X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=screenseqscommand.cpp;h=d2fbe935356a2f0752efa683a893a5892e1b2eb2;hp=586e436982c3629b842e0b9ddb0da73a9e3d5ebb;hb=c48d91112209b841444923670dca5454da0e2a4d;hpb=544469443afe44920bdf279aefd26d29534cabaf diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp index 586e436..d2fbe93 100644 --- a/screenseqscommand.cpp +++ b/screenseqscommand.cpp @@ -8,191 +8,2646 @@ */ #include "screenseqscommand.h" +#include "counttable.h" -//*************************************************************************************************************** +//********************************************************************************************************************** +vector ScreenSeqsCommand::setParameters(){ + try { + CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta); + CommandParameter pcontigsreport("contigsreport", "InputTypes", "", "", "report", "none", "none","contigsreport",false,true,true); parameters.push_back(pcontigsreport); + CommandParameter palignreport("alignreport", "InputTypes", "", "", "report", "none", "none","alignreport",false,false); parameters.push_back(palignreport); + CommandParameter psummary("summary", "InputTypes", "", "", "report", "none", "none","summary",false,false); parameters.push_back(psummary); + CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname); + CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount); + CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","group",false,false,true); parameters.push_back(pgroup); + CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none","qfile",false,false); parameters.push_back(pqfile); + + CommandParameter ptax("taxonomy", "InputTypes", "", "", "none", "none", "none","taxonomy",false,false); parameters.push_back(ptax); + CommandParameter pstart("start", "Number", "", "-1", "", "", "","",false,false,true); parameters.push_back(pstart); + CommandParameter pend("end", "Number", "", "-1", "", "", "","",false,false,true); parameters.push_back(pend); + CommandParameter pmaxambig("maxambig", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pmaxambig); + CommandParameter pmaxhomop("maxhomop", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pmaxhomop); + CommandParameter pminlength("minlength", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pminlength); + CommandParameter pmaxlength("maxlength", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pmaxlength); + CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors); + CommandParameter pcriteria("criteria", "Number", "", "90", "", "", "","",false,false); parameters.push_back(pcriteria); + CommandParameter poptimize("optimize", "Multiple", "none-start-end-maxambig-maxhomop-minlength-maxlength", "none", "", "", "","",true,false); parameters.push_back(poptimize); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir); + + //report parameters + CommandParameter pminoverlap("minoverlap", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pminoverlap); + CommandParameter postart("ostart", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(postart); + CommandParameter poend("oend", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(poend); + CommandParameter pmismatches("mismatches", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pmismatches); + CommandParameter pmaxn("maxn", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pmaxn); + CommandParameter pminscore("minscore", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pminscore); + CommandParameter pmaxinsert("maxinsert", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pmaxinsert); + CommandParameter pminsim("minsim", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pminsim); -ScreenSeqsCommand::ScreenSeqsCommand(){ + + + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ScreenSeqsCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string ScreenSeqsCommand::getHelpString(){ try { - globaldata = GlobalData::getInstance(); - if(globaldata->getFastaFile() == "") { cout << "you must provide a fasta formatted file" << endl; } + string helpString = ""; + helpString += "The screen.seqs command reads a fastafile and screens sequences.\n"; + helpString += "The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, group, count, qfile, alignreport, contigsreport, summary, taxonomy, optimize, criteria and processors.\n"; + helpString += "The fasta parameter is required.\n"; + helpString += "The contigsreport parameter allows you to use the contigsreport file to determine if a sequence is good. Screening parameters include: minoverlap, ostart, oend and mismatches. \n"; + helpString += "The alignreport parameter allows you to use the alignreport file to determine if a sequence is good. Screening parameters include: minsim, minscore and maxinsert. \n"; + helpString += "The summary parameter allows you to use the summary file from summary.seqs to save time processing.\n"; + helpString += "The taxonomy parameter allows you to remove bad seqs from taxonomy files.\n"; + helpString += "The start parameter is used to set a position the \"good\" sequences must start by. The default is -1.\n"; + helpString += "The end parameter is used to set a position the \"good\" sequences must end after. The default is -1.\n"; + helpString += "The maxambig parameter allows you to set the maximum number of ambigious bases allowed. The default is -1.\n"; + helpString += "The maxhomop parameter allows you to set a maximum homopolymer length. \n"; + helpString += "The minlength parameter allows you to set and minimum sequence length. \n"; + helpString += "The maxn parameter allows you to set and maximum number of N's allowed in a sequence. \n"; + helpString += "The minoverlap parameter allows you to set and minimum overlap. The default is -1. \n"; + helpString += "The ostart parameter is used to set an overlap position the \"good\" sequences must start by. The default is -1. \n"; + helpString += "The oend parameter is used to set an overlap position the \"good\" sequences must end after. The default is -1.\n"; + helpString += "The mismatches parameter allows you to set and maximum mismatches in the contigs.report. \n"; + helpString += "The minsim parameter allows you to set the minimum similarity to template sequences during alignment. Found in column \'SimBtwnQuery&Template\' in align.report file.\n"; + helpString += "The minscore parameter allows you to set the minimum search score during alignment. Found in column \'SearchScore\' in align.report file.\n"; + helpString += "The maxinsert parameter allows you to set the maximum number of insertions during alignment. Found in column \'LongestInsert\' in align.report file.\n"; + helpString += "The processors parameter allows you to specify the number of processors to use while running the command. The default is 1.\n"; + helpString += "The optimize and criteria parameters allow you set the start, end, maxabig, maxhomop, minlength and maxlength parameters relative to your set of sequences .\n"; + helpString += "For example optimize=start-end, criteria=90, would set the start and end values to the position 90% of your sequences started and ended.\n"; + helpString += "The name parameter allows you to provide a namesfile, and the group parameter allows you to provide a groupfile.\n"; + helpString += "The screen.seqs command should be in the following format: \n"; + helpString += "screen.seqs(fasta=yourFastaFile, name=youNameFile, group=yourGroupFIle, start=yourStart, end=yourEnd, maxambig=yourMaxambig, \n"; + helpString += "maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength) \n"; + helpString += "Example screen.seqs(fasta=abrecovery.fasta, name=abrecovery.names, group=abrecovery.groups, start=..., end=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n"; + helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n"; + return helpString; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the SeqCoordCommand class Function SeqCoordCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ScreenSeqsCommand", "getHelpString"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the SeqCoordCommand class function SeqCoordCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} +//********************************************************************************************************************** +string ScreenSeqsCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "fasta") { pattern = "[filename],good,[extension]"; } + else if (type == "taxonomy") { pattern = "[filename],good,[extension]"; } + else if (type == "name") { pattern = "[filename],good,[extension]"; } + else if (type == "group") { pattern = "[filename],good,[extension]"; } + else if (type == "count") { pattern = "[filename],good,[extension]"; } + else if (type == "accnos") { pattern = "[filename],bad.accnos"; } + else if (type == "qfile") { pattern = "[filename],good,[extension]"; } + else if (type == "alignreport") { pattern = "[filename],good.align.report"; } + else if (type == "contigsreport") { pattern = "[filename],good.contigs.report"; } + else if (type == "summary") { pattern = "[filename],good.summary"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "ScreenSeqsCommand", "getOutputPattern"); + exit(1); + } +} +//********************************************************************************************************************** +ScreenSeqsCommand::ScreenSeqsCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["name"] = tempOutNames; + outputTypes["group"] = tempOutNames; + outputTypes["alignreport"] = tempOutNames; + outputTypes["contigsreport"] = tempOutNames; + outputTypes["summary"] = tempOutNames; + outputTypes["accnos"] = tempOutNames; + outputTypes["qfile"] = tempOutNames; + outputTypes["taxonomy"] = tempOutNames; + outputTypes["count"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand"); exit(1); - } + } } - //*************************************************************************************************************** -ScreenSeqsCommand::~ScreenSeqsCommand(){ /* do nothing */ } +ScreenSeqsCommand::ScreenSeqsCommand(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 myArray = setParameters(); + + OptionParser parser(option); + map parameters = parser.getParameters(); + + ValidParameters validParameter("screen.seqs"); + map::iterator it; + + //check to make sure all parameters are valid for command + for (it = parameters.begin(); it != parameters.end(); it++) { + if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } + } + + //initialize outputTypes + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["name"] = tempOutNames; + outputTypes["group"] = tempOutNames; + outputTypes["alignreport"] = tempOutNames; + outputTypes["accnos"] = tempOutNames; + outputTypes["qfile"] = tempOutNames; + outputTypes["taxonomy"] = tempOutNames; + outputTypes["count"] = tempOutNames; + outputTypes["contigsreport"] = tempOutNames; + outputTypes["summary"] = 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("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; } + } + + 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("alignreport"); + //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["alignreport"] = inputDir + it->second; } + } + + it = parameters.find("contigsreport"); + //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["contigsreport"] = inputDir + it->second; } + } + + it = parameters.find("summary"); + //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["summary"] = inputDir + it->second; } + } + + it = parameters.find("qfile"); + //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["qfile"] = inputDir + it->second; } + } + + it = parameters.find("taxonomy"); + //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["taxonomy"] = inputDir + it->second; } + } + + it = parameters.find("count"); + //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["count"] = 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); } + + groupfile = validParameter.validFile(parameters, "group", true); + if (groupfile == "not open") { abort = true; } + else if (groupfile == "not found") { groupfile = ""; } + else { m->setGroupFile(groupfile); } + + qualfile = validParameter.validFile(parameters, "qfile", true); + if (qualfile == "not open") { abort = true; } + else if (qualfile == "not found") { qualfile = ""; } + else { m->setQualFile(qualfile); } + + namefile = validParameter.validFile(parameters, "name", true); + if (namefile == "not open") { namefile = ""; abort = true; } + else if (namefile == "not found") { namefile = ""; } + else { m->setNameFile(namefile); } + + countfile = validParameter.validFile(parameters, "count", true); + if (countfile == "not open") { countfile = ""; abort = true; } + else if (countfile == "not found") { countfile = ""; } + else { m->setCountTableFile(countfile); } + + contigsreport = validParameter.validFile(parameters, "contigsreport", true); + if (contigsreport == "not open") { contigsreport = ""; abort = true; } + else if (contigsreport == "not found") { contigsreport = ""; } + + summaryfile = validParameter.validFile(parameters, "summary", true); + if (summaryfile == "not open") { summaryfile = ""; abort = true; } + else if (summaryfile == "not found") { summaryfile = ""; } + else { m->setSummaryFile(summaryfile); } + + if ((namefile != "") && (countfile != "")) { + m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true; + } + + if ((groupfile != "") && (countfile != "")) { + m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true; + } + + alignreport = validParameter.validFile(parameters, "alignreport", true); + if (alignreport == "not open") { abort = true; } + else if (alignreport == "not found") { alignreport = ""; } + + taxonomy = validParameter.validFile(parameters, "taxonomy", true); + if (taxonomy == "not open") { abort = true; } + else if (taxonomy == "not found") { taxonomy = ""; } + + //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... + string temp; + temp = validParameter.validFile(parameters, "start", false); if (temp == "not found") { temp = "-1"; } + m->mothurConvert(temp, startPos); + + temp = validParameter.validFile(parameters, "end", false); if (temp == "not found") { temp = "-1"; } + m->mothurConvert(temp, endPos); + + temp = validParameter.validFile(parameters, "maxambig", false); if (temp == "not found") { temp = "-1"; } + m->mothurConvert(temp, maxAmbig); + + temp = validParameter.validFile(parameters, "maxhomop", false); if (temp == "not found") { temp = "-1"; } + m->mothurConvert(temp, maxHomoP); + + temp = validParameter.validFile(parameters, "minlength", false); if (temp == "not found") { temp = "-1"; } + m->mothurConvert(temp, minLength); + + temp = validParameter.validFile(parameters, "maxlength", false); if (temp == "not found") { temp = "-1"; } + m->mothurConvert(temp, maxLength); + + temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } + m->setProcessors(temp); + m->mothurConvert(temp, processors); + + temp = validParameter.validFile(parameters, "minoverlap", false); if (temp == "not found") { temp = "-1"; } + m->mothurConvert(temp, minOverlap); + + temp = validParameter.validFile(parameters, "ostart", false); if (temp == "not found") { temp = "-1"; } + m->mothurConvert(temp, oStart); + + temp = validParameter.validFile(parameters, "oend", false); if (temp == "not found") { temp = "-1"; } + m->mothurConvert(temp, oEnd); + + temp = validParameter.validFile(parameters, "mismatches", false); if (temp == "not found") { temp = "-1"; } + m->mothurConvert(temp, mismatches); + + temp = validParameter.validFile(parameters, "maxn", false); if (temp == "not found") { temp = "-1"; } + m->mothurConvert(temp, maxN); + + temp = validParameter.validFile(parameters, "minscore", false); if (temp == "not found") { temp = "-1"; } + m->mothurConvert(temp, minScore); + + temp = validParameter.validFile(parameters, "maxinsert", false); if (temp == "not found") { temp = "-1"; } + m->mothurConvert(temp, maxInsert); + + temp = validParameter.validFile(parameters, "minsim", false); if (temp == "not found") { temp = "-1"; } + m->mothurConvert(temp, minSim); + + temp = validParameter.validFile(parameters, "optimize", false); //optimizing trumps the optimized values original value + if (temp == "not found"){ temp = "none"; } + m->splitAtDash(temp, optimize); + + if ((contigsreport != "") && ((summaryfile != "") || ( alignreport != ""))) { + m->mothurOut("[ERROR]: You may only provide one of the following: contigsreport, alignreport or summary, aborting.\n"); abort=true; + } + + if ((alignreport != "") && ((summaryfile != "") || ( contigsreport != ""))) { + m->mothurOut("[ERROR]: You may only provide one of the following: contigsreport, alignreport or summary, aborting.\n"); abort=true; + } + + if ((summaryfile != "") && ((alignreport != "") || ( contigsreport != ""))) { + m->mothurOut("[ERROR]: You may only provide one of the following: contigsreport, alignreport or summary, aborting.\n"); abort=true; + } + + //check to make sure you have the files you need for certain screening + if ((contigsreport == "") && ((minOverlap != -1) || (oStart != -1) || (oEnd != -1) || (mismatches != -1))) { + m->mothurOut("[ERROR]: minoverlap, ostart, oend and mismatches can only be used with a contigs.report file, aborting.\n"); abort=true; + } + + if ((alignreport == "") && ((minScore != -1) || (maxInsert != -1) || (minSim != -1))) { + m->mothurOut("[ERROR]: minscore, maxinsert and minsim can only be used with a align.report file, aborting.\n"); abort=true; + } + + //check for invalid optimize options + set validOptimizers; + validOptimizers.insert("none"); validOptimizers.insert("start"); validOptimizers.insert("end"); validOptimizers.insert("maxambig"); validOptimizers.insert("maxhomop"); validOptimizers.insert("minlength"); validOptimizers.insert("maxlength"); validOptimizers.insert("maxn"); + if (contigsreport != "") { validOptimizers.insert("minoverlap"); validOptimizers.insert("ostart"); validOptimizers.insert("oend"); validOptimizers.insert("mismatches"); } + if (alignreport != "") { validOptimizers.insert("minscore"); validOptimizers.insert("maxinsert"); validOptimizers.insert("minsim"); } + + for (int i = 0; i < optimize.size(); i++) { + if (validOptimizers.count(optimize[i]) == 0) { + m->mothurOut(optimize[i] + " is not a valid optimizer with your input files. Valid options are "); + string valid = ""; + for (set::iterator it = validOptimizers.begin(); it != validOptimizers.end(); it++) { + valid += (*it) + ", "; + } + if (valid.length() != 0) { valid = valid.substr(0, valid.length()-2); } + m->mothurOut(valid + "."); + m->mothurOutEndLine(); + optimize.erase(optimize.begin()+i); + i--; + } + } + + if (optimize.size() == 1) { if (optimize[0] == "none") { optimize.clear(); } } + + temp = validParameter.validFile(parameters, "criteria", false); if (temp == "not found"){ temp = "90"; } + m->mothurConvert(temp, criteria); + + if (countfile == "") { + if (namefile == "") { + vector files; files.push_back(fastafile); + parser.getNameFile(files); + } + } + } + } + catch(exception& e) { + m->errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand"); + exit(1); + } +} //*************************************************************************************************************** int ScreenSeqsCommand::execute(){ try{ - int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength; - convert(globaldata->getStartPos(), startPos); - convert(globaldata->getEndPos(), endPos); - convert(globaldata->getMaxAmbig(), maxAmbig); - convert(globaldata->getMaxHomoPolymer(), maxHomoP); - convert(globaldata->getMinLength(), minLength); - convert(globaldata->getMaxLength(), maxLength); - ifstream inFASTA; - openInputFile(globaldata->getFastaFile(), inFASTA); + if (abort == true) { if (calledHelp) { return 0; } return 2; } - set badSeqNames; + map badSeqNames; + int start = time(NULL); + int numFastaSeqs = 0; + + if ((contigsreport == "") && (summaryfile == "") && (alignreport == "")) { numFastaSeqs = screenFasta(badSeqNames); } + else { numFastaSeqs = screenReports(badSeqNames); } - string goodSeqFile = getRootName(globaldata->inputFileName) + "good" + getExtension(globaldata->inputFileName); - string badSeqFile = getRootName(globaldata->inputFileName) + "bad" + getExtension(globaldata->inputFileName); + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } + + #ifdef USE_MPI + int pid; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + + if (pid == 0) { //only one process should fix files + #endif + + if(namefile != "" && groupfile != "") { + screenNameGroupFile(badSeqNames); + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } + }else if(namefile != "") { + screenNameGroupFile(badSeqNames); + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } + }else if(groupfile != "") { screenGroupFile(badSeqNames); } // this screens just the group + else if (countfile != "") { screenCountFile(badSeqNames); } + + + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } + + if(qualfile != "") { screenQual(badSeqNames); } + if(taxonomy != "") { screenTaxonomy(badSeqNames); } - ofstream goodSeqOut; openOutputFile(goodSeqFile, goodSeqOut); - ofstream badSeqOut; openOutputFile(badSeqFile, badSeqOut); + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } - while(!inFASTA.eof()){ - Sequence currSeq(inFASTA); - bool goodSeq = 1; // innocent until proven guilty - if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos()) { goodSeq = 0; } - if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos()) { goodSeq = 0; } - if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases()) { goodSeq = 0; } - if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer()) { goodSeq = 0; } - if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases()) { goodSeq = 0; } - if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases()) { goodSeq = 0; } - - if(goodSeq == 1){ - currSeq.printSequence(goodSeqOut); - } - else{ - currSeq.printSequence(badSeqOut); - badSeqNames.insert(currSeq.getName()); + #ifdef USE_MPI } - gobble(inFASTA); - } + #endif + + 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(); + 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); } + } + + itTypes = outputTypes.find("group"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); } + } + + itTypes = outputTypes.find("qfile"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); } + } + itTypes = outputTypes.find("taxonomy"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); } + } + + itTypes = outputTypes.find("count"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); } + } + + m->mothurOut("It took " + toString(time(NULL) - start) + " secs to screen " + toString(numFastaSeqs) + " sequences."); + m->mothurOutEndLine(); + return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "ScreenSeqsCommand", "execute"); + exit(1); + } +} +//***************************************************************************************************************/ +int ScreenSeqsCommand::runFastaScreening(map& badSeqNames){ + try{ + int numFastaSeqs = 0; + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile)); + string badAccnosFile = getOutputFileName("accnos",variables); + variables["[extension]"] = m->getExtension(fastafile); + string goodSeqFile = getOutputFileName("fasta", variables); + outputNames.push_back(goodSeqFile); outputTypes["fasta"].push_back(goodSeqFile); + outputNames.push_back(badAccnosFile); outputTypes["accnos"].push_back(badAccnosFile); + +#ifdef USE_MPI + int pid, numSeqsPerProcessor; + int tag = 2001; + vector MPIPos; + + MPI_Status status; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are + MPI_Comm_size(MPI_COMM_WORLD, &processors); + + MPI_File inMPI; + MPI_File outMPIGood; + MPI_File outMPIBadAccnos; + + int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; + int inMode=MPI_MODE_RDONLY; + + char outGoodFilename[1024]; + strcpy(outGoodFilename, goodSeqFile.c_str()); + + char outBadAccnosFilename[1024]; + strcpy(outBadAccnosFilename, badAccnosFile.c_str()); + + char inFileName[1024]; + strcpy(inFileName, fastafile.c_str()); + + MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer + MPI_File_open(MPI_COMM_WORLD, outGoodFilename, outMode, MPI_INFO_NULL, &outMPIGood); + MPI_File_open(MPI_COMM_WORLD, outBadAccnosFilename, outMode, MPI_INFO_NULL, &outMPIBadAccnos); + + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBadAccnos); return 0; } + + if (pid == 0) { //you are the root process + + MPIPos = m->setFilePosFasta(fastafile, numFastaSeqs); //fills MPIPos, returns numSeqs + + //send file positions to all processes + for(int i = 1; i < processors; i++) { + MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD); + MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD); + } + + //figure out how many sequences you have to align + numSeqsPerProcessor = numFastaSeqs / processors; + int startIndex = pid * numSeqsPerProcessor; + if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; } + + //align your part + driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames); + + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBadAccnos); return 0; } + + for (int i = 1; i < processors; i++) { + //get bad lists + int badSize; + MPI_Recv(&badSize, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status); + } + }else{ //you are a child process + MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status); + MPIPos.resize(numFastaSeqs+1); + MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status); + + //figure out how many sequences you have to align + numSeqsPerProcessor = numFastaSeqs / processors; + int startIndex = pid * numSeqsPerProcessor; + if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; } + + //align your part + driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames); + + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBadAccnos); return 0; } + + //send bad list + int badSize = badSeqNames.size(); + MPI_Send(&badSize, 1, MPI_INT, 0, tag, MPI_COMM_WORLD); + } + + //close files + MPI_File_close(&inMPI); + MPI_File_close(&outMPIGood); + MPI_File_close(&outMPIBadAccnos); + MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case + +#else + if(processors == 1){ numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames); } + else{ numFastaSeqs = createProcesses(goodSeqFile, badAccnosFile, fastafile, badSeqNames); } + + if (m->control_pressed) { m->mothurRemove(goodSeqFile); return numFastaSeqs; } +#endif + +#ifdef USE_MPI + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + + if (pid == 0) { //only one process should fix files + + //read accnos file with all names in it, process 0 just has its names + MPI_File inMPIAccnos; + MPI_Offset size; + + char inFileName[1024]; + strcpy(inFileName, badAccnosFile.c_str()); + + MPI_File_open(MPI_COMM_SELF, inFileName, inMode, MPI_INFO_NULL, &inMPIAccnos); //comm, filename, mode, info, filepointer + MPI_File_get_size(inMPIAccnos, &size); + + char* buffer = new char[size]; + MPI_File_read(inMPIAccnos, buffer, size, MPI_CHAR, &status); + + string tempBuf = buffer; + if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size); } + istringstream iss (tempBuf,istringstream::in); + + delete buffer; + MPI_File_close(&inMPIAccnos); + + badSeqNames.clear(); + string tempName, trashCode; + while (!iss.eof()) { + iss >> tempName >> trashCode; m->gobble(iss); + badSeqNames[tempName] = trashCode; + } + } +#endif + + + return numFastaSeqs; + + } + catch(exception& e) { + m->errorOut(e, "ScreenSeqsCommand", "runFastaScreening"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the FilterSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} +//***************************************************************************************************************/ +int ScreenSeqsCommand::screenReports(map& badSeqNames){ + try{ + int numFastaSeqs = 0; + bool summarizedFasta = false; + + //did not provide a summary file, but set a parameter that requires summarizing the fasta file + //or did provide a summary file, but set maxn parameter so we must summarize the fasta file + vector positions; + if (((summaryfile == "") && ((m->inUsersGroups("maxambig", optimize)) ||(m->inUsersGroups("maxhomop", optimize)) ||(m->inUsersGroups("maxlength", optimize)) || (m->inUsersGroups("minlength", optimize)) || (m->inUsersGroups("start", optimize)) || (m->inUsersGroups("end", optimize)))) || ((summaryfile != "") && m->inUsersGroups("maxn", optimize))) { + //use the namefile to optimize correctly + if (namefile != "") { nameMap = m->readNames(namefile); } + else if (countfile != "") { + CountTable ct; + ct.readTable(countfile); + nameMap = ct.getNameMap(); + } + getSummary(positions); + summarizedFasta = true; + } else { + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + positions = m->divideFile(fastafile, processors); + for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); } + #else + if(processors == 1){ lines.push_back(linePair(0, 1000)); } + else { + int numFastaSeqs = 0; + positions = m->setFilePosFasta(fastafile, numFastaSeqs); + if (positions.size() < processors) { processors = positions.size(); } + + //figure out how many sequences you have to process + int numSeqsPerProcessor = numFastaSeqs / processors; + for (int i = 0; i < processors; i++) { + int startIndex = i * numSeqsPerProcessor; + if(i == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; } + lines.push_back(linePair(positions[startIndex], numSeqsPerProcessor)); + } + } + #endif + } + + if ((summaryfile != "") && ((m->inUsersGroups("maxambig", optimize)) ||(m->inUsersGroups("maxhomop", optimize)) ||(m->inUsersGroups("maxlength", optimize)) || (m->inUsersGroups("minlength", optimize)) || (m->inUsersGroups("start", optimize)) || (m->inUsersGroups("end", optimize))) && !summarizedFasta) { //summarize based on summaryfile + if (namefile != "") { nameMap = m->readNames(namefile); } + else if (countfile != "") { + CountTable ct; + ct.readTable(countfile); + nameMap = ct.getNameMap(); + } + getSummaryReport(); + }else if ((contigsreport != "") && ((m->inUsersGroups("minoverlap", optimize)) || (m->inUsersGroups("ostart", optimize)) || (m->inUsersGroups("oend", optimize)) || (m->inUsersGroups("mismatches", optimize)))) { //optimize settings based on contigs file + optimizeContigs(); + }else if ((alignreport != "") && ((m->inUsersGroups("minsim", optimize)) || (m->inUsersGroups("minscore", optimize)) || (m->inUsersGroups("maxinsert", optimize)))) { //optimize settings based on contigs file + optimizeAlign(); + } + + + //provided summary file, and did not set maxn so no need to summarize fasta + if (summaryfile != "") { numFastaSeqs = screenSummary(badSeqNames); } + //add in any seqs that fail due to contigs report results + else if (contigsreport != "") { numFastaSeqs = screenContigs(badSeqNames); } + //add in any seqs that fail due to align report + else if (alignreport != "") { numFastaSeqs = screenAlignReport(badSeqNames); } + + return numFastaSeqs; + } + catch(exception& e) { + m->errorOut(e, "ScreenSeqsCommand", "screenReports"); exit(1); } - } - //*************************************************************************************************************** +int ScreenSeqsCommand::screenAlignReport(map& badSeqNames){ + try { + + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(alignreport)); + string outSummary = getOutputFileName("alignreport",variables); + outputNames.push_back(outSummary); outputTypes["alignreport"].push_back(outSummary); + + string name, TemplateName, SearchMethod, AlignmentMethod; + //QueryName QueryLength TemplateName TemplateLength SearchMethod SearchScore AlignmentMethod QueryStart QueryEnd TemplateStart TemplateEnd PairwiseAlignmentLength GapsInQuery GapsInTemplate LongestInsert SimBtwnQuery&Template + //checking for minScore, maxInsert, minSim + int length, TemplateLength, QueryStart, QueryEnd, TemplateStart, TemplateEnd, PairwiseAlignmentLength, GapsInQuery, GapsInTemplate, LongestInsert; + float SearchScore, SimBtwnQueryTemplate; + + ofstream out; + m->openOutputFile(outSummary, out); + + //read summary file + ifstream in; + m->openInputFile(alignreport, in); + out << (m->getline(in)) << endl; //skip headers + + int count = 0; + + while (!in.eof()) { + + if (m->control_pressed) { in.close(); out.close(); return 0; } + + //seqname start end nbases ambigs polymer numSeqs + in >> name >> length >> TemplateName >> TemplateLength >> SearchMethod >> SearchScore >> AlignmentMethod >> QueryStart >> QueryEnd >> TemplateStart >> TemplateEnd >> PairwiseAlignmentLength >> GapsInQuery >> GapsInTemplate >> LongestInsert >> SimBtwnQueryTemplate; m->gobble(in); -void ScreenSeqsCommand::screenNameGroupFile(set badSeqNames){ + bool goodSeq = 1; // innocent until proven guilty + string trashCode = ""; + if(maxInsert != -1 && maxInsert < LongestInsert) { goodSeq = 0; trashCode += "insert|"; } + if(minScore != -1 && minScore > SearchScore) { goodSeq = 0; trashCode += "score|"; } + if(minSim != -1 && minSim > SimBtwnQueryTemplate) { goodSeq = 0; trashCode += "sim|"; } + + if(goodSeq == 1){ + out << name << '\t' << length << '\t' << TemplateName << '\t' << TemplateLength << '\t' << SearchMethod << '\t' << SearchScore << '\t' << AlignmentMethod << '\t' << QueryStart << '\t' << QueryEnd << '\t' << TemplateStart << '\t' << TemplateEnd << '\t' << PairwiseAlignmentLength << '\t' << GapsInQuery << '\t' << GapsInTemplate << '\t' << LongestInsert << '\t' << SimBtwnQueryTemplate << endl; + } + else{ badSeqNames[name] = trashCode; } + count++; + } + in.close(); + out.close(); + + int oldBadSeqsCount = badSeqNames.size(); + + int numFastaSeqs = runFastaScreening(badSeqNames); + + if (oldBadSeqsCount != badSeqNames.size()) { //more seqs were removed by maxns + m->renameFile(outSummary, outSummary+".temp"); + + ofstream out2; + m->openOutputFile(outSummary, out2); + + //read summary file + ifstream in2; + m->openInputFile(outSummary+".temp", in2); + out2 << (m->getline(in2)) << endl; //skip headers + + while (!in2.eof()) { + + if (m->control_pressed) { in2.close(); out2.close(); return 0; } + + //seqname start end nbases ambigs polymer numSeqs + in2 >> name >> length >> TemplateName >> TemplateLength >> SearchMethod >> SearchScore >> AlignmentMethod >> QueryStart >> QueryEnd >> TemplateStart >> TemplateEnd >> PairwiseAlignmentLength >> GapsInQuery >> GapsInTemplate >> LongestInsert >> SimBtwnQueryTemplate; m->gobble(in2); + + if (badSeqNames.count(name) == 0) { //are you good? + out2 << name << '\t' << length << '\t' << TemplateName << '\t' << TemplateLength << '\t' << SearchMethod << '\t' << SearchScore << '\t' << AlignmentMethod << '\t' << QueryStart << '\t' << QueryEnd << '\t' << TemplateStart << '\t' << TemplateEnd << '\t' << PairwiseAlignmentLength << '\t' << GapsInQuery << '\t' << GapsInTemplate << '\t' << LongestInsert << '\t' << SimBtwnQueryTemplate << endl; + } + } + in2.close(); + out2.close(); + m->mothurRemove(outSummary+".temp"); + } + + if (numFastaSeqs != count) { m->mothurOut("[ERROR]: found " + toString(numFastaSeqs) + " sequences in your fasta file, and " + toString(count) + " sequences in your contigs report file, quitting.\n"); m->control_pressed = true; } + + + return count; + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "ScreenSeqsCommand", "screenAlignReport"); + exit(1); + } + +} +//***************************************************************************************************************/ +int ScreenSeqsCommand::screenContigs(map& badSeqNames){ + try{ + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(contigsreport)); + string outSummary = getOutputFileName("contigsreport",variables); + outputNames.push_back(outSummary); outputTypes["contigsreport"].push_back(outSummary); + + string name; + //Name Length Overlap_Length Overlap_Start Overlap_End MisMatches Num_Ns + int length, OLength, thisOStart, thisOEnd, numMisMatches, numNs; + + ofstream out; + m->openOutputFile(outSummary, out); + + //read summary file + ifstream in; + m->openInputFile(contigsreport, in); + out << (m->getline(in)) << endl; //skip headers + + int count = 0; + + while (!in.eof()) { + + if (m->control_pressed) { in.close(); out.close(); return 0; } + + //seqname start end nbases ambigs polymer numSeqs + in >> name >> length >> OLength >> thisOStart >> thisOEnd >> numMisMatches >> numNs; m->gobble(in); + + bool goodSeq = 1; // innocent until proven guilty + string trashCode = ""; + if(oStart != -1 && oStart < thisOStart) { goodSeq = 0; trashCode += "ostart|"; } + if(oEnd != -1 && oEnd > thisOEnd) { goodSeq = 0; trashCode += "oend|"; } + if(maxN != -1 && maxN < numNs) { goodSeq = 0; trashCode += "n|"; } + if(minOverlap != -1 && minOverlap > OLength) { goodSeq = 0; trashCode += "olength|"; } + if(mismatches != -1 && mismatches < numMisMatches) { goodSeq = 0; trashCode += "mismatches|"; } + + if(goodSeq == 1){ + out << name << '\t' << length << '\t' << OLength << '\t' << thisOStart << '\t' << thisOEnd << '\t' << numMisMatches << '\t' << numNs << endl; + } + else{ badSeqNames[name] = trashCode; } + count++; + } + in.close(); + out.close(); + + int oldBadSeqsCount = badSeqNames.size(); + + int numFastaSeqs = runFastaScreening(badSeqNames); + + if (oldBadSeqsCount != badSeqNames.size()) { //more seqs were removed by maxns + m->renameFile(outSummary, outSummary+".temp"); + + ofstream out2; + m->openOutputFile(outSummary, out2); + + //read summary file + ifstream in2; + m->openInputFile(outSummary+".temp", in2); + out2 << (m->getline(in2)) << endl; //skip headers + + while (!in2.eof()) { + + if (m->control_pressed) { in2.close(); out2.close(); return 0; } + + //seqname start end nbases ambigs polymer numSeqs + in2 >> name >> length >> OLength >> thisOStart >> thisOEnd >> numMisMatches >> numNs; m->gobble(in2); + + if (badSeqNames.count(name) == 0) { //are you good? + out2 << name << '\t' << length << '\t' << OLength << '\t' << thisOStart << '\t' << thisOEnd << '\t' << numMisMatches << '\t' << numNs << endl; + } + } + in2.close(); + out2.close(); + m->mothurRemove(outSummary+".temp"); + } + + if (numFastaSeqs != count) { m->mothurOut("[ERROR]: found " + toString(numFastaSeqs) + " sequences in your fasta file, and " + toString(count) + " sequences in your contigs report file, quitting.\n"); m->control_pressed = true; } + + + return count; + + } + catch(exception& e) { + m->errorOut(e, "ScreenSeqsCommand", "screenContigs"); + exit(1); + } +} +//***************************************************************************************************************/ +int ScreenSeqsCommand::screenSummary(map& badSeqNames){ + try{ + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(summaryfile)); + string outSummary = getOutputFileName("summary",variables); + outputNames.push_back(outSummary); outputTypes["summary"].push_back(outSummary); + + string name; + int start, end, length, ambigs, polymer, numReps; + + ofstream out; + m->openOutputFile(outSummary, out); + + //read summary file + ifstream in; + m->openInputFile(summaryfile, in); + out << (m->getline(in)) << endl; //skip headers + + int count = 0; + + while (!in.eof()) { + + if (m->control_pressed) { in.close(); out.close(); return 0; } + + //seqname start end nbases ambigs polymer numSeqs + in >> name >> start >> end >> length >> ambigs >> polymer >> numReps; m->gobble(in); + + bool goodSeq = 1; // innocent until proven guilty + string trashCode = ""; + if(startPos != -1 && startPos < start) { goodSeq = 0; trashCode += "start|"; } + if(endPos != -1 && endPos > end) { goodSeq = 0; trashCode += "end|"; } + if(maxAmbig != -1 && maxAmbig < ambigs) { goodSeq = 0; trashCode += "ambig|"; } + if(maxHomoP != -1 && maxHomoP < polymer) { goodSeq = 0; trashCode += "homop|"; } + if(minLength != -1 && minLength > length) { goodSeq = 0; trashCode += "renameFile(outSummary, outSummary+".temp"); + + ofstream out2; + m->openOutputFile(outSummary, out2); + + //read summary file + ifstream in2; + m->openInputFile(outSummary+".temp", in2); + out2 << (m->getline(in2)) << endl; //skip headers + + while (!in2.eof()) { + + if (m->control_pressed) { in2.close(); out2.close(); return 0; } + + //seqname start end nbases ambigs polymer numSeqs + in2 >> name >> start >> end >> length >> ambigs >> polymer >> numReps; m->gobble(in2); + + if (badSeqNames.count(name) == 0) { //are you good? + out2 << name << '\t' << start << '\t' << end << '\t' << length << '\t' << ambigs << '\t' << polymer << '\t' << numReps << endl; + } + } + in2.close(); + out2.close(); + m->mothurRemove(outSummary+".temp"); + } + + if (numFastaSeqs != count) { m->mothurOut("[ERROR]: found " + toString(numFastaSeqs) + " sequences in your fasta file, and " + toString(count) + " sequences in your summary file, quitting.\n"); m->control_pressed = true; } + + + + return count; + } + catch(exception& e) { + m->errorOut(e, "ScreenSeqsCommand", "screenSummary"); + exit(1); + } +} +//***************************************************************************************************************/ +int ScreenSeqsCommand::screenFasta(map& badSeqNames){ + try{ + + + //if the user want to optimize we need to know the 90% mark + vector positions; + if (optimize.size() != 0) { //get summary is paralellized so we need to divideFile, no need to do this step twice so I moved it here + //use the namefile to optimize correctly + if (namefile != "") { nameMap = m->readNames(namefile); } + else if (countfile != "") { + CountTable ct; + ct.readTable(countfile); + nameMap = ct.getNameMap(); + } + getSummary(positions); + }else { +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + positions = m->divideFile(fastafile, processors); + for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); } +#else + if(processors == 1){ lines.push_back(linePair(0, 1000)); } + else { + int numFastaSeqs = 0; + positions = m->setFilePosFasta(fastafile, numFastaSeqs); + if (positions.size() < processors) { processors = positions.size(); } + + //figure out how many sequences you have to process + int numSeqsPerProcessor = numFastaSeqs / processors; + for (int i = 0; i < processors; i++) { + int startIndex = i * numSeqsPerProcessor; + if(i == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; } + lines.push_back(linePair(positions[startIndex], numSeqsPerProcessor)); + } + } +#endif + } + + if (m->control_pressed) { return 0; } + + int numFastaSeqs = runFastaScreening(badSeqNames); + + return numFastaSeqs; + + } + catch(exception& e) { + m->errorOut(e, "ScreenSeqsCommand", "screenFasta"); + exit(1); + } +} +//*************************************************************************************************************** - ifstream inputNames; - openInputFile(globaldata->getNameFile(), inputNames); - set badSeqGroups; - string seqName, seqList, group; - set::iterator it; +int ScreenSeqsCommand::screenNameGroupFile(map badSeqNames){ + try { + ifstream inputNames; + m->openInputFile(namefile, inputNames); + map badSeqGroups; + string seqName, seqList, group; + map::iterator it; + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(namefile)); + variables["[extension]"] = m->getExtension(namefile); + string goodNameFile = getOutputFileName("name", variables); + outputNames.push_back(goodNameFile); outputTypes["name"].push_back(goodNameFile); + + ofstream goodNameOut; m->openOutputFile(goodNameFile, goodNameOut); + + while(!inputNames.eof()){ + if (m->control_pressed) { goodNameOut.close(); inputNames.close(); m->mothurRemove(goodNameFile); return 0; } - string goodNameFile = getRootName(globaldata->getNameFile()) + "good" + getExtension(globaldata->getNameFile()); - string badNameFile = getRootName(globaldata->getNameFile()) + "bad" + getExtension(globaldata->getNameFile()); + inputNames >> seqName; m->gobble(inputNames); inputNames >> seqList; + it = badSeqNames.find(seqName); + + if(it != badSeqNames.end()){ + if(namefile != ""){ + int start = 0; + for(int i=0;isecond; + start = i+1; + } + } + badSeqGroups[seqList.substr(start,seqList.length()-start)] = it->second; + } + badSeqNames.erase(it); + } + else{ + goodNameOut << seqName << '\t' << seqList << endl; + } + m->gobble(inputNames); + } + inputNames.close(); + goodNameOut.close(); - ofstream goodNameOut; openOutputFile(goodNameFile, goodNameOut); - ofstream badNameOut; openOutputFile(badNameFile, badNameOut); + //we were unable to remove some of the bad sequences + if (badSeqNames.size() != 0) { + for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) { + m->mothurOut("Your namefile does not include the sequence " + it->first + " please correct."); + m->mothurOutEndLine(); + } + } + + if(groupfile != ""){ + + ifstream inputGroups; + m->openInputFile(groupfile, inputGroups); + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(groupfile)); + variables["[extension]"] = m->getExtension(groupfile); + string goodGroupFile = getOutputFileName("group", variables); + + outputNames.push_back(goodGroupFile); outputTypes["group"].push_back(goodGroupFile); + + ofstream goodGroupOut; m->openOutputFile(goodGroupFile, goodGroupOut); + + while(!inputGroups.eof()){ + if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); m->mothurRemove(goodNameFile); m->mothurRemove(goodGroupFile); return 0; } + + inputGroups >> seqName; m->gobble(inputGroups); inputGroups >> group; + + it = badSeqGroups.find(seqName); + + if(it != badSeqGroups.end()){ + badSeqGroups.erase(it); + } + else{ + goodGroupOut << seqName << '\t' << group << endl; + } + m->gobble(inputGroups); + } + inputGroups.close(); + goodGroupOut.close(); + + //we were unable to remove some of the bad sequences + if (badSeqGroups.size() != 0) { + for (it = badSeqGroups.begin(); it != badSeqGroups.end(); it++) { + m->mothurOut("Your groupfile does not include the sequence " + it->first + " please correct."); + m->mothurOutEndLine(); + } + } + } + + + return 0; - while(!inputNames.eof()){ - inputNames >> seqName >> seqList; - it = badSeqNames.find(seqName); + } + catch(exception& e) { + m->errorOut(e, "ScreenSeqsCommand", "screenNameGroupFile"); + exit(1); + } +} +//*************************************************************************************************************** +int ScreenSeqsCommand::getSummaryReport(){ + try { - if(it != badSeqNames.end()){ - badSeqNames.erase(it); - badNameOut << seqName << '\t' << seqList << endl; - if(globaldata->getNameFile() != ""){ - int start = 0; - for(int i=0;i startPosition; + vector endPosition; + vector seqLength; + vector ambigBases; + vector longHomoPolymer; + +#ifdef USE_MPI + int pid; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + + if (pid == 0) { +#endif + + + //read summary file + ifstream in; + m->openInputFile(summaryfile, in); + m->getline(in); + + string name; + int start, end, length, ambigs, polymer, numReps; + + while (!in.eof()) { + + if (m->control_pressed) { in.close(); return 0; } + + //seqname start end nbases ambigs polymer numSeqs + in >> name >> start >> end >> length >> ambigs >> polymer >> numReps; m->gobble(in); + + int num = 1; + if ((namefile != "") || (countfile !="")) { + //make sure this sequence is in the namefile, else error + map::iterator it = nameMap.find(name); + + if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + name + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; } + else { num = it->second; } + } + + //for each sequence this sequence represents + for (int i = 0; i < num; i++) { + startPosition.push_back(start); + endPosition.push_back(end); + seqLength.push_back(length); + ambigBases.push_back(ambigs); + longHomoPolymer.push_back(polymer); } - badSeqGroups.insert(seqList.substr(start,seqList.length()-start)); + + } + in.close(); + + sort(startPosition.begin(), startPosition.end()); + sort(endPosition.begin(), endPosition.end()); + sort(seqLength.begin(), seqLength.end()); + sort(ambigBases.begin(), ambigBases.end()); + sort(longHomoPolymer.begin(), longHomoPolymer.end()); + + //numSeqs is the number of unique seqs, startPosition.size() is the total number of seqs, we want to optimize using all seqs + int criteriaPercentile = int(startPosition.size() * (criteria / (float) 100)); + + for (int i = 0; i < optimize.size(); i++) { + if (optimize[i] == "start") { startPos = startPosition[criteriaPercentile]; m->mothurOut("Optimizing start to " + toString(startPos) + "."); m->mothurOutEndLine(); } + else if (optimize[i] == "end") { int endcriteriaPercentile = int(endPosition.size() * ((100 - criteria) / (float) 100)); endPos = endPosition[endcriteriaPercentile]; m->mothurOut("Optimizing end to " + toString(endPos) + "."); m->mothurOutEndLine();} + else if (optimize[i] == "maxambig") { maxAmbig = ambigBases[criteriaPercentile]; m->mothurOut("Optimizing maxambig to " + toString(maxAmbig) + "."); m->mothurOutEndLine(); } + else if (optimize[i] == "maxhomop") { maxHomoP = longHomoPolymer[criteriaPercentile]; m->mothurOut("Optimizing maxhomop to " + toString(maxHomoP) + "."); m->mothurOutEndLine(); } + else if (optimize[i] == "minlength") { int mincriteriaPercentile = int(seqLength.size() * ((100 - criteria) / (float) 100)); minLength = seqLength[mincriteriaPercentile]; m->mothurOut("Optimizing minlength to " + toString(minLength) + "."); m->mothurOutEndLine(); } + else if (optimize[i] == "maxlength") { maxLength = seqLength[criteriaPercentile]; m->mothurOut("Optimizing maxlength to " + toString(maxLength) + "."); m->mothurOutEndLine(); } + } + +#ifdef USE_MPI + } + + MPI_Status status; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + MPI_Comm_size(MPI_COMM_WORLD, &processors); + + if (pid == 0) { + //send file positions to all processes + for(int i = 1; i < processors; i++) { + MPI_Send(&startPos, 1, MPI_INT, i, 2001, MPI_COMM_WORLD); + MPI_Send(&endPos, 1, MPI_INT, i, 2001, MPI_COMM_WORLD); + MPI_Send(&maxAmbig, 1, MPI_INT, i, 2001, MPI_COMM_WORLD); + MPI_Send(&maxHomoP, 1, MPI_INT, i, 2001, MPI_COMM_WORLD); + MPI_Send(&minLength, 1, MPI_INT, i, 2001, MPI_COMM_WORLD); + MPI_Send(&maxLength, 1, MPI_INT, i, 2001, MPI_COMM_WORLD); + } + }else { + MPI_Recv(&startPos, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + MPI_Recv(&endPos, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + MPI_Recv(&maxAmbig, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + MPI_Recv(&maxHomoP, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + MPI_Recv(&minLength, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + MPI_Recv(&maxLength, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + } + MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case +#endif + return 0; + + } + catch(exception& e) { + m->errorOut(e, "ScreenSeqsCommand", "getSummaryReport"); + exit(1); + } +} +//*************************************************************************************************************** +int ScreenSeqsCommand::optimizeContigs(){ + try { + vector olengths; + vector oStarts; + vector oEnds; + vector numMismatches; + vector numNs; + + vector positions; + vector contigsLines; +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + positions = m->divideFilePerLine(contigsreport, processors); + for (int i = 0; i < (positions.size()-1); i++) { contigsLines.push_back(linePair(positions[i], positions[(i+1)])); } +#else + if(processors == 1){ contigsLines.push_back(linePair(0, 1000)); } + else { + int numContigsSeqs = 0; + positions = m->setFilePosEachLine(contigsreport, numContigsSeqs); + if (positions.size() < processors) { processors = positions.size(); } + + //figure out how many sequences you have to process + int numSeqsPerProcessor = numContigsSeqs / processors; + for (int i = 0; i < processors; i++) { + int startIndex = i * numSeqsPerProcessor; + if(i == (processors - 1)){ numSeqsPerProcessor = numContigsSeqs - i * numSeqsPerProcessor; } + contigsLines.push_back(linePair(positions[startIndex], numSeqsPerProcessor)); + } + } +#endif + +#ifdef USE_MPI + int pid; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + + if (pid == 0) { + driverContigsSummary(olengths, oStarts, oEnds, numMismatches, numNs, contigsLines[0]); +#else + createProcessesContigsSummary(olengths, oStarts, oEnds, numMismatches, numNs, contigsLines); + + if (m->control_pressed) { return 0; } +#endif + sort(olengths.begin(), olengths.end()); + sort(oStarts.begin(), oStarts.end()); + sort(oEnds.begin(), oEnds.end()); + sort(numMismatches.begin(), numMismatches.end()); + sort(numNs.begin(), numNs.end()); + + //numSeqs is the number of unique seqs, startPosition.size() is the total number of seqs, we want to optimize using all seqs + int criteriaPercentile = int(oStarts.size() * (criteria / (float) 100)); + + for (int i = 0; i < optimize.size(); i++) { + if (optimize[i] == "ostart") { oStart = oStarts[criteriaPercentile]; m->mothurOut("Optimizing ostart to " + toString(oStart) + "."); m->mothurOutEndLine(); } + else if (optimize[i] == "oend") { int endcriteriaPercentile = int(oEnds.size() * ((100 - criteria) / (float) 100)); oEnd = oEnds[endcriteriaPercentile]; m->mothurOut("Optimizing oend to " + toString(oEnd) + "."); m->mothurOutEndLine();} + else if (optimize[i] == "mismatches") { mismatches = numMismatches[criteriaPercentile]; m->mothurOut("Optimizing mismatches to " + toString(mismatches) + "."); m->mothurOutEndLine(); } + else if (optimize[i] == "maxn") { maxN = numNs[criteriaPercentile]; m->mothurOut("Optimizing maxn to " + toString(maxN) + "."); m->mothurOutEndLine(); } + else if (optimize[i] == "minoverlap") { int mincriteriaPercentile = int(olengths.size() * ((100 - criteria) / (float) 100)); minOverlap = olengths[mincriteriaPercentile]; m->mothurOut("Optimizing minoverlap to " + toString(minOverlap) + "."); m->mothurOutEndLine(); } + + } + +#ifdef USE_MPI + } + + MPI_Status status; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + MPI_Comm_size(MPI_COMM_WORLD, &processors); + + if (pid == 0) { + //send file positions to all processes + for(int i = 1; i < processors; i++) { + MPI_Send(&minOverlap, 1, MPI_INT, i, 2001, MPI_COMM_WORLD); + MPI_Send(&oStart, 1, MPI_INT, i, 2001, MPI_COMM_WORLD); + MPI_Send(&oEnd, 1, MPI_INT, i, 2001, MPI_COMM_WORLD); + MPI_Send(&mismatches, 1, MPI_INT, i, 2001, MPI_COMM_WORLD); + MPI_Send(&maxN, 1, MPI_INT, i, 2001, MPI_COMM_WORLD); + } + }else { + MPI_Recv(&minOverlap, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + MPI_Recv(&oStart, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + MPI_Recv(&oEnd, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + MPI_Recv(&mismatches, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + MPI_Recv(&maxN, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + } + MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case +#endif + return 0; + } + catch(exception& e) { + m->errorOut(e, "ScreenSeqsCommand", "optimizeContigs"); + exit(1); + } +} +/**************************************************************************************/ +int ScreenSeqsCommand::driverContigsSummary(vector& oLength, vector& ostartPosition, vector& oendPosition, vector& omismatches, vector& numNs, linePair filePos) { + try { + + string name; + //Name Length Overlap_Length Overlap_Start Overlap_End MisMatches Num_Ns + int length, OLength, thisOStart, thisOEnd, numMisMatches, numns; + + ifstream in; + m->openInputFile(contigsreport, in); + + in.seekg(filePos.start); + if (filePos.start == 0) { //read headers + m->getline(in); m->gobble(in); + } + + bool done = false; + int count = 0; + + while (!done) { + + if (m->control_pressed) { in.close(); return 1; } + + //seqname start end nbases ambigs polymer numSeqs + in >> name >> length >> OLength >> thisOStart >> thisOEnd >> numMisMatches >> numns; m->gobble(in); + + int num = 1; + if ((namefile != "") || (countfile !="")){ + //make sure this sequence is in the namefile, else error + map::iterator it = nameMap.find(name); + + if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + name + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; } + else { num = it->second; } + } + + //for each sequence this sequence represents + for (int i = 0; i < num; i++) { + ostartPosition.push_back(thisOStart); + oendPosition.push_back(thisOEnd); + oLength.push_back(OLength); + omismatches.push_back(numMisMatches); + numNs.push_back(numns); + } + + count++; + + //if((count) % 100 == 0){ m->mothurOut("Optimizing sequence: " + toString(count)); m->mothurOutEndLine(); } +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + unsigned long long pos = in.tellg(); + if ((pos == -1) || (pos >= filePos.end)) { break; } +#else + if (in.eof()) { break; } +#endif + } + + in.close(); + + return count; + } + catch(exception& e) { + m->errorOut(e, "ScreenSeqsCommand", "driverContigsSummary"); + exit(1); + } +} + +/**************************************************************************************************/ +int ScreenSeqsCommand::createProcessesContigsSummary(vector& oLength, vector& ostartPosition, vector& oendPosition, vector& omismatches, vector& numNs, vector contigsLines) { + try { + + int process = 1; + int num = 0; + vector processIDS; + +#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){ + num = driverContigsSummary(oLength, ostartPosition, oendPosition, omismatches, numNs, contigsLines[process]); + + //pass numSeqs to parent + ofstream out; + string tempFile = contigsreport + toString(getpid()) + ".num.temp"; + m->openOutputFile(tempFile, out); + + out << num << endl; + out << ostartPosition.size() << endl; + for (int k = 0; k < ostartPosition.size(); k++) { out << ostartPosition[k] << '\t'; } out << endl; + for (int k = 0; k < oendPosition.size(); k++) { out << oendPosition[k] << '\t'; } out << endl; + for (int k = 0; k < oLength.size(); k++) { out << oLength[k] << '\t'; } out << endl; + for (int k = 0; k < omismatches.size(); k++) { out << omismatches[k] << '\t'; } out << endl; + for (int k = 0; k < numNs.size(); k++) { out << numNs[k] << '\t'; } out << endl; + + out.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); + } + } + + num = driverContigsSummary(oLength, ostartPosition, oendPosition, omismatches, numNs, contigsLines[0]); + + //force parent to wait until all the processes are done + for (int i=0;iopenInputFile(tempFilename, in); + + int temp, tempNum; + in >> tempNum; m->gobble(in); num += tempNum; + in >> tempNum; m->gobble(in); + for (int k = 0; k < tempNum; k++) { in >> temp; ostartPosition.push_back(temp); } m->gobble(in); + for (int k = 0; k < tempNum; k++) { in >> temp; oendPosition.push_back(temp); } m->gobble(in); + for (int k = 0; k < tempNum; k++) { in >> temp; oLength.push_back(temp); } m->gobble(in); + for (int k = 0; k < tempNum; k++) { in >> temp; omismatches.push_back(temp); } m->gobble(in); + for (int k = 0; k < tempNum; k++) { in >> temp; numNs.push_back(temp); } m->gobble(in); + + in.close(); + m->mothurRemove(tempFilename); + } + + +#else + ////////////////////////////////////////////////////////////////////////////////////////////////////// + //Windows version shared memory, so be careful when passing variables through the seqSumData struct. + //Above fork() will clone, so memory is separate, but that's not the case with windows, + //Taking advantage of shared memory to allow both threads to add info to vectors. + ////////////////////////////////////////////////////////////////////////////////////////////////////// + /* + vector pDataArray; + DWORD dwThreadIdArray[processors-1]; + HANDLE hThreadArray[processors-1]; + + //Create processor worker threads. + for( int i=0; icount; + if (pDataArray[i]->count != pDataArray[i]->end) { + m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true; + } + for (int k = 0; k < pDataArray[i]->ostartPosition.size(); k++) { ostartPosition.push_back(pDataArray[i]->ostartPosition[k]); } + for (int k = 0; k < pDataArray[i]->oendPosition.size(); k++) { oendPosition.push_back(pDataArray[i]->oendPosition[k]); } + for (int k = 0; k < pDataArray[i]->oLength.size(); k++) { oLength.push_back(pDataArray[i]->oLength[k]); } + for (int k = 0; k < pDataArray[i]->omismatches.size(); k++) { omismatches.push_back(pDataArray[i]->omismatches[k]); } + for (int k = 0; k < pDataArray[i]->numNs.size(); k++) { numNs.push_back(pDataArray[i]->numNs[k]); } + CloseHandle(hThreadArray[i]); + delete pDataArray[i]; + } + */ +#endif + return num; + } + catch(exception& e) { + m->errorOut(e, "ScreenSeqsCommand", "createProcessesContigsSummary"); + exit(1); + } +} +//*************************************************************************************************************** +int ScreenSeqsCommand::optimizeAlign(){ + try { + + vector sims; + vector scores; + vector inserts; + + vector positions; + vector alignLines; +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + positions = m->divideFilePerLine(alignreport, processors); + for (int i = 0; i < (positions.size()-1); i++) { alignLines.push_back(linePair(positions[i], positions[(i+1)])); } +#else + if(processors == 1){ alignLines.push_back(linePair(0, 1000)); } + else { + int numAlignSeqs = 0; + positions = m->setFilePosEachLine(alignreport, numAlignSeqs); + if (positions.size() < processors) { processors = positions.size(); } + + //figure out how many sequences you have to process + int numSeqsPerProcessor = numAlignSeqs / processors; + for (int i = 0; i < processors; i++) { + int startIndex = i * numSeqsPerProcessor; + if(i == (processors - 1)){ numSeqsPerProcessor = numAlignSeqs - i * numSeqsPerProcessor; } + alignLines.push_back(linePair(positions[startIndex], numSeqsPerProcessor)); + } + } +#endif + +#ifdef USE_MPI + int pid; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + + if (pid == 0) { + driverAlignSummary(sims, scores, inserts, alignLines[0]); +#else + createProcessesAlignSummary(sims, scores, inserts, alignLines); + + if (m->control_pressed) { return 0; } +#endif + sort(sims.begin(), sims.end()); + sort(scores.begin(), scores.end()); + sort(inserts.begin(), inserts.end()); + + //numSeqs is the number of unique seqs, startPosition.size() is the total number of seqs, we want to optimize using all seqs + int criteriaPercentile = int(sims.size() * (criteria / (float) 100)); + + for (int i = 0; i < optimize.size(); i++) { + if (optimize[i] == "minsim") { int mincriteriaPercentile = int(sims.size() * ((100 - criteria) / (float) 100)); minSim = sims[mincriteriaPercentile]; m->mothurOut("Optimizing minsim to " + toString(minSim) + "."); m->mothurOutEndLine();} + else if (optimize[i] == "minscore") { int mincriteriaPercentile = int(scores.size() * ((100 - criteria) / (float) 100)); minScore = scores[mincriteriaPercentile]; m->mothurOut("Optimizing minscore to " + toString(minScore) + "."); m->mothurOutEndLine(); } + else if (optimize[i] == "maxinsert") { maxInsert = inserts[criteriaPercentile]; m->mothurOut("Optimizing maxinsert to " + toString(maxInsert) + "."); m->mothurOutEndLine(); } + } + +#ifdef USE_MPI + } + + MPI_Status status; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + MPI_Comm_size(MPI_COMM_WORLD, &processors); + + if (pid == 0) { + //send file positions to all processes + for(int i = 1; i < processors; i++) { + MPI_Send(&minSim, 1, MPI_INT, i, 2001, MPI_COMM_WORLD); + MPI_Send(&minScore, 1, MPI_INT, i, 2001, MPI_COMM_WORLD); + MPI_Send(&maxInsert, 1, MPI_INT, i, 2001, MPI_COMM_WORLD); } + }else { + MPI_Recv(&minSim, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + MPI_Recv(&minScore, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + MPI_Recv(&maxInsert, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); } - else{ - goodNameOut << seqName << '\t' << seqList << endl; + MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case +#endif + return 0; + } + catch(exception& e) { + m->errorOut(e, "ScreenSeqsCommand", "optimizeContigs"); + exit(1); + } +} +/**************************************************************************************/ +int ScreenSeqsCommand::driverAlignSummary(vector& sims, vector& scores, vector& inserts, linePair filePos) { + try { + + string name, TemplateName, SearchMethod, AlignmentMethod; + //QueryName QueryLength TemplateName TemplateLength SearchMethod SearchScore AlignmentMethod QueryStart QueryEnd TemplateStart TemplateEnd PairwiseAlignmentLength GapsInQuery GapsInTemplate LongestInsert SimBtwnQuery&Template + //checking for minScore, maxInsert, minSim + int length, TemplateLength, QueryStart, QueryEnd, TemplateStart, TemplateEnd, PairwiseAlignmentLength, GapsInQuery, GapsInTemplate, LongestInsert; + float SearchScore, SimBtwnQueryTemplate; + + ifstream in; + m->openInputFile(alignreport, in); + + in.seekg(filePos.start); + if (filePos.start == 0) { //read headers + m->getline(in); m->gobble(in); + } + + bool done = false; + int count = 0; + + while (!done) { + + if (m->control_pressed) { in.close(); return 1; } + + in >> name >> length >> TemplateName >> TemplateLength >> SearchMethod >> SearchScore >> AlignmentMethod >> QueryStart >> QueryEnd >> TemplateStart >> TemplateEnd >> PairwiseAlignmentLength >> GapsInQuery >> GapsInTemplate >> LongestInsert >> SimBtwnQueryTemplate; m->gobble(in); + + int num = 1; + if ((namefile != "") || (countfile !="")){ + //make sure this sequence is in the namefile, else error + map::iterator it = nameMap.find(name); + + if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + name + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; } + else { num = it->second; } + } + + //for each sequence this sequence represents + for (int i = 0; i < num; i++) { + sims.push_back(SimBtwnQueryTemplate); + scores.push_back(SearchScore); + inserts.push_back(LongestInsert); + } + + count++; + + //if((count) % 100 == 0){ m->mothurOut("Optimizing sequence: " + toString(count)); m->mothurOutEndLine(); } +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + unsigned long long pos = in.tellg(); + if ((pos == -1) || (pos >= filePos.end)) { break; } +#else + if (in.eof()) { break; } +#endif } - gobble(inputNames); + + in.close(); + + return count; } - inputNames.close(); - goodNameOut.close(); - badNameOut.close(); + catch(exception& e) { + m->errorOut(e, "ScreenSeqsCommand", "driverAlignSummary"); + exit(1); + } +} + +/**************************************************************************************************/ +int ScreenSeqsCommand::createProcessesAlignSummary(vector& sims, vector& scores, vector& inserts, vector alignLines) { + try { + + int process = 1; + int num = 0; + vector processIDS; + +#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){ + num = driverAlignSummary(sims, scores, inserts, alignLines[process]); + + //pass numSeqs to parent + ofstream out; + string tempFile = alignreport + toString(getpid()) + ".num.temp"; + m->openOutputFile(tempFile, out); + + out << num << endl; + out << sims.size() << endl; + for (int k = 0; k < sims.size(); k++) { out << sims[k] << '\t'; } out << endl; + for (int k = 0; k < scores.size(); k++) { out << scores[k] << '\t'; } out << endl; + for (int k = 0; k < inserts.size(); k++) { out << inserts[k] << '\t'; } out << endl; + + out.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); + } + } + + num = driverAlignSummary(sims, scores, inserts, alignLines[0]); + + //force parent to wait until all the processes are done + for (int i=0;iopenInputFile(tempFilename, in); + + int temp, tempNum; + float temp2; + in >> tempNum; m->gobble(in); num += tempNum; + in >> tempNum; m->gobble(in); + for (int k = 0; k < tempNum; k++) { in >> temp2; sims.push_back(temp2); } m->gobble(in); + for (int k = 0; k < tempNum; k++) { in >> temp2; scores.push_back(temp2); } m->gobble(in); + for (int k = 0; k < tempNum; k++) { in >> temp; inserts.push_back(temp); } m->gobble(in); + + in.close(); + m->mothurRemove(tempFilename); + } + + +#else + ////////////////////////////////////////////////////////////////////////////////////////////////////// + //Windows version shared memory, so be careful when passing variables through the seqSumData struct. + //Above fork() will clone, so memory is separate, but that's not the case with windows, + //Taking advantage of shared memory to allow both threads to add info to vectors. + ////////////////////////////////////////////////////////////////////////////////////////////////////// + /* + vector pDataArray; + DWORD dwThreadIdArray[processors-1]; + HANDLE hThreadArray[processors-1]; + + //Create processor worker threads. + for( int i=0; icount; + if (pDataArray[i]->count != pDataArray[i]->end) { + m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true; + } + for (int k = 0; k < pDataArray[i]->sims.size(); k++) { sims.push_back(pDataArray[i]->sims[k]); } + for (int k = 0; k < pDataArray[i]->scores.size(); k++) { scores.push_back(pDataArray[i]->scores[k]); } + for (int k = 0; k < pDataArray[i]->inserts.size(); k++) { inserts.push_back(pDataArray[i]->inserts[k]); } + CloseHandle(hThreadArray[i]); + delete pDataArray[i]; + } + */ +#endif + return num; + } + catch(exception& e) { + m->errorOut(e, "ScreenSeqsCommand", "createProcessesAlignSummary"); + exit(1); + } +} +//*************************************************************************************************************** +int ScreenSeqsCommand::getSummary(vector& positions){ + try { + + vector startPosition; + vector endPosition; + vector seqLength; + vector ambigBases; + vector longHomoPolymer; + vector numNs; + + vector positions; +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + positions = m->divideFile(fastafile, processors); + for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); } +#else + if(processors == 1){ lines.push_back(linePair(0, 1000)); } + else { + int numFastaSeqs = 0; + positions = m->setFilePosFasta(fastafile, numFastaSeqs); + if (positions.size() < processors) { processors = positions.size(); } + + //figure out how many sequences you have to process + int numSeqsPerProcessor = numFastaSeqs / processors; + for (int i = 0; i < processors; i++) { + int startIndex = i * numSeqsPerProcessor; + if(i == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; } + lines.push_back(linePair(positions[startIndex], numSeqsPerProcessor)); + } + } +#endif + +#ifdef USE_MPI + int pid; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + + if (pid == 0) { + driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, numNs, fastafile, lines[0]); +#else + int numSeqs = 0; + //#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + if(processors == 1){ + numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, numNs, fastafile, lines[0]); + }else{ + numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, numNs, fastafile); + } + + if (m->control_pressed) { return 0; } +#endif + sort(startPosition.begin(), startPosition.end()); + sort(endPosition.begin(), endPosition.end()); + sort(seqLength.begin(), seqLength.end()); + sort(ambigBases.begin(), ambigBases.end()); + sort(longHomoPolymer.begin(), longHomoPolymer.end()); + sort(numNs.begin(), numNs.end()); + + //numSeqs is the number of unique seqs, startPosition.size() is the total number of seqs, we want to optimize using all seqs + int criteriaPercentile = int(startPosition.size() * (criteria / (float) 100)); + + for (int i = 0; i < optimize.size(); i++) { + if (optimize[i] == "start") { startPos = startPosition[criteriaPercentile]; m->mothurOut("Optimizing start to " + toString(startPos) + "."); m->mothurOutEndLine(); } + else if (optimize[i] == "end") { int endcriteriaPercentile = int(endPosition.size() * ((100 - criteria) / (float) 100)); endPos = endPosition[endcriteriaPercentile]; m->mothurOut("Optimizing end to " + toString(endPos) + "."); m->mothurOutEndLine();} + else if (optimize[i] == "maxambig") { maxAmbig = ambigBases[criteriaPercentile]; m->mothurOut("Optimizing maxambig to " + toString(maxAmbig) + "."); m->mothurOutEndLine(); } + else if (optimize[i] == "maxhomop") { maxHomoP = longHomoPolymer[criteriaPercentile]; m->mothurOut("Optimizing maxhomop to " + toString(maxHomoP) + "."); m->mothurOutEndLine(); } + else if (optimize[i] == "minlength") { int mincriteriaPercentile = int(seqLength.size() * ((100 - criteria) / (float) 100)); minLength = seqLength[mincriteriaPercentile]; m->mothurOut("Optimizing minlength to " + toString(minLength) + "."); m->mothurOutEndLine(); } + else if (optimize[i] == "maxlength") { maxLength = seqLength[criteriaPercentile]; m->mothurOut("Optimizing maxlength to " + toString(maxLength) + "."); m->mothurOutEndLine(); } + else if (optimize[i] == "maxn") { maxN = numNs[criteriaPercentile]; m->mothurOut("Optimizing maxn to " + toString(maxN) + "."); m->mothurOutEndLine(); } + } + +#ifdef USE_MPI + } + + MPI_Status status; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + MPI_Comm_size(MPI_COMM_WORLD, &processors); + + if (pid == 0) { + //send file positions to all processes + for(int i = 1; i < processors; i++) { + MPI_Send(&startPos, 1, MPI_INT, i, 2001, MPI_COMM_WORLD); + MPI_Send(&endPos, 1, MPI_INT, i, 2001, MPI_COMM_WORLD); + MPI_Send(&maxAmbig, 1, MPI_INT, i, 2001, MPI_COMM_WORLD); + MPI_Send(&maxHomoP, 1, MPI_INT, i, 2001, MPI_COMM_WORLD); + MPI_Send(&minLength, 1, MPI_INT, i, 2001, MPI_COMM_WORLD); + MPI_Send(&maxLength, 1, MPI_INT, i, 2001, MPI_COMM_WORLD); + MPI_Send(&maxN, 1, MPI_INT, i, 2001, MPI_COMM_WORLD); + } + }else { + MPI_Recv(&startPos, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + MPI_Recv(&endPos, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + MPI_Recv(&maxAmbig, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + MPI_Recv(&maxHomoP, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + MPI_Recv(&minLength, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + MPI_Recv(&maxLength, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + MPI_Recv(&maxN, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + } + MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case +#endif + return 0; + } + catch(exception& e) { + m->errorOut(e, "ScreenSeqsCommand", "getSummary"); + exit(1); + } +} +/**************************************************************************************/ +int ScreenSeqsCommand::driverCreateSummary(vector& startPosition, vector& endPosition, vector& seqLength, vector& ambigBases, vector& longHomoPolymer, vector& numNs, string filename, linePair filePos) { + try { + + ifstream in; + m->openInputFile(filename, in); + + in.seekg(filePos.start); + + bool done = false; + int count = 0; - if(globaldata->getGroupFile() != ""){ + while (!done) { + + if (m->control_pressed) { in.close(); return 1; } + + Sequence current(in); m->gobble(in); + + if (current.getName() != "") { + int num = 1; + if ((namefile != "") || (countfile !="")){ + //make sure this sequence is in the namefile, else error + map::iterator it = nameMap.find(current.getName()); + + if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; } + else { num = it->second; } + } + + //for each sequence this sequence represents + int numns = current.getNumNs(); + for (int i = 0; i < num; i++) { + startPosition.push_back(current.getStartPos()); + endPosition.push_back(current.getEndPos()); + seqLength.push_back(current.getNumBases()); + ambigBases.push_back(current.getAmbigBases()); + longHomoPolymer.push_back(current.getLongHomoPolymer()); + numNs.push_back(numns); + } + + count++; + } + //if((count) % 100 == 0){ m->mothurOut("Optimizing sequence: " + toString(count)); m->mothurOutEndLine(); } + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + unsigned long long pos = in.tellg(); + if ((pos == -1) || (pos >= filePos.end)) { break; } + #else + if (in.eof()) { break; } + #endif + + } - ifstream inputGroups; - openInputFile(globaldata->getGroupFile(), inputGroups); + in.close(); + + return count; + } + catch(exception& e) { + m->errorOut(e, "ScreenSeqsCommand", "driverCreateSummary"); + exit(1); + } +} +/**************************************************************************************************/ +int ScreenSeqsCommand::createProcessesCreateSummary(vector& startPosition, vector& endPosition, vector& seqLength, vector& ambigBases, vector& longHomoPolymer, vector& numNs, string filename) { + try { + + int process = 1; + int num = 0; + vector processIDS; - string goodGroupFile = getRootName(globaldata->getGroupFile()) + "good" + getExtension(globaldata->getGroupFile()); - string badGroupFile = getRootName(globaldata->getGroupFile()) + "bad" + getExtension(globaldata->getGroupFile()); +#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){ + num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, numNs, fastafile, lines[process]); + + //pass numSeqs to parent + ofstream out; + string tempFile = fastafile + toString(getpid()) + ".num.temp"; + m->openOutputFile(tempFile, out); + + out << num << endl; + out << startPosition.size() << endl; + for (int k = 0; k < startPosition.size(); k++) { out << startPosition[k] << '\t'; } out << endl; + for (int k = 0; k < endPosition.size(); k++) { out << endPosition[k] << '\t'; } out << endl; + for (int k = 0; k < seqLength.size(); k++) { out << seqLength[k] << '\t'; } out << endl; + for (int k = 0; k < ambigBases.size(); k++) { out << ambigBases[k] << '\t'; } out << endl; + for (int k = 0; k < longHomoPolymer.size(); k++) { out << longHomoPolymer[k] << '\t'; } out << endl; + for (int k = 0; k < numNs.size(); k++) { out << numNs[k] << '\t'; } out << endl; + + out.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); + } + } + + num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, numNs, fastafile, lines[0]); + + //force parent to wait until all the processes are done + for (int i=0;iopenInputFile(tempFilename, in); + + int temp, tempNum; + in >> tempNum; m->gobble(in); num += tempNum; + in >> tempNum; m->gobble(in); + for (int k = 0; k < tempNum; k++) { in >> temp; startPosition.push_back(temp); } m->gobble(in); + for (int k = 0; k < tempNum; k++) { in >> temp; endPosition.push_back(temp); } m->gobble(in); + for (int k = 0; k < tempNum; k++) { in >> temp; seqLength.push_back(temp); } m->gobble(in); + for (int k = 0; k < tempNum; k++) { in >> temp; ambigBases.push_back(temp); } m->gobble(in); + for (int k = 0; k < tempNum; k++) { in >> temp; longHomoPolymer.push_back(temp); } m->gobble(in); + for (int k = 0; k < tempNum; k++) { in >> temp; numNs.push_back(temp); } m->gobble(in); + + in.close(); + m->mothurRemove(tempFilename); + } + + +#else + ////////////////////////////////////////////////////////////////////////////////////////////////////// + //Windows version shared memory, so be careful when passing variables through the seqSumData struct. + //Above fork() will clone, so memory is separate, but that's not the case with windows, + //Taking advantage of shared memory to allow both threads to add info to vectors. + ////////////////////////////////////////////////////////////////////////////////////////////////////// + + vector pDataArray; + DWORD dwThreadIdArray[processors-1]; + HANDLE hThreadArray[processors-1]; + + //Create processor worker threads. + for( int i=0; icount; + if (pDataArray[i]->count != pDataArray[i]->end) { + m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true; + } + for (int k = 0; k < pDataArray[i]->startPosition.size(); k++) { startPosition.push_back(pDataArray[i]->startPosition[k]); } + for (int k = 0; k < pDataArray[i]->endPosition.size(); k++) { endPosition.push_back(pDataArray[i]->endPosition[k]); } + for (int k = 0; k < pDataArray[i]->seqLength.size(); k++) { seqLength.push_back(pDataArray[i]->seqLength[k]); } + for (int k = 0; k < pDataArray[i]->ambigBases.size(); k++) { ambigBases.push_back(pDataArray[i]->ambigBases[k]); } + for (int k = 0; k < pDataArray[i]->longHomoPolymer.size(); k++) { longHomoPolymer.push_back(pDataArray[i]->longHomoPolymer[k]); } + for (int k = 0; k < pDataArray[i]->numNs.size(); k++) { numNs.push_back(pDataArray[i]->numNs[k]); } + CloseHandle(hThreadArray[i]); + delete pDataArray[i]; + } + +#endif + return num; + } + catch(exception& e) { + m->errorOut(e, "ScreenSeqsCommand", "createProcessesCreateSummary"); + exit(1); + } +} + +//*************************************************************************************************************** + +int ScreenSeqsCommand::screenGroupFile(map badSeqNames){ + try { + ifstream inputGroups; + m->openInputFile(groupfile, inputGroups); + string seqName, group; + map::iterator it; + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(groupfile)); + variables["[extension]"] = m->getExtension(groupfile); + string goodGroupFile = getOutputFileName("group", variables); + outputNames.push_back(goodGroupFile); outputTypes["group"].push_back(goodGroupFile); + ofstream goodGroupOut; m->openOutputFile(goodGroupFile, goodGroupOut); while(!inputGroups.eof()){ - inputGroups >> seqName >> group; + if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); m->mothurRemove(goodGroupFile); return 0; } - it = badSeqGroups.find(seqName); + inputGroups >> seqName; m->gobble(inputGroups); inputGroups >> group; + it = badSeqNames.find(seqName); - if(it != badSeqGroups.end()){ - badSeqGroups.erase(it); - badGroupOut << seqName << '\t' << group << endl; + if(it != badSeqNames.end()){ + badSeqNames.erase(it); } else{ goodGroupOut << seqName << '\t' << group << endl; } - gobble(inputGroups); + m->gobble(inputGroups); + } + + if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); m->mothurRemove(goodGroupFile); return 0; } + + //we were unable to remove some of the bad sequences + if (badSeqNames.size() != 0) { + for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) { + m->mothurOut("Your groupfile does not include the sequence " + it->first + " please correct."); + m->mothurOutEndLine(); + } } + inputGroups.close(); goodGroupOut.close(); - badGroupOut.close(); + + if (m->control_pressed) { m->mothurRemove(goodGroupFile); } + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "ScreenSeqsCommand", "screenGroupFile"); + exit(1); } } +//*************************************************************************************************************** +int ScreenSeqsCommand::screenCountFile(map badSeqNames){ + try { + ifstream in; + m->openInputFile(countfile, in); + map::iterator it; + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(countfile)); + variables["[extension]"] = m->getExtension(countfile); + string goodCountFile = getOutputFileName("count", variables); + + outputNames.push_back(goodCountFile); outputTypes["count"].push_back(goodCountFile); + ofstream goodCountOut; m->openOutputFile(goodCountFile, goodCountOut); + + string headers = m->getline(in); m->gobble(in); + goodCountOut << headers << endl; + + string name, rest; int thisTotal; + while (!in.eof()) { + if (m->control_pressed) { goodCountOut.close(); in.close(); m->mothurRemove(goodCountFile); return 0; } + + in >> name; m->gobble(in); + in >> thisTotal; m->gobble(in); + rest = m->getline(in); m->gobble(in); + + it = badSeqNames.find(name); + + if(it != badSeqNames.end()){ + badSeqNames.erase(it); + } + else{ + goodCountOut << name << '\t' << thisTotal << '\t' << rest << endl; + } + } + + if (m->control_pressed) { goodCountOut.close(); in.close(); m->mothurRemove(goodCountFile); return 0; } + + //we were unable to remove some of the bad sequences + if (badSeqNames.size() != 0) { + for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) { + m->mothurOut("Your count file does not include the sequence " + it->first + " please correct."); + m->mothurOutEndLine(); + } + } + + in.close(); + goodCountOut.close(); + + //check for groups that have been eliminated + CountTable ct; + if (ct.testGroups(goodCountFile)) { + ct.readTable(goodCountFile); + ct.printTable(goodCountFile); + } + + if (m->control_pressed) { m->mothurRemove(goodCountFile); } + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "ScreenSeqsCommand", "screenCountFile"); + exit(1); + } +} //*************************************************************************************************************** -void ScreenSeqsCommand::screenGroupFile(set badSeqNames){ +int ScreenSeqsCommand::screenTaxonomy(map badSeqNames){ + try { + ifstream input; + m->openInputFile(taxonomy, input); + string seqName, tax; + map::iterator it; + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(taxonomy)); + variables["[extension]"] = m->getExtension(taxonomy); + string goodTaxFile = getOutputFileName("taxonomy", variables); - ifstream inputGroups; - openInputFile(globaldata->getGroupFile(), inputGroups); - string seqName, group; - set::iterator it; - - string goodGroupFile = getRootName(globaldata->getGroupFile()) + "good" + getExtension(globaldata->getGroupFile()); - string badGroupFile = getRootName(globaldata->getGroupFile()) + "bad" + getExtension(globaldata->getGroupFile()); - - ofstream goodGroupOut; openOutputFile(goodGroupFile, goodGroupOut); - ofstream badGroupOut; openOutputFile(badGroupFile, badGroupOut); + outputNames.push_back(goodTaxFile); outputTypes["taxonomy"].push_back(goodTaxFile); + ofstream goodTaxOut; m->openOutputFile(goodTaxFile, goodTaxOut); + + while(!input.eof()){ + if (m->control_pressed) { goodTaxOut.close(); input.close(); m->mothurRemove(goodTaxFile); return 0; } + + input >> seqName; m->gobble(input); input >> tax; + it = badSeqNames.find(seqName); + + if(it != badSeqNames.end()){ badSeqNames.erase(it); } + else{ + goodTaxOut << seqName << '\t' << tax << endl; + } + m->gobble(input); + } + + if (m->control_pressed) { goodTaxOut.close(); input.close(); m->mothurRemove(goodTaxFile); return 0; } + + //we were unable to remove some of the bad sequences + if (badSeqNames.size() != 0) { + for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) { + m->mothurOut("Your taxonomy file does not include the sequence " + it->first + " please correct."); + m->mothurOutEndLine(); + } + } + + input.close(); + goodTaxOut.close(); + + if (m->control_pressed) { m->mothurRemove(goodTaxFile); return 0; } + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "ScreenSeqsCommand", "screenTaxonomy"); + exit(1); + } - while(!inputGroups.eof()){ - inputGroups >> seqName >> group; - it = badSeqNames.find(seqName); +} +//*************************************************************************************************************** + +int ScreenSeqsCommand::screenQual(map badSeqNames){ + try { + ifstream in; + m->openInputFile(qualfile, in); + map::iterator it; + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(qualfile)); + variables["[extension]"] = m->getExtension(qualfile); + string goodQualFile = getOutputFileName("qfile", variables); - if(it != badSeqNames.end()){ - badSeqNames.erase(it); - badGroupOut << seqName << '\t' << group << endl; + outputNames.push_back(goodQualFile); outputTypes["qfile"].push_back(goodQualFile); + ofstream goodQual; m->openOutputFile(goodQualFile, goodQual); + + while(!in.eof()){ + + if (m->control_pressed) { goodQual.close(); in.close(); m->mothurRemove(goodQualFile); return 0; } + + string saveName = ""; + string name = ""; + string scores = ""; + + in >> name; + + if (name.length() != 0) { + saveName = name.substr(1); + while (!in.eof()) { + char c = in.get(); + if (c == 10 || c == 13 || c == -1){ break; } + else { name += c; } + } + m->gobble(in); + } + + while(in){ + char letter= in.get(); + if(letter == '>'){ in.putback(letter); break; } + else{ scores += letter; } + } + + m->gobble(in); + + it = badSeqNames.find(saveName); + + if(it != badSeqNames.end()){ + badSeqNames.erase(it); + }else{ + goodQual << name << endl << scores; + } + + m->gobble(in); } - else{ - goodGroupOut << seqName << '\t' << group << endl; + + in.close(); + goodQual.close(); + + //we were unable to remove some of the bad sequences + if (badSeqNames.size() != 0) { + for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) { + m->mothurOut("Your qual file does not include the sequence " + it->first + " please correct."); + m->mothurOutEndLine(); + } } - gobble(inputGroups); + + if (m->control_pressed) { m->mothurRemove(goodQualFile); return 0; } + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "ScreenSeqsCommand", "screenQual"); + exit(1); } - inputGroups.close(); - goodGroupOut.close(); - badGroupOut.close(); } +//********************************************************************************************************************** + +int ScreenSeqsCommand::driver(linePair filePos, string goodFName, string badAccnosFName, string filename, map& badSeqNames){ + try { + ofstream goodFile; + m->openOutputFile(goodFName, goodFile); + + ofstream badAccnosFile; + m->openOutputFile(badAccnosFName, badAccnosFile); + + ifstream inFASTA; + m->openInputFile(filename, inFASTA); + + inFASTA.seekg(filePos.start); + + bool done = false; + int count = 0; + + while (!done) { + + if (m->control_pressed) { return 0; } + + Sequence currSeq(inFASTA); m->gobble(inFASTA); + if (currSeq.getName() != "") { + bool goodSeq = 1; // innocent until proven guilty + string trashCode = ""; + //have the report files found you bad + map::iterator it = badSeqNames.find(currSeq.getName()); + if (it != badSeqNames.end()) { goodSeq = 0; trashCode = it->second; } + + if (summaryfile == "") { //summaryfile includes these so no need to check again + if(startPos != -1 && startPos < currSeq.getStartPos()) { goodSeq = 0; trashCode += "start|"; } + if(endPos != -1 && endPos > currSeq.getEndPos()) { goodSeq = 0; trashCode += "end|";} + if(maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases()) { goodSeq = 0; trashCode += "ambig|";} + if(maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer()) { goodSeq = 0; trashCode += "homop|";} + if(minLength != -1 && minLength > currSeq.getNumBases()) { goodSeq = 0; trashCode += "= filePos.end)) { break; } + #else + if (inFASTA.eof()) { break; } + #endif + + //report progress + if((count) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count)+"\n"); } + } + //report progress + if((count) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count)+"\n"); } + + + goodFile.close(); + inFASTA.close(); + badAccnosFile.close(); + + return count; + } + catch(exception& e) { + m->errorOut(e, "ScreenSeqsCommand", "driver"); + exit(1); + } +} +//********************************************************************************************************************** +#ifdef USE_MPI +int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& goodFile, MPI_File& badAccnosFile, vector& MPIPos, map& badSeqNames){ + try { + string outputString = ""; + MPI_Status statusGood; + MPI_Status statusBadAccnos; + MPI_Status status; + int pid; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are + + for(int i=0;icontrol_pressed) { return 0; } + + //read next sequence + int length = MPIPos[start+i+1] - MPIPos[start+i]; + + char* buf4 = new char[length]; + + MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status); + + string tempBuf = buf4; delete buf4; + if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); } + istringstream iss (tempBuf,istringstream::in); + + Sequence currSeq(iss); + + //process seq + if (currSeq.getName() != "") { + bool goodSeq = 1; // innocent until proven guilty + string trashCode = ""; + //have the report files found you bad + map::iterator it = badSeqNames.find(currSeq.getName()); + if (it != badSeqNames.end()) { goodSeq = 0; trashCode = it->second; } + + if (summaryfile == "") { //summaryfile includes these so no need to check again + if(startPos != -1 && startPos < currSeq.getStartPos()) { goodSeq = 0; trashCode += "start|"; } + if(endPos != -1 && endPos > currSeq.getEndPos()) { goodSeq = 0; trashCode += "end|";} + if(maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases()) { goodSeq = 0; trashCode += "ambig|";} + if(maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer()) { goodSeq = 0; trashCode += "homop|";} + if(minLength != -1 && minLength > currSeq.getNumBases()) { goodSeq = 0; trashCode += "mothurOutJustToScreen("Processing sequence: " + toString(i)+"\n"); } + } + + return 1; + } + catch(exception& e) { + m->errorOut(e, "ScreenSeqsCommand", "driverMPI"); + exit(1); + } +} +#endif +/**************************************************************************************************/ + +int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, string filename, map& badSeqNames) { + try { + + vector processIDS; + int process = 1; + int num = 0; + +#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){ + num = driver(lines[process], goodFileName + toString(getpid()) + ".temp", badAccnos + toString(getpid()) + ".temp", filename, badSeqNames); + + //pass numSeqs to parent + ofstream out; + string tempFile = filename + toString(getpid()) + ".num.temp"; + m->openOutputFile(tempFile, out); + out << num << endl; + out.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); + } + } + + num = driver(lines[0], goodFileName, badAccnos, filename, badSeqNames); + + //force parent to wait until all the processes are done + for (int i=0;iopenInputFile(tempFile, in); + if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; } + in.close(); m->mothurRemove(tempFile); + + m->appendFiles((goodFileName + toString(processIDS[i]) + ".temp"), goodFileName); + m->mothurRemove((goodFileName + toString(processIDS[i]) + ".temp")); + + m->appendFiles((badAccnos + toString(processIDS[i]) + ".temp"), badAccnos); + m->mothurRemove((badAccnos + toString(processIDS[i]) + ".temp")); + } + + //read badSeqs in because root process doesnt know what other "bad" seqs the children found + ifstream inBad; + int ableToOpen = m->openInputFile(badAccnos, inBad, "no error"); + + if (ableToOpen == 0) { + badSeqNames.clear(); + string tempName, trashCode; + while (!inBad.eof()) { + inBad >> tempName >> trashCode; m->gobble(inBad); + badSeqNames[tempName] = trashCode; + } + inBad.close(); + } +#else + + ////////////////////////////////////////////////////////////////////////////////////////////////////// + //Windows version shared memory, so be careful when passing variables through the sumScreenData struct. + //Above fork() will clone, so memory is separate, but that's not the case with windows, + //Taking advantage of shared memory to allow both threads to add info to badSeqNames. + ////////////////////////////////////////////////////////////////////////////////////////////////////// + + vector pDataArray; + DWORD dwThreadIdArray[processors-1]; + HANDLE hThreadArray[processors-1]; + + //Create processor worker threads. + for( int i=0; icount; + if (pDataArray[i]->count != pDataArray[i]->end) { + m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true; + } + for (map::iterator it = pDataArray[i]->badSeqNames.begin(); it != pDataArray[i]->badSeqNames.end(); it++) { badSeqNames[it->first] = it->second; } + CloseHandle(hThreadArray[i]); + delete pDataArray[i]; + } + + for (int i = 0; i < processIDS.size(); i++) { + m->appendFiles((goodFileName + toString(processIDS[i]) + ".temp"), goodFileName); + m->mothurRemove((goodFileName + toString(processIDS[i]) + ".temp")); + + m->appendFiles((badAccnos + toString(processIDS[i]) + ".temp"), badAccnos); + m->mothurRemove((badAccnos + toString(processIDS[i]) + ".temp")); + } + +#endif + + return num; + + } + catch(exception& e) { + m->errorOut(e, "ScreenSeqsCommand", "createProcesses"); + exit(1); + } +} //***************************************************************************************************************