#include "sharedsobscollectsummary.h"
#include "sharedchao1.h"
#include "sharedace.h"
+#include "nseqs.h"
+//**********************************************************************************************************************
+vector<string> VennCommand::getValidParameters(){
+ try {
+ string Array[] = {"groups","label","calc","permute", "abund","nseqs","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "VennCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+VennCommand::VennCommand(){
+ try {
+ abort = true; calledHelp = true;
+ vector<string> tempOutNames;
+ outputTypes["svg"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "VennCommand", "VennCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> VennCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "VennCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> VennCommand::getRequiredFiles(){
+ try {
+ string Array[] = {"list","shared","or"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "VennCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
VennCommand::VennCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
- string AlignArray[] = {"groups","label","calc", "abund","outputdir","inputdir"};
+ string AlignArray[] = {"groups","label","calc","permute", "abund","nseqs","outputdir","inputdir"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
OptionParser parser(option);
//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 += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
+ outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
}
//check for optional parameter and set defaults
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
- if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else {
- splitAtDash(groups, Groups);
+ m->splitAtDash(groups, Groups);
globaldata->Groups = Groups;
}
else { calc = "sharedsobs"; }
}
}
- splitAtDash(calc, Estimators);
+ m->splitAtDash(calc, Estimators);
string temp;
temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; }
convert(temp, abund);
+
+ 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 = "f"; }
+ perm = m->isTrue(temp);
if (abort == false) {
validCalculator = new ValidCalculators();
}
}
- venn = new Venn(outputDir);
+ //if the users entered no valid calculators don't execute command
+ if (vennCalculators.size() == 0) { m->mothurOut("No valid calculators given, please correct."); m->mothurOutEndLine(); abort = true; }
+ else { venn = new Venn(outputDir, nseqs); }
}
+
}
void VennCommand::help(){
try {
m->mothurOut("The venn command can only be executed after a successful read.otu command.\n");
- m->mothurOut("The venn command parameters are groups, calc, abund and label. No parameters are required.\n");
+ m->mothurOut("The venn command parameters are groups, calc, abund, nseqs, permute and label. No parameters are required.\n");
m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included in your venn diagram, you may only use a maximum of 4 groups.\n");
m->mothurOut("The group names are separated by dashes. The label allows you to select what distance levels you would like a venn diagram created for, and are also separated by dashes.\n");
m->mothurOut("The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, label=yourLabels, abund=yourAbund).\n");
m->mothurOut("The default value for groups is all the groups in your groupfile up to 4, and all labels in your inputfile will be used.\n");
m->mothurOut("The default value for calc is sobs if you have only read a list file or if you have selected only one group, and sharedsobs if you have multiple groups.\n");
m->mothurOut("The default available estimators for calc are sobs, chao and ace if you have only read a list file, and sharedsobs, sharedchao and sharedace if you have read a list and group file or a shared file.\n");
- m->mothurOut("The only estmiator available four 4 groups is sharedsobs.\n");
+ m->mothurOut("The nseqs parameter will output the number of sequences represented by the otus in the picture, default=F.\n");
+ m->mothurOut("If you have more than 4 groups, the permute parameter will find all possible combos of 4 of your groups and create pictures for them, default=F.\n");
+ m->mothurOut("The only estimators available four 4 groups are sharedsobs and sharedchao.\n");
m->mothurOut("The venn command outputs a .svg file for each calculator you specify at each distance you choose.\n");
m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
}
int VennCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
string lastLabel;
- vector<string> outputNames;
-
- //if the users entered no valid calculators don't execute command
- if (vennCalculators.size() == 0) { return 0; }
if (format == "sharedfile") {
//you have groups
input = globaldata->ginput;
lookup = input->getSharedRAbundVectors();
lastLabel = lookup[0]->getLabel();
+
+ if ((lookup.size() > 4) && (perm)) { combosOfFour = findCombinations(lookup.size()); }
}else if (format == "list") {
//you are using just a list file and have only one group
read = new ReadOTUFile(globaldata->inputFileName);
//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;
-
+
if (format != "list") {
//as long as you are not at the end of the file or done wih the lines you want
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
- if (lookup.size() > 4) {
- m->mothurOut("Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile."); m->mothurOutEndLine();
+ if ((lookup.size() > 4) && (!perm)){
+ m->mothurOut("Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile. If you set perm=t, I will find all possible combos of 4 groups."); m->mothurOutEndLine();
for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
- }
- vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
- for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); } }
+ vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
+ for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
+
+ }else if ((lookup.size() > 4) && (perm)) {
+ set< set<int> >::iterator it3;
+ set<int>::iterator it2;
+ for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
+
+ set<int> poss = *it3;
+ vector<SharedRAbundVector*> subset;
+ for (it2 = poss.begin(); it2 != poss.end(); it2++) { subset.push_back(lookup[*it2]); }
+
+ vector<string> outfilenames = venn->getPic(subset, vennCalculators);
+ for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
+ }
+ }else {
+ vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
+ for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
+ }
}
- if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ 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]; }
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
- if (lookup.size() > 4) {
- m->mothurOut("Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile."); m->mothurOutEndLine();
+ if ((lookup.size() > 4) && (!perm)){
+ m->mothurOut("Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile. If you set perm=t, I will find all possible combos of 4 groups."); m->mothurOutEndLine();
for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
- }
- vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
- for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); } }
+ vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
+ for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
+
+ }else if ((lookup.size() > 4) && (perm)) {
+ set< set<int> >::iterator it3;
+ set<int>::iterator it2;
+ for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
+
+ set<int> poss = *it3;
+ vector<SharedRAbundVector*> subset;
+ for (it2 = poss.begin(); it2 != poss.end(); it2++) { subset.push_back(lookup[*it2]); }
+
+ vector<string> outfilenames = venn->getPic(subset, vennCalculators);
+ for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
+ }
+ }else {
+ vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
+ for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
+ }
+
//restore real lastlabel to save below
lookup[0]->setLabel(saveLabel);
}
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
- if (lookup.size() > 4) {
- m->mothurOut("Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile."); m->mothurOutEndLine();
+ if ((lookup.size() > 4) && (!perm)){
+ m->mothurOut("Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile. If you set perm=t, I will find all possible combos of 4 groups."); m->mothurOutEndLine();
for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
- }
- vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
- for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); } }
+
+ vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
+ for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
+ }else if ((lookup.size() > 4) && (perm)) {
+ set< set<int> >::iterator it3;
+ set<int>::iterator it2;
+ for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
+
+ set<int> poss = *it3;
+ vector<SharedRAbundVector*> subset;
+ for (it2 = poss.begin(); it2 != poss.end(); it2++) { subset.push_back(lookup[*it2]); }
+
+ vector<string> outfilenames = venn->getPic(subset, vennCalculators);
+ for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
+ }
+ }else {
+ vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
+ for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
+ }
+
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
- for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); } }
+ for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
}
- if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = sabund->getLabel();
delete sabund;
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
- for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); } }
+ for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
processedLabels.insert(sabund->getLabel());
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
- for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); } }
+ for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
delete sabund;
exit(1);
}
}
+//**********************************************************************************************************************
+//returns a vector of sets containing the 4 group combinations
+set< set<int> > VennCommand::findCombinations(int lookupSize){
+ try {
+ set< set<int> > combos;
+
+ set<int> possibles;
+ for (int i = 0; i < lookupSize; i++) { possibles.insert(i); }
+
+ getCombos(possibles, combos);
+
+ return combos;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "VennCommand", "findCombinations");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//recusively finds combos of 4
+int VennCommand::getCombos(set<int> possibles, set< set<int> >& combos){
+ try {
+
+ if (possibles.size() == 4) { //done
+ if (combos.count(possibles) == 0) { //no dups
+ combos.insert(possibles);
+ }
+ }else { //we still have work to do
+ set<int>::iterator it;
+ set<int>::iterator it2;
+ for (it = possibles.begin(); it != possibles.end(); it++) {
+
+ set<int> newPossibles;
+ for (it2 = possibles.begin(); it2 != possibles.end(); it2++) { //all possible combos of one length smaller
+ if (*it != *it2) {
+ newPossibles.insert(*it2);
+ }
+ }
+ getCombos(newPossibles, combos);
+ }
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "VennCommand", "getCombos");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
projects / mothur.git / blobdiff