*/
#include "subsamplecommand.h"
+#include "sharedutilities.h"
//**********************************************************************************************************************
vector<string> SubSampleCommand::getValidParameters(){
if ((groupfile != "") && ((fastafile == "") && (listfile == ""))) {
m->mothurOut("Group file only valid with listfile or fastafile."); m->mothurOutEndLine(); abort = true; }
+ if ((groupfile != "") && ((fastafile != "") && (listfile != ""))) {
+ m->mothurOut("A new group file can only be made from the subsample of a listfile or fastafile, not both. Please correct."); m->mothurOutEndLine(); abort = true; }
+
}
}
if (abort == true) { return 0; }
if (sharedfile != "") { getSubSampleShared(); }
- //if (listfile != "") { getSubSampleList(); }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); return 0; } }
+ if (listfile != "") { getSubSampleList(); }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); return 0; } }
//if (rabund != "") { getSubSampleRabund(); }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); return 0; } }
//if (sabundfile != "") { getSubSampleSabund(); }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); return 0; } }
//if (fastafile != "") { getSubSampleFasta(); }
+ 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();
InputData* input = new InputData(sharedfile, "sharedfile");
vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
string lastLabel = lookup[0]->getLabel();
-
+
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
set<string> userLabels = labels;
-
-
+
+
//as long as you are not at the end of the file or done wih the lines you want
while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (m->control_pressed) { out.close(); return 0; }
-
+ if (m->control_pressed) { delete input; out.close(); return 0; }
+
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
-
+
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
processShared(lookup, out);
-
+
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
}
if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = lookup[0]->getLabel();
-
+
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
-
+
lookup = input->getSharedRAbundVectors(lastLabel);
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
lastLabel = lookup[0]->getLabel();
//prevent memory leak
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
-
+
//get next line to process
lookup = input->getSharedRAbundVectors();
}
if (m->control_pressed) { out.close(); return 0; }
-
+
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
-
+
//run last label if you need to
if (needToRun == true) {
for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
-
+
+ delete input;
out.close();
-
+
return 0;
-
+
}
catch(exception& e) {
m->errorOut(e, "SubSampleCommand", "getSubSampleShared");
int SubSampleCommand::processShared(vector<SharedRAbundVector*>& thislookup, ofstream& out) {
try {
- if (pickedGroups) { eliminateZeroOTUS(thislookup); }
+ //if (pickedGroups) { eliminateZeroOTUS(thislookup); }
if (size == 0) { //user has not set size, set size = smallest samples size
size = thislookup[0]->getNumSeqs();
int numBins = thislookup[0]->getNumBins();
for (int i = 0; i < thislookup.size(); i++) {
int thisSize = thislookup[i]->getNumSeqs();
-
+
if (thisSize != size) {
string thisgroup = thislookup[i]->getGroup();
-
+
OrderVector* order = new OrderVector();
for(int p=0;p<numBins;p++){
for(int j=0;j<thislookup[i]->getAbundance(p);j++){
for (int j = 0; j < size; j++) {
+
+ if (m->control_pressed) { delete order; return 0; }
+
//get random number to sample from order between 0 and thisSize-1.
int myrand = (int)((float)(rand()) / (RAND_MAX / (thisSize-1) + 1));
//subsampling may have created some otus with no sequences in them
eliminateZeroOTUS(thislookup);
+ if (m->control_pressed) { return 0; }
+
for (int i = 0; i < thislookup.size(); i++) {
out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
thislookup[i]->print(out);
}
catch(exception& e) {
- m->errorOut(e, "SubSampleCommand", "eliminateZeroOTUS");
+ m->errorOut(e, "SubSampleCommand", "processShared");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int SubSampleCommand::getSubSampleList() {
+ try {
+
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "subsample" + m->getExtension(listfile);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ InputData* input;
+ //if you have a groupfile you want to read a shared list
+ if (groupfile != "") {
+
+ GroupMap* groupMap = new GroupMap(groupfile);
+ groupMap->readMap();
+
+ //takes care of user setting groupNames that are invalid or setting groups=all
+ SharedUtil* util = new SharedUtil();
+ util->setGroups(Groups, groupMap->namesOfGroups);
+ delete util;
+
+ //create outputfiles
+ string groupOutputDir = outputDir;
+ if (outputDir == "") { groupOutputDir += m->hasPath(groupfile); }
+ string groupOutputFileName = groupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "subsample" + m->getExtension(groupfile);
+
+ ofstream outGroup;
+ m->openOutputFile(groupOutputFileName, outGroup);
+ outputTypes["group"].push_back(groupOutputFileName); outputNames.push_back(groupOutputFileName);
+
+ globaldata->setGroupFile(groupfile); //shared list needs this
+
+ input = new InputData(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> processedLabels;
+ set<string> userLabels = labels;
+
+ //file mismatch quit
+ if (list->getNumSeqs() != groupMap->getNumSeqs()) {
+ m->mothurOut("[ERROR]: your list file contains " + toString(list->getNumSeqs()) + " sequences, and your groupfile contains " + toString(groupMap->getNumSeqs()) + ", please correct.");
+ m->mothurOutEndLine();
+ delete groupMap;
+ delete list;
+ delete input;
+ out.close();
+ outGroup.close();
+ return 0;
+ }
+
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if (m->control_pressed) { delete list; delete input; delete groupMap; out.close(); outGroup.close(); return 0; }
+
+ if(allLines == 1 || labels.count(list->getLabel()) == 1){
+
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+
+ processListGroup(list, groupMap, out, outGroup);
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+ }
+
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = list->getLabel();
+
+ delete list;
+
+ list = input->getListVector(lastLabel);
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+
+ processListGroup(list, groupMap, out, outGroup);
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+
+ //restore real lastlabel to save below
+ list->setLabel(saveLabel);
+ }
+
+ lastLabel = list->getLabel();
+
+ delete list; list = NULL;
+
+ //get next line to process
+ list = input->getListVector();
+ }
+
+
+ if (m->control_pressed) { if (list != NULL) { delete list; } delete input; delete groupMap; out.close(); outGroup.close(); return 0; }
+
+ //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);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+ needToRun = true;
+ }else {
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ }
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ if (list != NULL) { delete list; }
+
+ list = input->getListVector(lastLabel);
+
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+
+ processListGroup(list, groupMap, out, outGroup);
+
+ delete list; list = NULL;
+ }
+
+ out.close(); outGroup.close();
+ if (list != NULL) { delete list; }
+ delete groupMap;
+
+ }else {
+ //need to complete
+ }
+
+
+ delete input;
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SubSampleCommand", "getSubSampleList");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int SubSampleCommand::processListGroup(ListVector*& list, GroupMap*& groupMap, ofstream& out, ofstream& outGroup) {
+ try {
+
+ if (size == 0) { //user has not set size, set size = 10% samples size
+ size = int (list->getNumSeqs() * 0.10);
+ }
+
+ int numBins = list->getNumBins();
+ int thisSize = list->getNumSeqs();
+
+ if (size > thisSize) { m->mothurOut("Your list file only contains " + toString(thisSize) + " sequences. Setting size to " + toString(thisSize) + "."); m->mothurOutEndLine();
+ size = thisSize;
+ }
+
+ vector<nameToBin> seqs;
+ for (int i = 0; i < numBins; i++) {
+ string names = list->get(i);
+
+ //parse names
+ string individual = "";
+ int length = names.length();
+ for(int j=0;j<length;j++){
+ if(names[j] == ','){
+ nameToBin temp(individual, i);
+ seqs.push_back(temp);
+ individual = "";
+ }
+ else{
+ individual += names[j];
+ }
+ }
+ nameToBin temp(individual, i);
+ seqs.push_back(temp);
+ }
+
+
+ ListVector* temp = new ListVector(numBins);
+ temp->setLabel(list->getLabel());
+
+ delete list;
+ list = temp;
+
+ set<int> alreadySelected; //dont want repeat sequence names added
+ alreadySelected.insert(-1);
+ for (int j = 0; j < size; j++) {
+
+ if (m->control_pressed) { return 0; }
+
+ //get random sequence to add, making sure we have not already added it
+ int myrand = -1;
+ while (alreadySelected.count(myrand) != 0) {
+ myrand = (int)((float)(rand()) / (RAND_MAX / (thisSize-1) + 1));
+ }
+ alreadySelected.insert(myrand);
+
+ //update new list
+ string oldNames = temp->get(seqs[myrand].bin);
+ if (oldNames == "") { oldNames += seqs[myrand].name; }
+ else { oldNames += "," + seqs[myrand].name; }
+
+ temp->set(seqs[myrand].bin, oldNames);
+
+ //update group file
+ string group = groupMap->getGroup(seqs[myrand].name);
+ if (group == "not found") { m->mothurOut("[ERROR]: " + seqs[myrand].name + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
+
+ outGroup << seqs[myrand].name << '\t' << group << endl;
+ }
+
+ if (m->control_pressed) { return 0; }
+
+ list->print(out);
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SubSampleCommand", "processListGroup");
exit(1);
}
}
projects / mothur.git / blobdiff