//**********************************************************************************************************************
inline bool comparePriority(seqPNode first, seqPNode second) { return (first.numIdentical > second.numIdentical); }
+
+//**********************************************************************************************************************
+vector<string> PreClusterCommand::setParameters(){
+ try {
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+ CommandParameter pdiffs("diffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pdiffs);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PreClusterCommand", "setParameters");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
+string PreClusterCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The pre.cluster command groups sequences that are within a given number of base mismatches.\n";
+ helpString += "The pre.cluster command outputs a new fasta and name file.\n";
+ helpString += "The pre.cluster command parameters are fasta, names and diffs. The fasta parameter is required. \n";
+ helpString += "The names parameter allows you to give a list of seqs that are identical. This file is 2 columns, first column is name or representative sequence, second column is a list of its identical sequences separated by commas.\n";
+ helpString += "The diffs parameter allows you to specify maximum number of mismatched bases allowed between sequences in a grouping. The default is 1.\n";
+ helpString += "The pre.cluster command should be in the following format: \n";
+ helpString += "pre.cluster(fasta=yourFastaFile, names=yourNamesFile, diffs=yourMaxDiffs) \n";
+ helpString += "Example pre.cluster(fasta=amazon.fasta, diffs=2).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PreClusterCommand", "getHelpString");
+ exit(1);
+ }
+}
-PreClusterCommand::PreClusterCommand(string option){
+//**********************************************************************************************************************
+PreClusterCommand::PreClusterCommand(){
try {
- abort = false;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PreClusterCommand", "PreClusterCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+PreClusterCommand::PreClusterCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"fasta", "name", "diffs"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
ValidParameters validParameter;
+ map<string, string>::iterator it;
//check to make sure all parameters are valid for command
for (map<string, string>::iterator it2 = parameters.begin(); it2 != parameters.end(); it2++) {
if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = 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);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("fasta");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["fasta"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //user has given a template file
+ if(it != parameters.end()){
+ 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; }
+ }
+ }
+
//check for required parameters
fastafile = validParameter.validFile(parameters, "fasta", true);
- if (fastafile == "not found") { mothurOut("fasta is a required parameter for the pre.cluster command."); mothurOutEndLine(); abort = true; }
+ if (fastafile == "not found") {
+ fastafile = m->getFastaFile();
+ if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
else if (fastafile == "not open") { abort = true; }
+ //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 += m->hasPath(fastafile); //if user entered a file with a path then preserve it
+ }
+
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
namefile = validParameter.validFile(parameters, "name", true);
}
catch(exception& e) {
- errorOut(e, "PreClusterCommand", "PreClusterCommand");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-PreClusterCommand::~PreClusterCommand(){}
-//**********************************************************************************************************************
-
-void PreClusterCommand::help(){
- try {
- mothurOut("The pre.cluster command groups sequences that are within a given number of base mismatches.\n");
- mothurOut("The pre.cluster command outputs a new fasta and name file.\n");
- mothurOut("The pre.cluster command parameters are fasta, names and diffs. The fasta parameter is required. \n");
- mothurOut("The names parameter allows you to give a list of seqs that are identical. This file is 2 columns, first column is name or representative sequence, second column is a list of its identical sequences separated by commas.\n");
- mothurOut("The diffs parameter allows you to specify maximum number of mismatched bases allowed between sequences in a grouping. The default is 1.\n");
- mothurOut("The pre.cluster command should be in the following format: \n");
- mothurOut("pre.cluster(fasta=yourFastaFile, names=yourNamesFile, diffs=yourMaxDiffs) \n");
- mothurOut("Example pre.cluster(fasta=amazon.fasta, diffs=2).\n");
- mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
- }
- catch(exception& e) {
- errorOut(e, "PreClusterCommand", "help");
+ m->errorOut(e, "PreClusterCommand", "PreClusterCommand");
exit(1);
}
}
int PreClusterCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ int start = time(NULL);
//reads fasta file and return number of seqs
- int numSeqs = readSeqs(); //fills alignSeqs and makes all seqs active
+ int numSeqs = readFASTA(); //fills alignSeqs and makes all seqs active
+
+ if (m->control_pressed) { return 0; }
- if (numSeqs == 0) { mothurOut("Error reading fasta file...please correct."); mothurOutEndLine(); return 0; }
- if (diffs > length) { mothurOut("Error: diffs is greater than your sequence length."); mothurOutEndLine(); 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; }
//clear sizes since you only needed this info to build the alignSeqs seqPNode structs
- sizes.clear();
+// sizes.clear();
//sort seqs by number of identical seqs
sort(alignSeqs.begin(), alignSeqs.end(), comparePriority);
- //go through active list and cluster everthing you can, until all nodes are inactive
- //taking advantage of the fact that maps are already sorted
- map<string, bool>::iterator itActive;
- map<string, bool>::iterator it2Active;
int count = 0;
-
- for (int i = 0; i < alignSeqs.size(); i++) {
-
- //are you active
- itActive = active.find(alignSeqs[i].seq.getName());
+
+ //think about running through twice...
+ for (int i = 0; i < numSeqs; i++) {
- if (itActive != active.end()) { //this sequence has not been merged yet
+ //are you active
+ // itActive = active.find(alignSeqs[i].seq.getName());
+ if (alignSeqs[i].active) { //this sequence has not been merged yet
+
//try to merge it with all smaller seqs
- for (int j = i; j < alignSeqs.size(); j++) {
+ for (int j = i+1; j < numSeqs; j++) {
+
+ if (m->control_pressed) { return 0; }
- if (i != j) {
- //are you active
- it2Active = active.find(alignSeqs[j].seq.getName());
- if (it2Active != active.end()) { //this sequence has not been merged yet
- //are you within "diff" bases
- int mismatch = calcMisMatches(alignSeqs[i].seq.getAligned(), alignSeqs[j].seq.getAligned());
-
- if (mismatch <= diffs) {
- //merge
- names[alignSeqs[i].seq.getName()] += "," + names[alignSeqs[j].seq.getName()];
-
- //remove from active list
- active.erase(it2Active);
-
- //set numIdentical to 0, so you only print the representative seqs in the fasta file
- alignSeqs[j].numIdentical = 0;
- count++;
- }
- }//end if j active
- }//end if i != j
- }//end for loop
+ if (alignSeqs[j].active) { //this sequence has not been merged yet
+ //are you within "diff" bases
+ int mismatch = calcMisMatches(alignSeqs[i].seq.getAligned(), alignSeqs[j].seq.getAligned());
+
+ if (mismatch <= diffs) {
+ //merge
+ alignSeqs[i].names += ',' + alignSeqs[j].names;
+ alignSeqs[i].numIdentical += alignSeqs[j].numIdentical;
+
+ alignSeqs[j].active = 0;
+ alignSeqs[j].numIdentical = 0;
+ count++;
+ }
+ }//end if j active
+ }//end if i != j
+
+ //remove from active list
+ alignSeqs[i].active = 0;
- //remove from active list
- active.erase(itActive);
}//end if active i
+ if(i % 100 == 0) { m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); }
}
+
+ if(numSeqs % 100 != 0) { m->mothurOut(toString(numSeqs) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); }
- string newFastaFile = getRootName(fastafile) + "precluster" + getExtension(fastafile);
- string newNamesFile = getRootName(fastafile) + "precluster.names";
+ string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));
+
+ string newFastaFile = fileroot + "precluster" + m->getExtension(fastafile);
+ string newNamesFile = fileroot + "precluster.names";
+
+ if (m->control_pressed) { 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();
printData(newFastaFile, newNamesFile);
- mothurOut("Total number of sequences before precluster was " + toString(alignSeqs.size()) + "."); mothurOutEndLine();
- mothurOut("pre.cluster removed " + toString(count) + " sequences."); mothurOutEndLine();
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
+
+ if (m->control_pressed) { remove(newFastaFile.c_str()); remove(newNamesFile.c_str()); 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);
+ m->mothurOutEndLine();
+
+ //set fasta file as new current fastafile
+ string current = "";
+ itTypes = outputTypes.find("fasta");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+ }
+
+ itTypes = outputTypes.find("name");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
+ }
return 0;
}
catch(exception& e) {
- errorOut(e, "PreClusterCommand", "execute");
+ m->errorOut(e, "PreClusterCommand", "execute");
exit(1);
}
}
+
/**************************************************************************************************/
-int PreClusterCommand::readSeqs(){
+
+//this requires the names and fasta file to be in the same order
+
+int PreClusterCommand::readFASTA(){
try {
+ //ifstream inNames;
ifstream inFasta;
- openInputFile(fastafile, inFasta);
+
+ //m->openInputFile(namefile, inNames);
+ m->openInputFile(fastafile, inFasta);
+
+ //string firstCol, secondCol, nameString;
length = 0;
- map<string, string>::iterator it;
-
+
while (!inFasta.eof()) {
- Sequence temp(inFasta); //read seq
- if (temp.getName() != "") {
+ if (m->control_pressed) { inFasta.close(); return 0; }
+
+ //inNames >> firstCol >> secondCol;
+ //nameString = secondCol;
+
+ //m->gobble(inNames);
+ //int size = 1;
+ //while (secondCol.find_first_of(',') != -1) {
+ // size++;
+ // secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
+ //}
+
+ Sequence seq(inFasta); m->gobble(inFasta);
+
+ if (seq.getName() != "") { //can get "" if commented line is at end of fasta file
if (namefile != "") {
- //make sure fasta and name files match
- it = names.find(temp.getName());
- if (it == names.end()) { mothurOut(temp.getName() + " is not in your names file, please correct."); mothurOutEndLine(); exit(1); }
- }else { sizes[temp.getName()] = 1; }
-
- seqPNode tempNode(sizes[temp.getName()], temp);
- alignSeqs.push_back(tempNode);
- active[temp.getName()] = true;
+ itSize = sizes.find(seq.getName());
+
+ if (itSize == sizes.end()) { m->mothurOut(seq.getName() + " is not in your names file, please correct."); m->mothurOutEndLine(); exit(1); }
+ else{
+ seqPNode tempNode(itSize->second, seq, names[seq.getName()]);
+ alignSeqs.push_back(tempNode);
+ if (seq.getAligned().length() > length) { length = 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(); }
+ }
}
- gobble(inFasta);
}
inFasta.close();
-
- if (alignSeqs.size() != 0) { length = alignSeqs[0].seq.getAligned().length(); }
-
+ //inNames.close();
return alignSeqs.size();
}
+
catch(exception& e) {
- errorOut(e, "PreClusterCommand", "readSeqs");
- exit(1);
- }
-}
-/**************************************************************************************************/
-void PreClusterCommand::readNameFile(){
- try {
- ifstream in;
- openInputFile(namefile, in);
- string firstCol, secondCol;
-
- while (!in.eof()) {
- in >> firstCol >> secondCol; gobble(in);
- names[firstCol] = secondCol;
- int size = 1;
- while (secondCol.find_first_of(',') != -1) {
- size++;
- secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
- }
- sizes[firstCol] = size;
- }
- in.close();
- }
- catch(exception& e) {
- errorOut(e, "PreClusterCommand", "readNameFile");
+ m->errorOut(e, "PreClusterCommand", "readFASTA");
exit(1);
}
}
+
/**************************************************************************************************/
+
int PreClusterCommand::calcMisMatches(string seq1, string seq2){
try {
int numBad = 0;
return numBad;
}
catch(exception& e) {
- errorOut(e, "PreClusterCommand", "calcMisMatches");
+ m->errorOut(e, "PreClusterCommand", "calcMisMatches");
exit(1);
}
}
+
/**************************************************************************************************/
+
void PreClusterCommand::printData(string newfasta, string newname){
try {
ofstream outFasta;
ofstream outNames;
- openOutputFile(newfasta, outFasta);
- openOutputFile(newname, outNames);
+
+ m->openOutputFile(newfasta, outFasta);
+ m->openOutputFile(newname, outNames);
- map<string, string>::iterator itNames;
for (int i = 0; i < alignSeqs.size(); i++) {
if (alignSeqs[i].numIdentical != 0) {
alignSeqs[i].seq.printSequence(outFasta);
-
- itNames = names.find(alignSeqs[i].seq.getName());
-
- outNames << itNames->first << '\t' << itNames->second << endl;
+ outNames << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].names << endl;
}
}
}
catch(exception& e) {
- errorOut(e, "PreClusterCommand", "printData");
+ m->errorOut(e, "PreClusterCommand", "printData");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+void PreClusterCommand::readNameFile(){
+ try {
+ ifstream in;
+ m->openInputFile(namefile, in);
+ string firstCol, secondCol;
+
+ while (!in.eof()) {
+ in >> firstCol >> secondCol; m->gobble(in);
+ names[firstCol] = secondCol;
+ int size = 1;
+
+ for(int i=0;i<secondCol.size();i++){
+ if(secondCol[i] == ','){ size++; }
+ }
+ sizes[firstCol] = size;
+ }
+ in.close();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PreClusterCommand", "readNameFile");
exit(1);
}
}
projects / mothur.git / blobdiff