+++ /dev/null
-/*
- * preclustercommand.cpp
- * Mothur
- *
- * Created by westcott on 12/21/09.
- * Copyright 2009 Schloss Lab. All rights reserved.
- *
- */
-
-#include "preclustercommand.h"
-#include "deconvolutecommand.h"
-
-//**********************************************************************************************************************
-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 pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter pdiffs("diffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pdiffs);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- 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 group parameter allows you to provide a group file so you can cluster by group. \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(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["fasta"] = tempOutNames;
- outputTypes["name"] = tempOutNames;
- outputTypes["map"] = 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; calledHelp = true; }
- else if(option == "citation") { citation(); abort = true; calledHelp = true;}
-
- else {
- 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;
- 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);
- 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; }
- }
-
- it = parameters.find("group");
- //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["group"] = inputDir + it->second; }
- }
- }
-
- //check for required parameters
- fastafile = validParameter.validFile(parameters, "fasta", 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; }
- else { m->setFastaFile(fastafile); }
-
- //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);
- if (namefile == "not found") { namefile = ""; }
- else if (namefile == "not open") { namefile = ""; abort = true; }
- else { m->setNameFile(namefile); }
-
- groupfile = validParameter.validFile(parameters, "group", true);
- if (groupfile == "not found") { groupfile = ""; bygroup = false; }
- else if (groupfile == "not open") { abort = true; groupfile = ""; }
- else { m->setGroupFile(groupfile); bygroup = true; }
-
- string temp = validParameter.validFile(parameters, "diffs", false); if(temp == "not found"){ temp = "1"; }
- m->mothurConvert(temp, diffs);
-
- temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
- m->setProcessors(temp);
- m->mothurConvert(temp, processors);
-
- if (namefile == "") {
- vector<string> files; files.push_back(fastafile);
- parser.getNameFile(files);
- }
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "PreClusterCommand", "PreClusterCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int PreClusterCommand::execute(){
- try {
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- 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 newMapFile = fileroot + "precluster.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;
- if (namefile != "") { parser = new SequenceParser(groupfile, fastafile, namefile); }
- else { parser = new SequenceParser(groupfile, fastafile); }
-
- vector<string> groups = parser->getNamesOfGroups();
-
- 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) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
-
- //run unique.seqs for deconvolute results
- string inputString = "fasta=" + newFastaFile;
- if (namefile != "") { inputString += ", name=" + newNamesFile; }
- 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();
-
- }else {
- if (namefile != "") { readNameFile(); }
-
- //reads fasta file and return number of seqs
- int numSeqs = readFASTA(); //fills alignSeqs and makes all seqs active
-
- 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(newMapFile);
- outputNames.push_back(newMapFile); outputTypes["map"].push_back(newMapFile);
-
- 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();
- printData(newFastaFile, newNamesFile);
-
- m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
- }
-
- 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();
- for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
- 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) {
- m->errorOut(e, "PreClusterCommand", "execute");
- exit(1);
- }
-}
-/**************************************************************************************************/
-int PreClusterCommand::createProcessesGroups(SequenceParser* parser, string newFName, string newNName, string newMFile, vector<string> groups) {
- try {
-
- vector<int> processIDS;
- int process = 1;
- int num = 0;
-
- //sanity check
- if (groups.size() < processors) { processors = groups.size(); }
-
- //divide the groups between the processors
- vector<linePair> lines;
- int numGroupsPerProcessor = groups.size() / processors;
- for (int i = 0; i < processors; i++) {
- int startIndex = i * numGroupsPerProcessor;
- int endIndex = (i+1) * numGroupsPerProcessor;
- if(i == (processors - 1)){ endIndex = groups.size(); }
- lines.push_back(linePair(startIndex, endIndex));
- }
-
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
-
- //loop through and create all the processes you want
- while (process != processors) {
- int pid = fork();
-
- if (pid > 0) {
- 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){
- 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();
- for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
- exit(0);
- }
- }
-
- //do my part
- 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
-
- //////////////////////////////////////////////////////////////////////////////////////////////////////
- //Windows version shared memory, so be careful when passing variables through the preClusterData struct.
- //Above fork() will clone, so memory is separate, but that's not the case with windows,
- //////////////////////////////////////////////////////////////////////////////////////////////////////
-
- vector<preClusterData*> pDataArray;
- DWORD dwThreadIdArray[processors-1];
- HANDLE hThreadArray[processors-1];
-
- //Create processor worker threads.
- for( int i=1; i<processors; i++ ){
- // Allocate memory for thread data.
- string extension = toString(i) + ".temp";
-
- 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);
-
- //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
- //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
- hThreadArray[i-1] = CreateThread(NULL, 0, MyPreclusterThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
- }
-
-
- //using the main process as a worker saves time and memory
- 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];
- }
-
-#endif
-
- //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"));
-
- m->appendFiles((newNName + toString(processIDS[i]) + ".temp"), newNName);
- m->mothurRemove((newNName + toString(processIDS[i]) + ".temp"));
- }
-
- return num;
-
- }
- catch(exception& e) {
- m->errorOut(e, "PreClusterCommand", "createProcessesGroups");
- exit(1);
- }
-}
-/**************************************************************************************************/
-int PreClusterCommand::driverGroups(SequenceParser* parser, string newFFile, string newNFile, string newMFile, int start, int end, vector<string> groups){
- try {
-
- int numSeqs = 0;
-
- //precluster each group
- for (int i = start; i < end; i++) {
-
- start = time(NULL);
-
- if (m->control_pressed) { return 0; }
-
- m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[i] + ":"); m->mothurOutEndLine();
-
- map<string, string> thisNameMap;
- if (namefile != "") { thisNameMap = parser->getNameMap(groups[i]); }
- vector<Sequence> thisSeqs = parser->getSeqs(groups[i]);
-
- //fill alignSeqs with this groups info.
- numSeqs = loadSeqs(thisNameMap, thisSeqs);
-
- if (m->control_pressed) { return 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(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; }
-
- m->mothurOut("Total number of sequences before pre.cluster was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine();
- m->mothurOut("pre.cluster removed " + toString(count) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
- printData(newFFile, newNFile);
-
- m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
-
- }
-
- return numSeqs;
- }
- catch(exception& e) {
- m->errorOut(e, "PreClusterCommand", "driverGroups");
- exit(1);
- }
-}
-/**************************************************************************************************/
-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);
-
- int count = 0;
- int numSeqs = alignSeqs.size();
-
- //think about running through twice...
- for (int i = 0; i < numSeqs; i++) {
-
- //are you active
- // itActive = active.find(alignSeqs[i].seq.getName());
-
- 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) { out.close(); return 0; }
-
- 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;
-
- 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 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(); }
-
- return count;
-
- }
- catch(exception& e) {
- m->errorOut(e, "PreClusterCommand", "process");
- exit(1);
- }
-}
-/**************************************************************************************************/
-int PreClusterCommand::readFASTA(){
- try {
- //ifstream inNames;
- ifstream inFasta;
-
- //m->openInputFile(namefile, inNames);
- m->openInputFile(fastafile, inFasta);
-
- //string firstCol, secondCol, nameString;
- set<int> lengths;
-
- while (!inFasta.eof()) {
-
- 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 != "") {
- 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);
- lengths.insert(seq.getAligned().length());
- }
- }else { //no names file, you are identical to yourself
- seqPNode tempNode(1, seq, seq.getName());
- alignSeqs.push_back(tempNode);
- 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();
- }
-
- catch(exception& e) {
- m->errorOut(e, "PreClusterCommand", "readFASTA");
- exit(1);
- }
-}
-/**************************************************************************************************/
-int PreClusterCommand::loadSeqs(map<string, string>& thisName, vector<Sequence>& thisSeqs){
- try {
- set<int> lengths;
- alignSeqs.clear();
- map<string, string>::iterator it;
- bool error = false;
-
- for (int i = 0; i < thisSeqs.size(); i++) {
-
- if (m->control_pressed) { return 0; }
-
- if (namefile != "") {
- it = thisName.find(thisSeqs[i].getName());
-
- //should never be true since parser checks for this
- if (it == thisName.end()) { m->mothurOut(thisSeqs[i].getName() + " is not in your names file, please correct."); m->mothurOutEndLine(); error = true; }
- else{
- //get number of reps
- int numReps = 1;
- for(int j=0;j<(it->second).length();j++){
- if((it->second)[j] == ','){ numReps++; }
- }
-
- seqPNode tempNode(numReps, thisSeqs[i], it->second);
- alignSeqs.push_back(tempNode);
- 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);
- 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; }
-
- thisSeqs.clear();
-
- return alignSeqs.size();
- }
-
- catch(exception& e) {
- m->errorOut(e, "PreClusterCommand", "loadSeqs");
- exit(1);
- }
-}
-
-/**************************************************************************************************/
-
-int PreClusterCommand::calcMisMatches(string seq1, string seq2){
- try {
- int numBad = 0;
-
- for (int i = 0; i < seq1.length(); i++) {
- //do they match
- if (seq1[i] != seq2[i]) { numBad++; }
- if (numBad > diffs) { return length; } //to far to cluster
- }
-
- return numBad;
- }
- catch(exception& e) {
- m->errorOut(e, "PreClusterCommand", "calcMisMatches");
- exit(1);
- }
-}
-
-/**************************************************************************************************/
-
-void PreClusterCommand::printData(string newfasta, string newname){
- try {
- ofstream outFasta;
- ofstream outNames;
-
- if (bygroup) {
- m->openOutputFileAppend(newfasta, outFasta);
- m->openOutputFileAppend(newname, outNames);
- }else {
- 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);
- outNames << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].names << endl;
- }
- }
-
- outFasta.close();
- outNames.close();
-
- }
- catch(exception& e) {
- 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