attributes = {
ORGANIZATIONNAME = "Schloss Lab";
};
- buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */;
+ buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */;
compatibilityVersion = "Xcode 3.1";
developmentRegion = English;
hasScannedForEncodings = 1;
"VERSION=\"\\\"1.15.0\\\"\"",
"RELEASE_DATE=\"\\\"12/10/2010\\\"\"",
);
+ GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
GCC_WARN_ABOUT_RETURN_TYPE = YES;
GCC_WARN_UNUSED_VARIABLE = YES;
INSTALL_PATH = "";
defaultConfigurationIsVisible = 0;
defaultConfigurationName = Release;
};
- 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */ = {
+ 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */ = {
isa = XCConfigurationList;
buildConfigurations = (
1DEB928A08733DD80010E9CD /* Debug */,
*/
#include "matrixoutputcommand.h"
+#include "sharedsobscollectsummary.h"
+#include "sharedchao1.h"
+#include "sharedace.h"
+#include "sharednseqs.h"
#include "sharedjabund.h"
#include "sharedsorabund.h"
#include "sharedjclass.h"
#include "sharedsorest.h"
#include "sharedthetayc.h"
#include "sharedthetan.h"
+#include "sharedkstest.h"
+#include "whittaker.h"
+#include "sharedochiai.h"
+#include "sharedanderbergs.h"
+#include "sharedkulczynski.h"
+#include "sharedkulczynskicody.h"
+#include "sharedlennon.h"
#include "sharedmorisitahorn.h"
#include "sharedbraycurtis.h"
-
+#include "sharedjackknife.h"
+#include "whittaker.h"
+#include "odum.h"
+#include "canberra.h"
+#include "structeuclidean.h"
+#include "structchord.h"
+#include "hellinger.h"
+#include "manhattan.h"
+#include "structpearson.h"
+#include "soergel.h"
+#include "spearman.h"
+#include "structkulczynski.h"
+#include "structchi2.h"
+#include "speciesprofile.h"
+#include "hamming.h"
+#include "gower.h"
+#include "memchi2.h"
+#include "memchord.h"
+#include "memeuclidean.h"
+#include "mempearson.h"
//**********************************************************************************************************************
vector<string> MatrixOutputCommand::getValidParameters(){
try {
int i;
for (i=0; i<Estimators.size(); i++) {
if (validCalculator->isValidCalculator("matrix", Estimators[i]) == true) {
- if (Estimators[i] == "jabund") {
+ if (Estimators[i] == "sharedsobs") {
+ matrixCalculators.push_back(new SharedSobsCS());
+ }else if (Estimators[i] == "sharedchao") {
+ matrixCalculators.push_back(new SharedChao1());
+ }else if (Estimators[i] == "sharedace") {
+ matrixCalculators.push_back(new SharedAce());
+ }else if (Estimators[i] == "jabund") {
matrixCalculators.push_back(new JAbund());
}else if (Estimators[i] == "sorabund") {
matrixCalculators.push_back(new SorAbund());
matrixCalculators.push_back(new ThetaYC());
}else if (Estimators[i] == "thetan") {
matrixCalculators.push_back(new ThetaN());
+ }else if (Estimators[i] == "kstest") {
+ matrixCalculators.push_back(new KSTest());
+ }else if (Estimators[i] == "sharednseqs") {
+ matrixCalculators.push_back(new SharedNSeqs());
+ }else if (Estimators[i] == "ochiai") {
+ matrixCalculators.push_back(new Ochiai());
+ }else if (Estimators[i] == "anderberg") {
+ matrixCalculators.push_back(new Anderberg());
+ }else if (Estimators[i] == "kulczynski") {
+ matrixCalculators.push_back(new Kulczynski());
+ }else if (Estimators[i] == "kulczynskicody") {
+ matrixCalculators.push_back(new KulczynskiCody());
+ }else if (Estimators[i] == "lennon") {
+ matrixCalculators.push_back(new Lennon());
}else if (Estimators[i] == "morisitahorn") {
matrixCalculators.push_back(new MorHorn());
}else if (Estimators[i] == "braycurtis") {
matrixCalculators.push_back(new BrayCurtis());
+ }else if (Estimators[i] == "whittaker") {
+ matrixCalculators.push_back(new Whittaker());
+ }else if (Estimators[i] == "odum") {
+ matrixCalculators.push_back(new Odum());
+ }else if (Estimators[i] == "canberra") {
+ matrixCalculators.push_back(new Canberra());
+ }else if (Estimators[i] == "structeuclidean") {
+ matrixCalculators.push_back(new StructEuclidean());
+ }else if (Estimators[i] == "structchord") {
+ matrixCalculators.push_back(new StructChord());
+ }else if (Estimators[i] == "hellinger") {
+ matrixCalculators.push_back(new Hellinger());
+ }else if (Estimators[i] == "manhattan") {
+ matrixCalculators.push_back(new Manhattan());
+ }else if (Estimators[i] == "structpearson") {
+ matrixCalculators.push_back(new StructPearson());
+ }else if (Estimators[i] == "soergel") {
+ matrixCalculators.push_back(new Soergel());
+ }else if (Estimators[i] == "spearman") {
+ matrixCalculators.push_back(new Spearman());
+ }else if (Estimators[i] == "structkulczynski") {
+ matrixCalculators.push_back(new StructKulczynski());
+ }else if (Estimators[i] == "speciesprofile") {
+ matrixCalculators.push_back(new SpeciesProfile());
+ }else if (Estimators[i] == "hamming") {
+ matrixCalculators.push_back(new Hamming());
+ }else if (Estimators[i] == "structchi2") {
+ matrixCalculators.push_back(new StructChi2());
+ }else if (Estimators[i] == "gower") {
+ matrixCalculators.push_back(new Gower());
+ }else if (Estimators[i] == "memchi2") {
+ matrixCalculators.push_back(new MemChi2());
+ }else if (Estimators[i] == "memchord") {
+ matrixCalculators.push_back(new MemChord());
+ }else if (Estimators[i] == "memeuclidean") {
+ matrixCalculators.push_back(new MemEuclidean());
+ }else if (Estimators[i] == "mempearson") {
+ matrixCalculators.push_back(new MemPearson());
}
}
}
//add new pair of sharedrabunds
subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
+ //if this calc needs all groups to calculate the pair load all groups
+ if (matrixCalculators[i]->getNeedsAll()) {
+ //load subset with rest of lookup for those calcs that need everyone to calc for a pair
+ for (int w = 0; w < thisLookup.size(); w++) {
+ if ((w != k) && (w != l)) { subset.push_back(thisLookup[w]); }
+ }
+ }
+
data = matrixCalculators[i]->getValues(subset); //saves the calculator outputs
//save values in similarity matrix
simMatrix[k][l] = 1.0 - data[0]; //convert similiarity to distance
//**********************************************************************************************************************
vector<string> RemoveRareCommand::getValidParameters(){
try {
- string Array[] = {"rabund","sabund", "group", "list", "shared", "nseqs","groups","label","outputdir","inputdir"};
+ string Array[] = {"rabund","sabund", "group", "list", "shared","bygroup","nseqs","groups","label","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
return myArray;
}
//**********************************************************************************************************************
RemoveRareCommand::RemoveRareCommand(string option) {
try {
+ globaldata = GlobalData::getInstance();
abort = false;
allLines = 1;
else {
//valid paramters for this command
- string Array[] = {"rabund","sabund", "group", "list", "shared", "nseqs","groups","label","outputdir","inputdir"};
+ string Array[] = {"rabund","sabund", "group", "list", "shared", "bygroup", "nseqs","groups","label","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
else if (rabundfile == "not found") { rabundfile = ""; }
groupfile = validParameter.validFile(parameters, "group", true);
- if (groupfile == "not open") { abort = true; }
+ if (groupfile == "not open") { groupfile = ""; abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
sharedfile = validParameter.validFile(parameters, "shared", true);
- if (sharedfile == "not open") { abort = true; }
+ if (sharedfile == "not open") { sharedfile = ""; abort = true; }
else if (sharedfile == "not found") { sharedfile = ""; }
if ((sabundfile == "") && (rabundfile == "") && (sharedfile == "") && (listfile == "")) { m->mothurOut("You must provide at least one of the following: rabund, sabund, shared or list."); m->mothurOutEndLine(); abort = true; }
string temp = validParameter.validFile(parameters, "nseqs", false);
if (temp == "not found") { m->mothurOut("nseqs is a required parameter."); m->mothurOutEndLine(); abort = true; }
else { convert(temp, nseqs); }
+
+ temp = validParameter.validFile(parameters, "bygroup", false); if (temp == "not found") { temp = "f"; }
+ byGroup = m->isTrue(temp);
+
+ if (byGroup && (sharedfile == "")) { m->mothurOut("The byGroup parameter is only valid with a shared file."); m->mothurOutEndLine(); }
+
+ if ((groupfile != "") && (listfile == "")) { m->mothurOut("A groupfile is only valid with a list file."); m->mothurOutEndLine(); groupfile = ""; }
}
}
void RemoveRareCommand::help(){
try {
- //m->mothurOut("The remove.seqs command reads an .accnos file and at least one of the following file types: fasta, name, group, list, taxonomy, quality or alignreport file.\n");
- //m->mothurOut("It outputs a file containing the sequences NOT in the .accnos file.\n");
- //m->mothurOut("The remove.seqs command parameters are accnos, fasta, name, group, list, taxonomy, qfile, alignreport and dups. You must provide accnos and at least one of the file parameters.\n");
- //m->mothurOut("The dups parameter allows you to remove the entire line from a name file if you remove any name from the line. default=true. \n");
- //m->mothurOut("The remove.seqs command should be in the following format: remove.seqs(accnos=yourAccnos, fasta=yourFasta).\n");
- //m->mothurOut("Example remove.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n");
- //m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
+ m->mothurOut("The remove.rare command parameters are list, rabund, sabund, shared, group, label, groups, bygroup and nseqs.\n");
+ m->mothurOut("The remove.rare command reads one of the following file types: list, rabund, sabund or shared file. It outputs a new file after removing the rare otus.\n");
+ m->mothurOut("The groups parameter allows you to specify which of the groups you would like analyzed. Default=all. You may separate group names with dashes.\n");
+ m->mothurOut("The label parameter is used to analyze specific labels in your input. default=all. You may separate label names with dashes.\n");
+ m->mothurOut("The bygroup parameter is only valid with the shared file. default=f, meaning remove any OTU that has nseqs or fewer sequences across all groups.\n");
+ m->mothurOut("bygroups=T means remove any OTU that has nseqs or fewer sequences in each group (if groupA has 1 sequence and group B has 100 sequences in OTUZ and nseqs=1, then set the groupA count for OTUZ to 0 and keep groupB's count at 100.) \n");
+ m->mothurOut("The nseqs parameter allows you to set the cutoff for an otu to be deemed rare. It is required.\n");
+ m->mothurOut("The remove.rare command should be in the following format: remove.rare(shared=yourSharedFile, nseqs=yourRareCutoff).\n");
+ m->mothurOut("Example remove.rare(shared=amazon.fn.shared, nseqs=2).\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. shared), '=' and parameters (i.e.yourSharedFile).\n\n");
}
catch(exception& e) {
m->errorOut(e, "RemoveRareCommand", "help");
if (sabundfile != "") { processSabund(); }
if (rabundfile != "") { processRabund(); }
if (listfile != "") { processList(); }
- //if (sharedfile != "") { processShared(); }
+ if (sharedfile != "") { processShared(); }
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
return 0;
}
+ catch(exception& e) {
+ m->errorOut(e, "RemoveRareCommand", "processRabund");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int RemoveRareCommand::processShared(){
+ try {
+ globaldata->Groups = Groups;
+
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + "pick" + m->getExtension(sharedfile);
+ outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ InputData input(sharedfile, "sharedfile");
+ vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
+ string lastLabel = lookup[0]->getLabel();
+ set<string> processedLabels;
+ set<string> userLabels = labels;
+
+ while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } out.close(); return 0; }
+
+ if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
+
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+
+ processLookup(lookup, out);
+ }
+
+ 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();
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+
+ processLookup(lookup, out);
+
+ //restore real lastlabel to save below
+ lookup[0]->setLabel(saveLabel);
+ }
+
+ lastLabel = lookup[0]->getLabel();
+
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ 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;
+ 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) {
+ for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
+ lookup = input.getSharedRAbundVectors(lastLabel);
+
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+
+ processLookup(lookup, out);
+
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ }
+
+ return 0;
+ }
catch(exception& e) {
m->errorOut(e, "RemoveRareCommand", "processSabund");
exit(1);
}
}
//**********************************************************************************************************************
+int RemoveRareCommand::processLookup(vector<SharedRAbundVector*>& lookup, ofstream& out){
+ try {
+
+ vector<SharedRAbundVector> newRabunds; newRabunds.resize(lookup.size());
+ for (int i = 0; i < lookup.size(); i++) {
+ newRabunds[i].setGroup(lookup[i]->getGroup());
+ newRabunds[i].setLabel(lookup[i]->getLabel());
+ }
+
+ if (byGroup) {
+
+ //for each otu
+ for (int i = 0; i < lookup[0]->getNumBins(); i++) {
+ bool allZero = true;
+
+ if (m->control_pressed) { return 0; }
+
+ //for each group
+ for (int j = 0; j < lookup.size(); j++) {
+
+ //are you rare?
+ if (lookup[j]->getAbundance(i) > nseqs) {
+ newRabunds[j].push_back(lookup[j]->getAbundance(i), newRabunds[j].getGroup());
+ allZero = false;
+ }else {
+ newRabunds[j].push_back(0, newRabunds[j].getGroup());
+ }
+ }
+
+ //eliminates zero otus
+ if (allZero) { for (int j = 0; j < newRabunds.size(); j++) { newRabunds[j].pop_back(); } }
+ }
+ }else {
+ //for each otu
+ for (int i = 0; i < lookup[0]->getNumBins(); i++) {
+
+ if (m->control_pressed) { return 0; }
+
+ int totalAbund = 0;
+ //get total otu abundance
+ for (int j = 0; j < lookup.size(); j++) {
+ newRabunds[j].push_back(lookup[j]->getAbundance(i), newRabunds[j].getGroup());
+ totalAbund += lookup[j]->getAbundance(i);
+ }
+
+ //eliminates otus below rare cutoff
+ if (totalAbund <= nseqs) { for (int j = 0; j < newRabunds.size(); j++) { newRabunds[j].pop_back(); } }
+ }
+ }
+
+ //do we have any otus above the rare cutoff
+ if (newRabunds[0].getNumBins() != 0) {
+ for (int j = 0; j < newRabunds.size(); j++) {
+ out << newRabunds[j].getLabel() << '\t' << newRabunds[j].getGroup() << '\t';
+ newRabunds[j].print(out);
+ }
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveRareCommand", "processLookup");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
#include "command.hpp"
#include "listvector.hpp"
+#include "globaldata.hpp"
class RemoveRareCommand : public Command {
void help();
private:
+ GlobalData* globaldata;
string sabundfile, rabundfile, sharedfile, groupfile, listfile, outputDir, groups, label;
int nseqs, allLines;
bool abort, byGroup;
int processRabund();
int processList();
int processShared();
+ int processLookup(vector<SharedRAbundVector*>&, ofstream&);
};
};
-#endif
\ No newline at end of file
+#endif
+
/***********************************************************************/
-#endif
\ No newline at end of file
+#endif
+
+
+
/***********************************************************************/
-#endif
\ No newline at end of file
+#endif
+
+
+
+
+
/***********************************************************************/
-#endif
\ No newline at end of file
+#endif
+
+
+
+
//add new pair of sharedrabunds
subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
+ //if this calc needs all groups to calculate the pair load all groups
+ if (treeCalculators[i]->getNeedsAll()) {
+ //load subset with rest of lookup for those calcs that need everyone to calc for a pair
+ for (int w = 0; w < thisLookup.size(); w++) {
+ if ((w != k) && (w != l)) { subset.push_back(thisLookup[w]); }
+ }
+ }
+
data = treeCalculators[i]->getValues(subset); //saves the calculator outputs
//cout << thisLookup[k]->getGroup() << '\t' << thisLookup[l]->getGroup() << '\t' << (1.0 - data[0]) << endl;
if (m->control_pressed) { return 1; }
/********************************************************************/
void ValidCalculators::initialMatrix() {
try {
- matrix["jabund"] = "jabund";
+ matrix["sharedsobs"] = "sharedsobs";
+ matrix["sharedchao"] = "sharedchao";
+ matrix["sharedace"] = "sharedace";
+ matrix["jabund"] = "jabund";
matrix["sorabund"] = "sorabund";
- matrix["jclass"] = "jclass";
+ matrix["jclass"] = "jclass";
matrix["sorclass"] = "sorclass";
matrix["jest"] = "jest";
- matrix["sorest"] = "sorest";
+ matrix["sorest"] = "sorest";
matrix["thetayc"] = "thetayc";
- matrix["thetan"] = "thetan";
+ matrix["thetan"] = "thetan";
+ matrix["kstest"] = "kstest";
+ matrix["whittaker"] = "whittaker";
+ matrix["sharednseqs"] = "sharednseqs";
+ matrix["ochiai"] = "ochiai";
+ matrix["anderberg"] = "anderberg";
+ matrix["kulczynski"] = "kulczynski";
+ matrix["kulczynskicody"] = "kulczynskicody";
+ matrix["lennon"] = "lennon";
matrix["morisitahorn"] = "morisitahorn";
- matrix["braycurtis"] = "braycurtis";
+ matrix["braycurtis"] = "braycurtis";
+ matrix["odum"] = "odum";
+ matrix["canberra"] = "canberra";
+ matrix["structeuclidean"] = "structeuclidean";
+ matrix["structchord"] = "structchord";
+ matrix["hellinger"] = "hellinger";
+ matrix["manhattan"] = "manhattan";
+ matrix["structpearson"] = "structpearson";
+ matrix["structkulczynski"] = "structkulczynski";
+ matrix["structchi2"] = "structchi2";
+ matrix["soergel"] = "soergel";
+ matrix["spearman"] = "spearman";
+ matrix["speciesprofile"] = "speciesprofile";
+ matrix["hamming"] = "hamming";
+ matrix["gower"] = "gower";
+ matrix["memchi2"] = "memchi2";
+ matrix["memchord"] = "memchord";
+ matrix["memeuclidean"] = "memeuclidean";
+ matrix["mempearson"] = "mempearson";
+
}
catch(exception& e) {
m->errorOut(e, "ValidCalculator", "initialMatrix");
projects / mothur.git / commitdiff