],[tag],mix.relabund"; }
- else if (type == "design") { pattern = "[filename],[distance],mix.design"; }
- else if (type == "matrix") { pattern = "[filename],[distance],[tag],mix.posterior"; }
- else if (type == "parameters") { pattern = "[filename],[distance],mix.parameters"; }
- else if (type == "summary") { pattern = "[filename],[distance],mix.summary"; }
+ if (type == "fit") { pattern = "[filename],[distance],[method],mix.fit"; }
+ else if (type == "relabund") { pattern = "[filename],[distance],[method],[tag],mix.relabund"; }
+ else if (type == "design") { pattern = "[filename],[distance],[method],mix.design"; }
+ else if (type == "matrix") { pattern = "[filename],[distance],[method],[tag],mix.posterior"; }
+ else if (type == "parameters") { pattern = "[filename],[distance],[method],mix.parameters"; }
+ else if (type == "summary") { pattern = "[filename],[distance],[method],mix.summary"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
variables["[distance]"] = thislookup[0]->getLabel();
+ variables["[method]"] = method;
string outputFileName = getOutputFileName("fit", variables);
outputNames.push_back(outputFileName); outputTypes["fit"].push_back(outputFileName);
map<string, string> variables;
variables["[filename]"] = v["[filename]"];
variables["[distance]"] = v["[distance]"];
+ variables["]method]"] = method;
variables["[tag]"] = "1";
string reference = getOutputFileName("relabund", variables);
m->openInputFile(reference, referenceFile); //((fileRoot + label + ".1mix.relabund").c_str());
else {
userGroups = "unique." + groups;
m->splitAtDash(groups, Groups);
+ if (Groups.size() > 4) { userGroups = "unique.selected_groups"; } //if too many groups then the filename becomes too big.
}
groups = validParameter.validFile(parameters, "sharedgroups", false);
else {
userGroups = groups;
m->splitAtDash(groups, Groups);
+ if (Groups.size() > 4) { userGroups = "selected_groups"; } //if too many groups then the filename becomes too big.
unique = false;
}
userGroups = "unique.";
for(int i = 0; i < Groups.size(); i++) { userGroups += Groups[i] + "-"; }
userGroups = userGroups.substr(0, userGroups.length()-1);
+ if (Groups.size() > 4) { userGroups = "unique.selected_groups"; } //if too many groups then the filename becomes too big.
}else{
//sanity check for group names
SharedUtil util;
userGroups = "unique.";
for(int i = 0; i < Groups.size(); i++) { userGroups += Groups[i] + "-"; }
userGroups = userGroups.substr(0, userGroups.length()-1);
+ if (Groups.size() > 4) { userGroups = "unique.selected_groups"; } //if too many groups then the filename becomes too big.
}else {
//sanity check for group names
SharedUtil util;
ifstream in;
string thisLabel;
m->openInputFile(filename, in);
+ m->saveNextLabel = "";
if(in){
string thisLabel;
fileHandle.clear();
fileHandle.seekg(0);
+ m->saveNextLabel = "";
if(fileHandle){
ifstream in;
string thisLabel;
m->openInputFile(filename, in);
+ m->saveNextLabel = "";
if(in){
if(in){
if((format == "list") || (format == "listorder")) {
-
+ m->saveNextLabel = "";
while (in.eof() != true) {
input = new ListVector(in);
}
}
else if (format == "shared") {
-
+ m->saveNextLabel = "";
while (in.eof() != true) {
input = new SharedListVector(in);
if(in){
if (format == "list") {
-
+ m->saveNextLabel = "";
while (in.eof() != true) {
input = new ListVector(in);
}
}
else if (format == "shared") {
-
+ m->saveNextLabel = "";
while (in.eof() != true) {
input = new SharedListVector(in);
if(in){
if (format == "list") {
+ m->saveNextLabel = "";
while (in.eof() != true) {
}
}
else if (format == "shared") {
+ m->saveNextLabel = "";
while (in.eof() != true) {
try {
CommandParameter psff("sff", "InputTypes", "", "", "sffFile", "sffFile", "none","sff",false,false); parameters.push_back(psff);
CommandParameter pfile("file", "InputTypes", "", "", "sffFile", "sffFile", "none","sff",false,false); parameters.push_back(pfile);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutput("output", "String", "", "", "", "", "","",false,true,true); parameters.push_back(poutput);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
string MergeSfffilesCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The merge.sfffiles command reads a sff set of files or a file containing a list of sff files and merges the individual files into a single sff file.\n";
- helpString += "The merge.sfffiles command parameters are sff and file. sff or file is required. \n";
+ helpString += "The merge.sfffiles command reads a sff file or a file containing a list of sff files and merges the individual files into a single sff file. \n";
+ helpString += "The merge.sfffiles command parameters are sff, file and output. sff or file is required. \n";
helpString += "The sff parameter allows you to enter the sff list of sff files separated by -'s.\n";
helpString += "The file parameter allows you to provide a file containing a list of sff files to merge. \n";
+ helpString += "The output parameter allows you to provide an output filename. \n";
helpString += "Example sffinfo(sff=mySffFile.sff-mySecond.sff).\n";
helpString += "Note: No spaces between parameter labels (i.e. sff), '=' and parameters (i.e.yourSffFileName).\n";
return helpString;
try {
string pattern = "";
- if (type == "sff") { pattern = "[filename],merge.sff"; }
+ if (type == "sff") { pattern = "[filename],"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
m->mothurOut("[ERROR]: cannot use file option and sff option at the same time, choose one."); m->mothurOutEndLine(); abort = true;
}
+ outputFile = validParameter.validFile(parameters, "output", false);
+ if (outputFile == "not found") { m->mothurOut("you must enter an output file name"); m->mothurOutEndLine(); abort=true; }
+ if (outputDir != "") { outputFile = outputDir + m->getSimpleName(outputFile); }
+
}
}
catch(exception& e) {
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- map<string, string> variables;
if (file != "") {
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(file); }
- variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(file));
readFile();
- }else {
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(filenames[0]); }
- variables["[filename]"] = thisOutputDir + "mergedSff";
+ if (outputDir == "") { outputDir = m->hasPath(file); }
}
ofstream out;
+ map<string, string> variables;
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(outputFile); }
+ variables["[filename]"] = thisOutputDir + m->getSimpleName(outputFile);
outputFile = getOutputFileName("sff",variables);
m->openOutputFile(outputFile, out);
outputNames.push_back(outputFile); outputTypes["sff"].push_back(outputFile);
*/
#include "otuhierarchycommand.h"
+#include "inputdata.h"
//**********************************************************************************************************************
vector<string> OtuHierarchyCommand::setParameters(){
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { m->mothurOut("label is a required parameter for the otu.hierarchy command."); m->mothurOutEndLine(); abort = true; }
else {
- m->splitAtDash(label, labels);
- if (labels.size() != 2) { m->mothurOut("You must provide 2 labels."); m->mothurOutEndLine(); abort = true; }
+ m->splitAtDash(label, mylabels);
+ if (mylabels.size() != 2) { m->mothurOut("You must provide 2 labels."); m->mothurOutEndLine(); abort = true; }
}
output = validParameter.validFile(parameters, "output", false); if (output == "not found") { output = "name"; }
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//get listvectors that correspond to labels requested, (or use smart distancing to get closest listvector)
- vector<ListVector> lists = getListVectors();
+ vector< vector<string> > lists = getListVectors();
if (m->control_pressed) { outputTypes.clear(); return 0; }
//determine which is little and which is big, putting little first
- if (lists.size() == 2) {
+ if (lists.size() == 4) {
//if big is first swap them
- if (lists[0].getNumBins() < lists[1].getNumBins()) {
- reverse(lists.begin(), lists.end());
+ if (lists[0].size() < lists[2].size()) {
+ vector< vector<string> > tempLists;
+ tempLists.push_back(lists[2]);
+ tempLists.push_back(lists[3]);
+ tempLists.push_back(lists[0]);
+ tempLists.push_back(lists[1]);
+ lists = tempLists;
+ string tempLabel = list2Label;
+ list2Label = list1Label;
+ list1Label = tempLabel;
}
}else{
m->mothurOut("error getting listvectors, unable to read 2 different vectors, check your label inputs."); m->mothurOutEndLine(); return 0;
//map sequences to bin number in the "little" otu
map<string, int> littleBins;
- vector<string> binLabels0 = lists[0].getLabels();
- for (int i = 0; i < lists[0].getNumBins(); i++) {
+ vector<string> binLabels0 = lists[0];
+ for (int i = 0; i < lists[0].size(); i++) {
if (m->control_pressed) { return 0; }
- string bin = lists[0].get(i);
+ string bin = lists[1][i];
vector<string> names; m->splitAtComma(bin, names);
for (int j = 0; j < names.size(); j++) { littleBins[names[j]] = i; }
}
ofstream out;
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listFile));
- variables["[distance1]"] = lists[0].getLabel();
+ variables["[distance1]"] = list1Label;
variables["[tag]"] = "-";
- variables["[distance2]"] = lists[1].getLabel();
+ variables["[distance2]"] = list2Label;
string outputFileName = getOutputFileName("otuheirarchy",variables);
m->openOutputFile(outputFileName, out);
//go through each bin in "big" otu and output the bins in "little" otu which created it
- vector<string> binLabels1 = lists[1].getLabels();
- for (int i = 0; i < lists[1].getNumBins(); i++) {
+ vector<string> binLabels1 = lists[2];
+ for (int i = 0; i < lists[2].size(); i++) {
if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(outputFileName); return 0; }
- string binnames = lists[1].get(i);
+ string binnames = lists[3][i];
vector<string> names; m->splitAtComma(binnames, names);
//output column 1
string col2 = "";
for (it = bins.begin(); it != bins.end(); it++) {
- if (output == "name") { col2 += lists[0].get(it->first) + "\t"; }
+ if (output == "name") { col2 += lists[1][it->first] + "\t"; }
else { col2 += binLabels0[it->first] + "\t"; }
}
//**********************************************************************************************************************
//returns a vector of listVectors where "little" vector is first
-vector<ListVector> OtuHierarchyCommand::getListVectors() {
+vector< vector<string> > OtuHierarchyCommand::getListVectors() { //return value [0] -> otulabelsFirstLabel [1] -> binsFirstLabel [2] -> otulabelsSecondLabel [3] -> binsSecondLabel
try {
-
- int pos; //to use in smart distancing, position of last read in file
- int lastPos;
- vector<ListVector> lists;
+ vector< vector<string> > lists;
+
+ int count = 0;
+ for (set<string>::iterator it = mylabels.begin(); it != mylabels.end(); it++) {
+ string realLabel;
+ vector< vector<string> > thisList = getListVector(*it, realLabel);
+
+ if (m->control_pressed) { return lists; }
+
+ for (int i = 0; i < thisList.size(); i++) { lists.push_back(thisList[i]); }
+
+ if (count == 0) { list1Label = realLabel; count++; }
+ else { list2Label = realLabel; }
+ }
+
+ return lists;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OtuHierarchyCommand", "getListVectors");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector< vector<string> > OtuHierarchyCommand::getListVector(string label, string& realLabel){ //return value [0] -> otulabels [1] -> bins
+ try {
+ vector< vector<string> > myList;
+
+ InputData input(listFile, "list");
+ ListVector* list = input.getListVector();
+ string lastLabel = list->getLabel();
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> labels; labels.insert(label);
set<string> processedLabels;
set<string> userLabels = labels;
-
- //open file
- ifstream in;
- m->openInputFile(listFile, in);
-
- //get first list vector in file
- ListVector* list = NULL;
- string lastLabel = "";
- if (!in.eof()) {
- pos = in.tellg();
- lastPos = pos;
- list = new ListVector(in);
- m->gobble(in);
- lastLabel = list->getLabel();
- }
-
- while ((list != NULL) && (userLabels.size() != 0)) {
- if (m->control_pressed) { in.close(); delete list; return lists; }
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((list != NULL) && (userLabels.size() != 0)) {
+ if (m->control_pressed) { return myList; }
- //is this a listvector that we want?
if(labels.count(list->getLabel()) == 1){
-
- //make copy of listvector
- ListVector temp(*list);
- lists.push_back(temp);
-
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
+ break;
}
-
- //you have a label the user want that is smaller than this label and the last label has not already been processed
+
if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = list->getLabel();
- int savePos = in.tellg();
- //get smart distance line
delete list;
- in.seekg(lastPos);
- if (!in.eof()) {
- list = new ListVector(in);
- }else { list = NULL; }
+ list = input.getListVector(lastLabel);
- //make copy of listvector
- ListVector temp(*list);
- lists.push_back(temp);
-
processedLabels.insert(list->getLabel());
- userLabels.erase(list->getLabel());
-
+ userLabels.erase(list->getLabel());
+
//restore real lastlabel to save below
- list->setLabel(saveLabel);
- in.seekg(savePos);
+ //list->setLabel(saveLabel);
+ break;
}
lastLabel = list->getLabel();
- lastPos = pos;
- //get next line
+ //get next line to process
+ //prevent memory leak
delete list;
- if (!in.eof()) {
- pos = in.tellg();
- list = new ListVector(in);
- m->gobble(in);
- }else { list = NULL; }
+ list = input.getListVector();
}
- if (m->control_pressed) { in.close(); return lists; }
+
+ if (m->control_pressed) { return myList; }
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
- for (it = userLabels.begin(); it != userLabels.end(); it++) {
- m->mothurOut("Your file does not include the label " + *it);
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}
}
- if (m->control_pressed) { in.close(); return lists; }
-
//run last label if you need to
if (needToRun == true) {
- if (list != NULL) { delete list; }
-
- in.seekg(lastPos);
- if (!in.eof()) {
- list = new ListVector(in);
-
- //make copy of listvector
- ListVector temp(*list);
- lists.push_back(temp);
-
- delete list;
- }
+ delete list;
+ list = input.getListVector(lastLabel);
}
- in.close();
- return lists;
+ //at this point the list vector has the right distance
+ myList.push_back(list->getLabels());
+ vector<string> bins;
+ for (int i = 0; i < list->getNumBins(); i++) {
+ if (m->control_pressed) { return myList; }
+ bins.push_back(list->get(i));
+ }
+ myList.push_back(bins);
+ realLabel = list->getLabel();
+
+ delete list;
+
+ return myList;
}
catch(exception& e) {
- m->errorOut(e, "OtuHierarchyCommand", "getListVectors");
+ m->errorOut(e, "OtuHierarchyCommand", "getListVector");
exit(1);
}
}
private:
bool abort;
- set<string> labels; //holds labels to be used
- string label, listFile, outputDir, output;
+ set<string> mylabels; //holds labels to be used
+ string label, listFile, outputDir, output, list1Label, list2Label;
vector<string> outputNames;
- vector<ListVector> getListVectors();
+ vector< vector<string> > getListVectors();
+ vector< vector<string> > getListVector(string, string&);
};
temp = validParameter.validFile(parameters, "nseqs", false); if (temp == "not found"){ temp = "f"; }
nseqs = m->isTrue(temp);
- temp = validParameter.validFile(parameters, "permute", false); if (temp == "not found"){ temp = "4"; }
+ temp = validParameter.validFile(parameters, "permute", false);
+ if (temp == "not found"){ temp = "4"; }
+ else {
+ if ((temp == "1") || (temp == "2") || (temp == "3") || (temp == "4")) {}
+ else {
+ bool permTrue = m->isTrue(temp);
+ if (permTrue) { temp = "4"; }
+ else { }
+ }
+ }
m->mothurConvert(temp, perm);
if ((perm == 1) || (perm == 2) || (perm == 3) || (perm == 4)) { }
- else { m->mothurOut("[ERROR]: Not a valid permute value. Valid values are 1, 2, 3, and 4."); m->mothurOutEndLine(); abort = true; }
+ else { m->mothurOut("[ERROR]: Not a valid permute value. Valid values are 1, 2, 3, 4 and true."); m->mothurOutEndLine(); abort = true; }
temp = validParameter.validFile(parameters, "sharedotus", false); if (temp == "not found"){ temp = "t"; }
sharedOtus = m->isTrue(temp);
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