#include "mgclustercommand.h"
//**********************************************************************************************************************
-MGClusterCommand::MGClusterCommand(string option){
+MGClusterCommand::MGClusterCommand(string option) {
try {
globaldata = GlobalData::getInstance();
abort = false;
else {
//valid paramters for this command
- string Array[] = {"blast", "method", "name", "cutoff", "precision", "length", "min", "penalty", "hcluster","merge","outputdir","inputdir"};
+ string Array[] = {"blast", "method", "name", "hard", "cutoff", "precision", "length", "min", "penalty", "hcluster","merge","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
it = parameters.find("blast");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["blast"] = inputDir + it->second; }
}
it = parameters.find("name");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["name"] = inputDir + it->second; }
}
//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(blastfile); //if user entered a file with a path then preserve it
+ outputDir += m->hasPath(blastfile); //if user entered a file with a path then preserve it
}
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { abort = true; }
else if (namefile == "not found") { namefile = ""; }
- if ((blastfile == "")) { mothurOut("When executing a mgcluster command you must provide a blastfile."); mothurOutEndLine(); abort = true; }
+ if ((blastfile == "")) { m->mothurOut("When executing a mgcluster command you must provide a blastfile."); m->mothurOutEndLine(); abort = true; }
//check for optional parameter and set defaults
string temp;
if (method == "not found") { method = "furthest"; }
if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
- else { mothurOut("Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average."); mothurOutEndLine(); abort = true; }
+ else { m->mothurOut("Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average."); m->mothurOutEndLine(); abort = true; }
temp = validParameter.validFile(parameters, "length", false); if (temp == "not found") { temp = "5"; }
convert(temp, length);
convert(temp, penalty);
temp = validParameter.validFile(parameters, "min", false); if (temp == "not found") { temp = "true"; }
- minWanted = isTrue(temp);
+ minWanted = m->isTrue(temp);
temp = validParameter.validFile(parameters, "merge", false); if (temp == "not found") { temp = "true"; }
- merge = isTrue(temp);
+ merge = m->isTrue(temp);
temp = validParameter.validFile(parameters, "hcluster", false); if (temp == "not found") { temp = "false"; }
- hclusterWanted = isTrue(temp);
+ hclusterWanted = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "hard", false); if (temp == "not found") { temp = "F"; }
+ hard = m->isTrue(temp);
}
}
catch(exception& e) {
- errorOut(e, "MGClusterCommand", "MGClusterCommand");
+ m->errorOut(e, "MGClusterCommand", "MGClusterCommand");
exit(1);
}
}
void MGClusterCommand::help(){
try {
- mothurOut("The mgcluster command parameter options are blast, name, cutoff, precision, method, merge, min, length, penalty and hcluster. The blast parameter is required.\n");
- mothurOut("The mgcluster command reads a blast and name file and clusters the sequences into OPF units similiar to the OTUs.\n");
- mothurOut("This command outputs a .list, .rabund and .sabund file that can be used with mothur other commands to estimate richness.\n");
- mothurOut("The cutoff parameter is used to specify the maximum distance you would like to cluster to. The default is 0.70.\n");
- mothurOut("The precision parameter's default value is 100. \n");
- mothurOut("The acceptable mgcluster methods are furthest, nearest and average. If no method is provided then furthest is assumed.\n\n");
- mothurOut("The min parameter allows you to specify is you want the minimum or maximum blast score ratio used in calculating the distance. The default is true, meaning you want the minimum.\n");
- mothurOut("The length parameter is used to specify the minimum overlap required. The default is 5.\n");
- mothurOut("The penalty parameter is used to adjust the error rate. The default is 0.10.\n");
- mothurOut("The merge parameter allows you to shut off merging based on overlaps and just cluster. By default merge is true, meaning you want to merge.\n");
- mothurOut("The hcluster parameter allows you to use the hcluster algorithm when clustering. This may be neccessary if your file is too large to fit into RAM. The default is false.\n");
- mothurOut("The mgcluster command should be in the following format: \n");
- mothurOut("mgcluster(blast=yourBlastfile, name=yourNameFile, cutoff=yourCutOff).\n");
- mothurOut("Note: No spaces between parameter labels (i.e. balst), '=' and parameters (i.e.yourBlastfile).\n\n");
+ m->mothurOut("The mgcluster command parameter options are blast, name, cutoff, precision, method, merge, min, length, penalty and hcluster. The blast parameter is required.\n");
+ m->mothurOut("The mgcluster command reads a blast and name file and clusters the sequences into OPF units similiar to the OTUs.\n");
+ m->mothurOut("This command outputs a .list, .rabund and .sabund file that can be used with mothur other commands to estimate richness.\n");
+ m->mothurOut("The cutoff parameter is used to specify the maximum distance you would like to cluster to. The default is 0.70.\n");
+ m->mothurOut("The precision parameter's default value is 100. \n");
+ m->mothurOut("The acceptable mgcluster methods are furthest, nearest and average. If no method is provided then furthest is assumed.\n\n");
+ m->mothurOut("The min parameter allows you to specify is you want the minimum or maximum blast score ratio used in calculating the distance. The default is true, meaning you want the minimum.\n");
+ m->mothurOut("The length parameter is used to specify the minimum overlap required. The default is 5.\n");
+ m->mothurOut("The penalty parameter is used to adjust the error rate. The default is 0.10.\n");
+ m->mothurOut("The merge parameter allows you to shut off merging based on overlaps and just cluster. By default merge is true, meaning you want to merge.\n");
+ m->mothurOut("The hcluster parameter allows you to use the hcluster algorithm when clustering. This may be neccessary if your file is too large to fit into RAM. The default is false.\n");
+ m->mothurOut("The mgcluster command should be in the following format: \n");
+ m->mothurOut("mgcluster(blast=yourBlastfile, name=yourNameFile, cutoff=yourCutOff).\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. balst), '=' and parameters (i.e.yourBlastfile).\n\n");
}
catch(exception& e) {
- errorOut(e, "MGClusterCommand", "help");
+ m->errorOut(e, "MGClusterCommand", "help");
exit(1);
}
}
nameMap->readMap();
}else{ nameMap= new NameAssignment(); }
- string fileroot = outputDir + getRootName(getSimpleName(blastfile));
+ string fileroot = outputDir + m->getRootName(m->getSimpleName(blastfile));
string tag = "";
time_t start;
float previousDist = 0.00000;
list = new ListVector(nameMap->getListVector());
RAbundVector* rabund = new RAbundVector(list->getRAbundVector());
+ if (m->control_pressed) { delete nameMap; delete read; delete list; delete rabund; return 0; }
+
start = time(NULL);
oldList = *list;
+ map<string, int> Seq2Bin;
+ map<string, int> oldSeq2Bin;
if (method == "furthest") { tag = "fn"; }
else if (method == "nearest") { tag = "nn"; }
else { tag = "an"; }
//open output files
- openOutputFile(fileroot+ tag + ".list", listFile);
- openOutputFile(fileroot+ tag + ".rabund", rabundFile);
- openOutputFile(fileroot+ tag + ".sabund", sabundFile);
+ m->openOutputFile(fileroot+ tag + ".list", listFile);
+ m->openOutputFile(fileroot+ tag + ".rabund", rabundFile);
+ m->openOutputFile(fileroot+ tag + ".sabund", sabundFile);
+
+ if (m->control_pressed) {
+ delete nameMap; delete read; delete list; delete rabund;
+ listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+ return 0;
+ }
if (!hclusterWanted) {
//get distmatrix and overlap
delete read;
//create cluster
- if (method == "furthest") { cluster = new CompleteLinkage(rabund, list, distMatrix, cutoff); }
- else if(method == "nearest"){ cluster = new SingleLinkage(rabund, list, distMatrix, cutoff); }
- else if(method == "average"){ cluster = new AverageLinkage(rabund, list, distMatrix, cutoff); }
+ if (method == "furthest") { cluster = new CompleteLinkage(rabund, list, distMatrix, cutoff, method); }
+ else if(method == "nearest"){ cluster = new SingleLinkage(rabund, list, distMatrix, cutoff, method); }
+ else if(method == "average"){ cluster = new AverageLinkage(rabund, list, distMatrix, cutoff, method); }
cluster->setMapWanted(true);
+ Seq2Bin = cluster->getSeqtoBin();
+ oldSeq2Bin = Seq2Bin;
+ if (m->control_pressed) {
+ delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster;
+ listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+ return 0;
+ }
+
//cluster using cluster classes
while (distMatrix->getSmallDist() < cutoff && distMatrix->getNNodes() > 0){
- cluster->update();
+ cluster->update(cutoff);
+
+ if (m->control_pressed) {
+ delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster;
+ listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+ return 0;
+ }
+
float dist = distMatrix->getSmallDist();
- float rndDist = roundDist(dist, precision);
+ float rndDist;
+ if (hard) {
+ rndDist = m->ceilDist(dist, precision);
+ }else{
+ rndDist = m->roundDist(dist, precision);
+ }
if(previousDist <= 0.0000 && dist != previousDist){
oldList.setLabel("unique");
}
else if(rndDist != rndPreviousDist){
if (merge) {
- map<string, int> seq2Bin = cluster->getSeqtoBin();
- ListVector* temp = mergeOPFs(seq2Bin, rndPreviousDist);
+ ListVector* temp = mergeOPFs(oldSeq2Bin, rndPreviousDist);
+
+ if (m->control_pressed) {
+ delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster; delete temp;
+ listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+ return 0;
+ }
+
temp->setLabel(toString(rndPreviousDist, precisionLength-1));
printData(temp);
delete temp;
printData(&oldList);
}
}
-
+
previousDist = dist;
rndPreviousDist = rndDist;
oldList = *list;
+ Seq2Bin = cluster->getSeqtoBin();
+ oldSeq2Bin = Seq2Bin;
}
if(previousDist <= 0.0000){
}
else if(rndPreviousDist<cutoff){
if (merge) {
- map<string, int> seq2Bin = cluster->getSeqtoBin();
- ListVector* temp = mergeOPFs(seq2Bin, rndPreviousDist);
+ ListVector* temp = mergeOPFs(oldSeq2Bin, rndPreviousDist);
+
+ if (m->control_pressed) {
+ delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster; delete temp;
+ listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+ return 0;
+ }
+
temp->setLabel(toString(rndPreviousDist, precisionLength-1));
printData(temp);
delete temp;
//sort the distance and overlap files
sortHclusterFiles(distFile, overlapFile);
+
+ if (m->control_pressed) {
+ delete nameMap; delete list; delete rabund;
+ listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+ return 0;
+ }
//create cluster
hcluster = new HCluster(rabund, list, method, distFile, nameMap, cutoff);
hcluster->setMapWanted(true);
+ Seq2Bin = cluster->getSeqtoBin();
+ oldSeq2Bin = Seq2Bin;
vector<seqDist> seqs; seqs.resize(1); // to start loop
//ifstream inHcluster;
- //openInputFile(distFile, inHcluster);
+ //m->openInputFile(distFile, inHcluster);
+
+ if (m->control_pressed) {
+ delete nameMap; delete list; delete rabund; delete hcluster;
+ listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+ return 0;
+ }
while (seqs.size() != 0){
seqs = hcluster->getSeqs();
+ if (m->control_pressed) {
+ delete nameMap; delete list; delete rabund; delete hcluster;
+ listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+ remove(distFile.c_str());
+ remove(overlapFile.c_str());
+ return 0;
+ }
+
for (int i = 0; i < seqs.size(); i++) { //-1 means skip me
if (seqs[i].seq1 != seqs[i].seq2) {
hcluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist);
+
+ if (m->control_pressed) {
+ delete nameMap; delete list; delete rabund; delete hcluster;
+ listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+ remove(distFile.c_str());
+ remove(overlapFile.c_str());
+ return 0;
+ }
- float rndDist = roundDist(seqs[i].dist, precision);
+ float rndDist;
+ if (hard) {
+ rndDist = m->ceilDist(seqs[i].dist, precision);
+ }else{
+ rndDist = m->roundDist(seqs[i].dist, precision);
+ }
if((previousDist <= 0.0000) && (seqs[i].dist != previousDist)){
oldList.setLabel("unique");
}
else if((rndDist != rndPreviousDist)){
if (merge) {
- map<string, int> seq2Bin = hcluster->getSeqtoBin();
- ListVector* temp = mergeOPFs(seq2Bin, rndPreviousDist);
+ ListVector* temp = mergeOPFs(oldSeq2Bin, rndPreviousDist);
+
+ if (m->control_pressed) {
+ delete nameMap; delete list; delete rabund; delete hcluster; delete temp;
+ listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+ remove(distFile.c_str());
+ remove(overlapFile.c_str());
+ return 0;
+ }
+
temp->setLabel(toString(rndPreviousDist, precisionLength-1));
printData(temp);
delete temp;
previousDist = seqs[i].dist;
rndPreviousDist = rndDist;
oldList = *list;
+ Seq2Bin = cluster->getSeqtoBin();
+ oldSeq2Bin = Seq2Bin;
}
}
}
}
else if(rndPreviousDist<cutoff){
if (merge) {
- map<string, int> seq2Bin = hcluster->getSeqtoBin();
- ListVector* temp = mergeOPFs(seq2Bin, rndPreviousDist);
+ ListVector* temp = mergeOPFs(oldSeq2Bin, rndPreviousDist);
+
+ if (m->control_pressed) {
+ delete nameMap; delete list; delete rabund; delete hcluster; delete temp;
+ listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+ remove(distFile.c_str());
+ remove(overlapFile.c_str());
+ return 0;
+ }
+
temp->setLabel(toString(rndPreviousDist, precisionLength-1));
printData(temp);
delete temp;
globaldata->setListFile(fileroot+ tag + ".list");
globaldata->setFormat("list");
-
- mothurOut("It took " + toString(time(NULL) - start) + " seconds to cluster."); mothurOutEndLine();
+
+ if (m->control_pressed) {
+ delete nameMap;
+ listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str());
+ globaldata->setListFile("");
+ globaldata->setFormat("");
+ return 0;
+ }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ m->mothurOut(fileroot+ tag + ".list"); m->mothurOutEndLine();
+ m->mothurOut(fileroot+ tag + ".rabund"); m->mothurOutEndLine();
+ m->mothurOut(fileroot+ tag + ".sabund"); m->mothurOutEndLine();
+ m->mothurOutEndLine();
+
+ m->mothurOut("It took " + toString(time(NULL) - start) + " seconds to cluster."); m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
- errorOut(e, "MGClusterCommand", "execute");
+ m->errorOut(e, "MGClusterCommand", "execute");
exit(1);
}
}
sabund.print(sabundFile);
}
catch(exception& e) {
- errorOut(e, "MGClusterCommand", "printData");
+ m->errorOut(e, "MGClusterCommand", "printData");
exit(1);
}
}
try {
//create new listvector so you don't overwrite the clustering
ListVector* newList = new ListVector(oldList);
+
bool done = false;
ifstream inOverlap;
int count = 0;
if (hclusterWanted) {
- openInputFile(overlapFile, inOverlap);
+ m->openInputFile(overlapFile, inOverlap);
if (inOverlap.eof()) { done = true; }
}else { if (overlapMatrix.size() == 0) { done = true; } }
while (!done) {
+ if (m->control_pressed) {
+ if (hclusterWanted) { inOverlap.close(); }
+ return newList;
+ }
//get next overlap
seqDist overlapNode;
if (!inOverlap.eof()) {
string firstName, secondName;
float overlapDistance;
- inOverlap >> firstName >> secondName >> overlapDistance; gobble(inOverlap);
+ inOverlap >> firstName >> secondName >> overlapDistance; m->gobble(inOverlap);
- map<string,int>::iterator itA = nameMap->find(firstName);
- map<string,int>::iterator itB = nameMap->find(secondName);
- if(itA == nameMap->end()){ cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n"; exit(1); }
- if(itB == nameMap->end()){ cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1); }
+ //commented out because we check this in readblast already
+ //map<string,int>::iterator itA = nameMap->find(firstName);
+ //map<string,int>::iterator itB = nameMap->find(secondName);
+ //if(itA == nameMap->end()){ cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n"; exit(1); }
+ //if(itB == nameMap->end()){ cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1); }
- overlapNode.seq1 = itA->second;
- overlapNode.seq2 = itB->second;
+ //overlapNode.seq1 = itA->second;
+ //overlapNode.seq2 = itB->second;
+ overlapNode.seq1 = nameMap->get(firstName);
+ overlapNode.seq2 = nameMap->get(secondName);
overlapNode.dist = overlapDistance;
}else { inOverlap.close(); break; }
}
//get names of seqs that overlap
string name1 = nameMap->get(overlapNode.seq1);
string name2 = nameMap->get(overlapNode.seq2);
-
+
//use binInfo to find out if they are already in the same bin
+ //map<string, int>::iterator itBin1 = binInfo.find(name1);
+ //map<string, int>::iterator itBin2 = binInfo.find(name2);
+
+ //if(itBin1 == binInfo.end()){ cerr << "AAError: Sequence '" << name1 << "' does not have any bin info.\n"; exit(1); }
+ //if(itBin2 == binInfo.end()){ cerr << "ABError: Sequence '" << name2 << "' does not have any bin info.\n"; exit(1); }
+
+ //int binKeep = itBin1->second;
+ //int binRemove = itBin2->second;
+
int binKeep = binInfo[name1];
int binRemove = binInfo[name2];
-
+
//if not merge bins and update binInfo
if(binKeep != binRemove) {
+
//save names in old bin
- string names = list->get(binRemove);
-
+ string names = newList->get(binRemove);
+
//merge bins into name1s bin
newList->set(binKeep, newList->get(binRemove)+','+newList->get(binKeep));
newList->set(binRemove, "");
}
catch(exception& e) {
- errorOut(e, "MGClusterCommand", "mergeOPFs");
+ m->errorOut(e, "MGClusterCommand", "mergeOPFs");
exit(1);
}
}
void MGClusterCommand::sortHclusterFiles(string unsortedDist, string unsortedOverlap) {
try {
//sort distFile
- string sortedDistFile = sortFile(unsortedDist);
+ string sortedDistFile = m->sortFile(unsortedDist, outputDir);
remove(unsortedDist.c_str()); //delete unsorted file
distFile = sortedDistFile;
//sort overlap file
- string sortedOverlapFile = sortFile(unsortedOverlap);
+ string sortedOverlapFile = m->sortFile(unsortedOverlap, outputDir);
remove(unsortedOverlap.c_str()); //delete unsorted file
overlapFile = sortedOverlapFile;
}
catch(exception& e) {
- errorOut(e, "MGClusterCommand", "sortHclusterFiles");
+ m->errorOut(e, "MGClusterCommand", "sortHclusterFiles");
exit(1);
}
}
projects / mothur.git / blobdiff