X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=preclustercommand.cpp;h=8e4f3274a490679c85f992f8584605c877c84850;hb=d6c0a11d1cecfac18b323285e7ffadb7f58e848f;hp=cab29633c8528c30fe0ba032cc6d76bfea44eccb;hpb=94ba64671398f3c9e591df90536833123de0fd34;p=mothur.git diff --git a/preclustercommand.cpp b/preclustercommand.cpp index cab2963..8e4f327 100644 --- a/preclustercommand.cpp +++ b/preclustercommand.cpp @@ -8,22 +8,77 @@ */ #include "preclustercommand.h" +#include "deconvolutecommand.h" //********************************************************************************************************************** -inline bool comparePriority(seqPNode first, seqPNode second) { return (first.numIdentical > second.numIdentical); } +vector 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 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 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; + 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", "outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -36,6 +91,12 @@ PreClusterCommand::PreClusterCommand(string option) { if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) { abort = true; } } + //initialize outputTypes + vector 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 = ""; } @@ -44,7 +105,7 @@ PreClusterCommand::PreClusterCommand(string option) { it = parameters.find("fasta"); //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["fasta"] = inputDir + it->second; } } @@ -52,32 +113,59 @@ PreClusterCommand::PreClusterCommand(string option) { 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; } } + + 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") { m->mothurOut("fasta is a required parameter for the pre.cluster command."); m->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; } + 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 += hasPath(fastafile); //if user entered a file with a path then preserve it + 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") { abort = true; } - else { readNameFile(); } + 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); - string temp = validParameter.validFile(parameters, "diffs", false); if(temp == "not found"){ temp = "1"; } - convert(temp, diffs); + if (namefile == "") { + vector files; files.push_back(fastafile); + parser.getNameFile(files); + } } } @@ -86,137 +174,347 @@ PreClusterCommand::PreClusterCommand(string option) { exit(1); } } - -//********************************************************************************************************************** -PreClusterCommand::~PreClusterCommand(){} //********************************************************************************************************************** -void PreClusterCommand::help(){ +int PreClusterCommand::execute(){ try { - m->mothurOut("The pre.cluster command groups sequences that are within a given number of base mismatches.\n"); - m->mothurOut("The pre.cluster command outputs a new fasta and name file.\n"); - m->mothurOut("The pre.cluster command parameters are fasta, names and diffs. The fasta parameter is required. \n"); - m->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"); - m->mothurOut("The diffs parameter allows you to specify maximum number of mismatched bases allowed between sequences in a grouping. The default is 1.\n"); - m->mothurOut("The pre.cluster command should be in the following format: \n"); - m->mothurOut("pre.cluster(fasta=yourFastaFile, names=yourNamesFile, diffs=yourMaxDiffs) \n"); - m->mothurOut("Example pre.cluster(fasta=amazon.fasta, diffs=2).\n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n"); + + 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 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(); + + Command* uniqueCommand = new DeconvoluteCommand(inputString); + uniqueCommand->execute(); + + map > filenames = uniqueCommand->getOutputFiles(); + + delete uniqueCommand; + + m->mothurOut("/******************************************/"); m->mothurOutEndLine(); + + m->renameFile(filenames["fasta"][0], newFastaFile); + + 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", "help"); + m->errorOut(e, "PreClusterCommand", "execute"); exit(1); } } -//********************************************************************************************************************** - -int PreClusterCommand::execute(){ +/**************************************************************************************************/ +int PreClusterCommand::createProcessesGroups(SequenceParser* parser, string newFName, string newNName, string newMFile, vector groups) { try { - if (abort == true) { return 0; } + vector processIDS; + int process = 1; + int num = 0; - //reads fasta file and return number of seqs - int numSeqs = readFASTA(); //fills alignSeqs and makes all seqs active + //sanity check + if (groups.size() < processors) { processors = groups.size(); } - if (m->control_pressed) { 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; } + //divide the groups between the processors + vector 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)); + } - string fileroot = outputDir + getRootName(getSimpleName(fastafile)); - string newFastaFile = fileroot + "precluster" + getExtension(fastafile); - string newNamesFile = fileroot + "precluster.names"; - ofstream outFasta; - ofstream outNames; +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - openOutputFile(newFastaFile, outFasta); - openOutputFile(newNamesFile, outNames); - - //sort seqs by number of identical seqs - alignSeqs.sort(comparePriority); - - int count = 0; - int i = 0; - //think about running through twice... - list::iterator itList; - list::iterator itList2; - for (itList = alignSeqs.begin(); itList != alignSeqs.end();) { + //loop through and create all the processes you want + while (process != processors) { + int pid = fork(); - //try to merge it with all smaller seqs - for (itList2 = alignSeqs.begin(); itList2 != alignSeqs.end();) { - - if (m->control_pressed) { outFasta.close(); outNames.close(); remove(newFastaFile.c_str()); remove(newNamesFile.c_str()); return 0; } - + 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){ + num = driverGroups(parser, newFName + toString(getpid()) + ".temp", newNName + toString(getpid()) + ".temp", newMFile, lines[process].start, lines[process].end, groups); + 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 pDataArray; + DWORD dwThreadIdArray[processors-1]; + HANDLE hThreadArray[processors-1]; + + //Create processor worker threads. + for( int i=1; iseq.getName() != itList2->seq.getName()) { //you don't want to merge with yourself - //are you within "diff" bases - - int mismatch = calcMisMatches((*itList).seq.getAligned(), (*itList2).seq.getAligned()); - - if (mismatch <= diffs) { - //merge - (*itList).names += ',' + (*itList2).names; - (*itList).numIdentical += (*itList2).numIdentical; - - itList2 = alignSeqs.erase(itList2); //itList2--; - count++; - }else{ itList2++; } - }else{ itList2++; } - + 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]); } - - //ouptut this sequence - printData(outFasta, outNames, (*itList)); + CloseHandle(hThreadArray[i]); + delete pDataArray[i]; + } + +#endif + + //append output files + for(int i=0;igetFullPathName(".\\" + newFName); + //newNName = m->getFullPathName(".\\" + newNName); + + m->appendFiles((newFName + toString(processIDS[i]) + ".temp"), newFName); + m->mothurRemove((newFName + toString(processIDS[i]) + ".temp")); - //remove sequence - itList = alignSeqs.erase(itList); + 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 groups){ + try { + + int numSeqs = 0; + + //precluster each group + for (int i = start; i < end; i++) { - i++; + start = time(NULL); + + if (m->control_pressed) { return 0; } + + m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[i] + ":"); m->mothurOutEndLine(); + + map thisNameMap; + if (namefile != "") { thisNameMap = parser->getNameMap(groups[i]); } + vector 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(); - if(i % 100 == 0) { m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); } } - - if(i % 100 != 0) { m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); } - outFasta.close(); - outNames.close(); + return numSeqs; + } + catch(exception& e) { + m->errorOut(e, "PreClusterCommand", "driverGroups"); + exit(1); + } +} +/**************************************************************************************************/ +int PreClusterCommand::process(string newMapFile){ + try { + ofstream out; + m->openOutputFile(newMapFile, out); - if (m->control_pressed) { remove(newFastaFile.c_str()); remove(newNamesFile.c_str()); return 0; } + //sort seqs by number of identical seqs + sort(alignSeqs.begin(), alignSeqs.end(), comparePriority); + + int count = 0; + int numSeqs = alignSeqs.size(); - m->mothurOut("Total number of sequences before precluster was " + toString(numSeqs) + "."); m->mothurOutEndLine(); - m->mothurOut("pre.cluster removed " + toString(count) + " sequences."); m->mothurOutEndLine(); + //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 (m->control_pressed) { remove(newFastaFile.c_str()); remove(newNamesFile.c_str()); return 0; } + if(numSeqs % 100 != 0) { m->mothurOut(toString(numSeqs) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); } - m->mothurOutEndLine(); - m->mothurOut("Output File Names: "); m->mothurOutEndLine(); - m->mothurOut(newFastaFile); m->mothurOutEndLine(); - m->mothurOut(newNamesFile); m->mothurOutEndLine(); - m->mothurOutEndLine(); - - return 0; + return count; } catch(exception& e) { - m->errorOut(e, "PreClusterCommand", "execute"); + m->errorOut(e, "PreClusterCommand", "process"); exit(1); } } - /**************************************************************************************************/ - -//this requires the names and fasta file to be in the same order - int PreClusterCommand::readFASTA(){ try { //ifstream inNames; ifstream inFasta; - //openInputFile(namefile, inNames); - openInputFile(fastafile, inFasta); + //m->openInputFile(namefile, inNames); + m->openInputFile(fastafile, inFasta); //string firstCol, secondCol, nameString; - length = 0; + set lengths; while (!inFasta.eof()) { @@ -225,14 +523,14 @@ int PreClusterCommand::readFASTA(){ //inNames >> firstCol >> secondCol; //nameString = secondCol; - //gobble(inNames); + //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); gobble(inFasta); + Sequence seq(inFasta); m->gobble(inFasta); if (seq.getName() != "") { //can get "" if commented line is at end of fasta file if (namefile != "") { @@ -242,17 +540,20 @@ int PreClusterCommand::readFASTA(){ 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(); } + return alignSeqs.size(); } @@ -261,7 +562,57 @@ int PreClusterCommand::readFASTA(){ exit(1); } } - +/**************************************************************************************************/ +int PreClusterCommand::loadSeqs(map& thisName, vector& thisSeqs){ + try { + set lengths; + alignSeqs.clear(); + map::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(); } + + //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){ @@ -284,10 +635,29 @@ int PreClusterCommand::calcMisMatches(string seq1, string seq2){ /**************************************************************************************************/ -void PreClusterCommand::printData(ofstream& outFasta, ofstream& outNames, seqPNode thisSeq){ +void PreClusterCommand::printData(string newfasta, string newname){ try { - thisSeq.seq.printSequence(outFasta); - outNames << thisSeq.seq.getName() << '\t' << thisSeq.names << endl; + 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"); @@ -299,16 +669,16 @@ void PreClusterCommand::printData(ofstream& outFasta, ofstream& outNames, seqPNo void PreClusterCommand::readNameFile(){ try { ifstream in; - openInputFile(namefile, in); + m->openInputFile(namefile, in); string firstCol, secondCol; while (!in.eof()) { - in >> firstCol >> secondCol; gobble(in); + in >> firstCol >> secondCol; m->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()); + + for(int i=0;i