exit(1);
}
}
-
+//**********************************************************************************************************************
+string PreClusterCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "fasta") { outputFileName = "precluster" + m->getExtension(inputName); }
+ else if (type == "name") { outputFileName = "precluster.names"; }
+ else if (type == "map") { outputFileName = "precluster.map"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PreClusterCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
PreClusterCommand::PreClusterCommand(){
try {
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["name"] = tempOutNames;
+ outputTypes["map"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "PreClusterCommand", "PreClusterCommand");
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["name"] = tempOutNames;
+ outputTypes["map"] = tempOutNames;
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
// ...at some point should added some additional type checking...
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not found") { namefile = ""; }
- else if (namefile == "not open") { abort = true; }
+ else if (namefile == "not open") { namefile = ""; abort = true; }
else { m->setNameFile(namefile); }
groupfile = validParameter.validFile(parameters, "group", true);
else { m->setGroupFile(groupfile); bygroup = true; }
string temp = validParameter.validFile(parameters, "diffs", false); if(temp == "not found"){ temp = "1"; }
- convert(temp, diffs);
+ m->mothurConvert(temp, diffs);
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
-
+ m->mothurConvert(temp, processors);
+ if (namefile == "") {
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
}
}
int start = time(NULL);
string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));
- string newFastaFile = fileroot + "precluster" + m->getExtension(fastafile);
- string newNamesFile = fileroot + "precluster.names";
+ string newFastaFile = fileroot + getOutputFileNameTag("fasta", fastafile);
+ string newNamesFile = fileroot + getOutputFileNameTag("name");
+ string newMapFile = fileroot + getOutputFileNameTag("map"); //add group name if by group
+ outputNames.push_back(newFastaFile); outputTypes["fasta"].push_back(newFastaFile);
+ outputNames.push_back(newNamesFile); outputTypes["name"].push_back(newNamesFile);
+
if (bygroup) {
//clear out old files
ofstream outFasta; m->openOutputFile(newFastaFile, outFasta); outFasta.close();
ofstream outNames; m->openOutputFile(newNamesFile, outNames); outNames.close();
+ newMapFile = fileroot + "precluster.";
//parse fasta and name file by group
SequenceParser* parser;
vector<string> groups = parser->getNamesOfGroups();
-//#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- if(processors == 1) { driverGroups(parser, newFastaFile, newNamesFile, 0, groups.size(), groups); }
- else { createProcessesGroups(parser, newFastaFile, newNamesFile, groups); }
-//#else
-// driverGroups(parser, newFastaFile, newNamesFile, 0, groups.size(), groups);
-//#endif
+ if(processors == 1) { driverGroups(parser, newFastaFile, newNamesFile, newMapFile, 0, groups.size(), groups); }
+ else { createProcessesGroups(parser, newFastaFile, newNamesFile, newMapFile, groups); }
delete parser;
- if (m->control_pressed) { m->mothurRemove(newFastaFile); m->mothurRemove(newNamesFile); return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
//run unique.seqs for deconvolute results
string inputString = "fasta=" + newFastaFile;
m->mothurOutEndLine();
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
-
+ m->mothurCalling = true;
+
Command* uniqueCommand = new DeconvoluteCommand(inputString);
uniqueCommand->execute();
map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
delete uniqueCommand;
-
+ m->mothurCalling = false;
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
m->renameFile(filenames["fasta"][0], newFastaFile);
+ m->renameFile(filenames["name"][0], newNamesFile);
m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run pre.cluster."); m->mothurOutEndLine();
//reads fasta file and return number of seqs
int numSeqs = readFASTA(); //fills alignSeqs and makes all seqs active
- if (m->control_pressed) { return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if (numSeqs == 0) { m->mothurOut("Error reading fasta file...please correct."); m->mothurOutEndLine(); return 0; }
if (diffs > length) { m->mothurOut("Error: diffs is greater than your sequence length."); m->mothurOutEndLine(); return 0; }
- int count = process();
+ int count = process(newMapFile);
+ outputNames.push_back(newMapFile); outputTypes["map"].push_back(newMapFile);
- if (m->control_pressed) { return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
m->mothurOut("Total number of sequences before precluster was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine();
m->mothurOut("pre.cluster removed " + toString(count) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
}
-
- if (m->control_pressed) { m->mothurRemove(newFastaFile); m->mothurRemove(newNamesFile); return 0; }
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
- m->mothurOut(newFastaFile); m->mothurOutEndLine(); outputNames.push_back(newFastaFile); outputTypes["fasta"].push_back(newFastaFile);
- m->mothurOut(newNamesFile); m->mothurOutEndLine(); outputNames.push_back(newNamesFile); outputTypes["name"].push_back(newNamesFile);
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
//set fasta file as new current fastafile
}
}
/**************************************************************************************************/
-int PreClusterCommand::createProcessesGroups(SequenceParser* parser, string newFName, string newNName, vector<string> groups) {
+int PreClusterCommand::createProcessesGroups(SequenceParser* parser, string newFName, string newNName, string newMFile, vector<string> groups) {
try {
vector<int> processIDS;
lines.push_back(linePair(startIndex, endIndex));
}
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//loop through and create all the processes you want
while (process != processors) {
processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
process++;
}else if (pid == 0){
- num = driverGroups(parser, newFName + toString(getpid()) + ".temp", newNName + toString(getpid()) + ".temp", lines[process].start, lines[process].end, groups);
+ outputNames.clear();
+ num = driverGroups(parser, newFName + toString(getpid()) + ".temp", newNName + toString(getpid()) + ".temp", newMFile, lines[process].start, lines[process].end, groups);
+
+ string tempFile = toString(getpid()) + ".outputNames.temp";
+ ofstream outTemp;
+ m->openOutputFile(tempFile, outTemp);
+
+ outTemp << outputNames.size();
+ for (int i = 0; i < outputNames.size(); i++) { outTemp << outputNames[i] << endl; }
+ outTemp.close();
+
exit(0);
}else {
m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
}
//do my part
- num = driverGroups(parser, newFName, newNName, lines[0].start, lines[0].end, groups);
+ num = driverGroups(parser, newFName, newNName, newMFile, lines[0].start, lines[0].end, groups);
//force parent to wait until all the processes are done
for (int i=0;i<processIDS.size();i++) {
int temp = processIDS[i];
wait(&temp);
}
-
+
+ for (int i = 0; i < processIDS.size(); i++) {
+ string tempFile = toString(processIDS[i]) + ".outputNames.temp";
+ ifstream intemp;
+ m->openInputFile(tempFile, intemp);
+
+ int num;
+ intemp >> num;
+ for (int k = 0; k < num; k++) {
+ string name = "";
+ intemp >> name; m->gobble(intemp);
+
+ outputNames.push_back(name); outputTypes["map"].push_back(name);
+ }
+ intemp.close();
+ m->mothurRemove(tempFile);
+ }
#else
//////////////////////////////////////////////////////////////////////////////////////////////////////
// Allocate memory for thread data.
string extension = toString(i) + ".temp";
- preClusterData* tempPreCluster = new preClusterData(fastafile, namefile, groupfile, (newFName+extension), (newNName+extension), groups, m, lines[i].start, lines[i].end, diffs, i);
+ preClusterData* tempPreCluster = new preClusterData(fastafile, namefile, groupfile, (newFName+extension), (newNName+extension), newMFile, groups, m, lines[i].start, lines[i].end, diffs, i);
pDataArray.push_back(tempPreCluster);
processIDS.push_back(i);
//using the main process as a worker saves time and memory
- num = driverGroups(parser, newFName, newNName, lines[0].start, lines[0].end, groups);
+ num = driverGroups(parser, newFName, newNName, newMFile, lines[0].start, lines[0].end, groups);
//Wait until all threads have terminated.
WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
//Close all thread handles and free memory allocations.
for(int i=0; i < pDataArray.size(); i++){
+ for (int j = 0; j < pDataArray[i]->mapFileNames.size(); j++) {
+ outputNames.push_back(pDataArray[i]->mapFileNames[j]); outputTypes["map"].push_back(pDataArray[i]->mapFileNames[j]);
+ }
CloseHandle(hThreadArray[i]);
delete pDataArray[i];
}
//append output files
for(int i=0;i<processIDS.size();i++){
+ //newFName = m->getFullPathName(".\\" + newFName);
+ //newNName = m->getFullPathName(".\\" + newNName);
+
m->appendFiles((newFName + toString(processIDS[i]) + ".temp"), newFName);
m->mothurRemove((newFName + toString(processIDS[i]) + ".temp"));
}
}
/**************************************************************************************************/
-int PreClusterCommand::driverGroups(SequenceParser* parser, string newFFile, string newNFile, int start, int end, vector<string> groups){
+int PreClusterCommand::driverGroups(SequenceParser* parser, string newFFile, string newNFile, string newMFile, int start, int end, vector<string> groups){
try {
int numSeqs = 0;
if (diffs > length) { m->mothurOut("Error: diffs is greater than your sequence length."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }
- int count = process();
+ int count = process(newMFile+groups[i]+".map");
+ outputNames.push_back(newMFile+groups[i]+".map"); outputTypes["map"].push_back(newMFile+groups[i]+".map");
if (m->control_pressed) { return 0; }
}
}
/**************************************************************************************************/
-int PreClusterCommand::process(){
+int PreClusterCommand::process(string newMapFile){
try {
+ ofstream out;
+ m->openOutputFile(newMapFile, out);
//sort seqs by number of identical seqs
sort(alignSeqs.begin(), alignSeqs.end(), comparePriority);
if (alignSeqs[i].active) { //this sequence has not been merged yet
+ string chunk = alignSeqs[i].seq.getName() + "\t" + toString(alignSeqs[i].numIdentical) + "\t" + toString(0) + "\t" + alignSeqs[i].seq.getAligned() + "\n";
+
//try to merge it with all smaller seqs
for (int j = i+1; j < numSeqs; j++) {
- if (m->control_pressed) { return 0; }
+ if (m->control_pressed) { out.close(); return 0; }
if (alignSeqs[j].active) { //this sequence has not been merged yet
//are you within "diff" bases
alignSeqs[i].names += ',' + alignSeqs[j].names;
alignSeqs[i].numIdentical += alignSeqs[j].numIdentical;
+ chunk += alignSeqs[j].seq.getName() + "\t" + toString(alignSeqs[j].numIdentical) + "\t" + toString(mismatch) + "\t" + alignSeqs[j].seq.getAligned() + "\n";
+
alignSeqs[j].active = 0;
alignSeqs[j].numIdentical = 0;
count++;
}
}//end if j active
- }//end if i != j
+ }//end for loop j
//remove from active list
alignSeqs[i].active = 0;
+ out << "ideal_seq_" << (i+1) << '\t' << alignSeqs[i].numIdentical << endl << chunk << endl;;
+
}//end if active i
if(i % 100 == 0) { m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); }
}
+ out.close();
if(numSeqs % 100 != 0) { m->mothurOut(toString(numSeqs) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); }
m->openInputFile(fastafile, inFasta);
//string firstCol, secondCol, nameString;
- length = 0;
+ set<int> lengths;
while (!inFasta.eof()) {
else{
seqPNode tempNode(itSize->second, seq, names[seq.getName()]);
alignSeqs.push_back(tempNode);
- if (seq.getAligned().length() > length) { length = seq.getAligned().length(); }
+ lengths.insert(seq.getAligned().length());
}
}else { //no names file, you are identical to yourself
seqPNode tempNode(1, seq, seq.getName());
alignSeqs.push_back(tempNode);
- if (seq.getAligned().length() > length) { length = seq.getAligned().length(); }
+ lengths.insert(seq.getAligned().length());
}
}
}
inFasta.close();
//inNames.close();
+
+ if (lengths.size() > 1) { m->control_pressed = true; m->mothurOut("[ERROR]: your sequences are not all the same length. pre.cluster requires sequences to be aligned."); m->mothurOutEndLine(); }
+ else if (lengths.size() == 1) { length = *(lengths.begin()); }
+
return alignSeqs.size();
}
/**************************************************************************************************/
int PreClusterCommand::loadSeqs(map<string, string>& thisName, vector<Sequence>& thisSeqs){
try {
- length = 0;
+ set<int> lengths;
alignSeqs.clear();
map<string, string>::iterator it;
bool error = false;
seqPNode tempNode(numReps, thisSeqs[i], it->second);
alignSeqs.push_back(tempNode);
- if (thisSeqs[i].getAligned().length() > length) { length = thisSeqs[i].getAligned().length(); }
+ lengths.insert(thisSeqs[i].getAligned().length());
}
}else { //no names file, you are identical to yourself
seqPNode tempNode(1, thisSeqs[i], thisSeqs[i].getName());
alignSeqs.push_back(tempNode);
- if (thisSeqs[i].getAligned().length() > length) { length = thisSeqs[i].getAligned().length(); }
+ lengths.insert(thisSeqs[i].getAligned().length());
}
}
+ if (lengths.size() > 1) { error = true; m->mothurOut("[ERROR]: your sequences are not all the same length. pre.cluster requires sequences to be aligned."); m->mothurOutEndLine(); }
+ else if (lengths.size() == 1) { length = *(lengths.begin()); }
+
//sanity check
if (error) { m->control_pressed = true; }
m->openOutputFile(newfasta, outFasta);
m->openOutputFile(newname, outNames);
}
-
+
for (int i = 0; i < alignSeqs.size(); i++) {
if (alignSeqs[i].numIdentical != 0) {
alignSeqs[i].seq.printSequence(outFasta);
projects / mothur.git / blobdiff