X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=screenseqscommand.cpp;h=5a9c0c8320b7305834cdf4bb544effd515728417;hb=f12174bc43f9e8ad536f2a37fb3a763b1ac90ba9;hp=ec2d8e003a31a712de8c32d255d164b6b13cd46c;hpb=7f0cae4f4853cc3f12bc751ee06ea31c7c97496e;p=mothur.git diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp index ec2d8e0..5a9c0c8 100644 --- a/screenseqscommand.cpp +++ b/screenseqscommand.cpp @@ -8,28 +8,29 @@ */ #include "screenseqscommand.h" -#include "sequence.hpp" +#include "counttable.h" //********************************************************************************************************************** vector ScreenSeqsCommand::setParameters(){ try { - CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta); - CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname); - CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup); - CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pqfile); - CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(palignreport); - CommandParameter ptax("taxonomy", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(ptax); - CommandParameter pstart("start", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pstart); - CommandParameter pend("end", "Number", "", "-1", "", "", "",false,false); 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); 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); + CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta); + 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 palignreport("alignreport", "InputTypes", "", "", "none", "none", "none","alignreport",false,false); parameters.push_back(palignreport); + 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); vector myArray; for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } @@ -44,12 +45,12 @@ vector ScreenSeqsCommand::setParameters(){ string ScreenSeqsCommand::getHelpString(){ try { string helpString = ""; - helpString += "The screen.seqs command reads a fastafile and creates .....\n"; - helpString += "The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, group, qfile, alignreport, taxonomy, optimize, criteria and processors.\n"; + 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, taxonomy, optimize, criteria and processors.\n"; helpString += "The fasta parameter is required.\n"; helpString += "The alignreport and taxonomy parameters allow you to remove bad seqs from taxonomy and alignreport files.\n"; - helpString += "The start parameter .... The default is -1.\n"; - helpString += "The end parameter .... The default is -1.\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"; @@ -71,6 +72,28 @@ string ScreenSeqsCommand::getHelpString(){ } } //********************************************************************************************************************** +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 { 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; @@ -83,6 +106,7 @@ ScreenSeqsCommand::ScreenSeqsCommand(){ outputTypes["accnos"] = tempOutNames; outputTypes["qfile"] = tempOutNames; outputTypes["taxonomy"] = tempOutNames; + outputTypes["count"] = tempOutNames; } catch(exception& e) { m->errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand"); @@ -122,6 +146,7 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option) { outputTypes["accnos"] = tempOutNames; outputTypes["qfile"] = tempOutNames; outputTypes["taxonomy"] = tempOutNames; + outputTypes["count"] = 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); @@ -175,6 +200,14 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option) { //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 @@ -202,6 +235,19 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option) { 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); } + + 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 = ""; } @@ -220,26 +266,26 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option) { // ...at some point should added some additional type checking... string temp; temp = validParameter.validFile(parameters, "start", false); if (temp == "not found") { temp = "-1"; } - convert(temp, startPos); + m->mothurConvert(temp, startPos); temp = validParameter.validFile(parameters, "end", false); if (temp == "not found") { temp = "-1"; } - convert(temp, endPos); + m->mothurConvert(temp, endPos); temp = validParameter.validFile(parameters, "maxambig", false); if (temp == "not found") { temp = "-1"; } - convert(temp, maxAmbig); + m->mothurConvert(temp, maxAmbig); temp = validParameter.validFile(parameters, "maxhomop", false); if (temp == "not found") { temp = "-1"; } - convert(temp, maxHomoP); + m->mothurConvert(temp, maxHomoP); temp = validParameter.validFile(parameters, "minlength", false); if (temp == "not found") { temp = "-1"; } - convert(temp, minLength); + m->mothurConvert(temp, minLength); temp = validParameter.validFile(parameters, "maxlength", false); if (temp == "not found") { temp = "-1"; } - convert(temp, maxLength); + m->mothurConvert(temp, maxLength); temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } m->setProcessors(temp); - convert(temp, processors); + m->mothurConvert(temp, processors); temp = validParameter.validFile(parameters, "optimize", false); //optimizing trumps the optimized values original value if (temp == "not found"){ temp = "none"; } @@ -259,7 +305,14 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option) { if (optimize.size() == 1) { if (optimize[0] == "none") { optimize.clear(); } } temp = validParameter.validFile(parameters, "criteria", false); if (temp == "not found"){ temp = "90"; } - convert(temp, criteria); + m->mothurConvert(temp, criteria); + + if (countfile == "") { + if (namefile == "") { + vector files; files.push_back(fastafile); + parser.getNameFile(files); + } + } } } @@ -280,22 +333,41 @@ int ScreenSeqsCommand::execute(){ 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) - positions = m->divideFile(fastafile, processors); - for (int i = 0; i < (positions.size()-1); i++) { - lines.push_back(new linePair(positions[i], positions[(i+1)])); - } + #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 - positions.push_back(0); positions.push_back(1000); - lines.push_back(new linePair(0, 1000)); + 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 } - - string goodSeqFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "good" + m->getExtension(fastafile); - string badAccnosFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "bad.accnos"; + + 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); + int numFastaSeqs = 0; set badSeqNames; @@ -346,29 +418,16 @@ int ScreenSeqsCommand::execute(){ numSeqsPerProcessor = numFastaSeqs / processors; int startIndex = pid * numSeqsPerProcessor; if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; } - // cout << pid << '\t' << numSeqsPerProcessor << '\t' << startIndex << endl; + //align your part driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames); - //cout << pid << " done" << endl; + 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); - /*for (int j = 0; j < badSize; j++) { - int length; - MPI_Recv(&length, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status); //recv the length of the name - char* buf2 = new char[length]; //make space to recieve it - MPI_Recv(buf2, length, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status); //get name - - string tempBuf = buf2; - if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); } - delete buf2; - - badSeqNames.insert(tempBuf); - }*/ } }else{ //you are a child process MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status); @@ -379,27 +438,15 @@ int ScreenSeqsCommand::execute(){ numSeqsPerProcessor = numFastaSeqs / processors; int startIndex = pid * numSeqsPerProcessor; if(pid == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor; } - //cout << pid << '\t' << numSeqsPerProcessor << '\t' << startIndex << endl; + //align your part driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames); -//cout << pid << " done" << endl; + 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); - - /* - set::iterator it; - for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) { - string name = *it; - int length = name.length(); - char* buf2 = new char[length]; - memcpy(buf2, name.c_str(), length); - - MPI_Send(&length, 1, MPI_INT, 0, tag, MPI_COMM_WORLD); - MPI_Send(buf2, length, MPI_CHAR, 0, tag, MPI_COMM_WORLD); - }*/ } //close files @@ -409,53 +456,10 @@ int ScreenSeqsCommand::execute(){ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case #else - - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - if(processors == 1){ - numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames); - - if (m->control_pressed) { m->mothurRemove(goodSeqFile); return 0; } - - }else{ - processIDS.resize(0); - - numFastaSeqs = createProcesses(goodSeqFile, badAccnosFile, fastafile, badSeqNames); - - rename((goodSeqFile + toString(processIDS[0]) + ".temp").c_str(), goodSeqFile.c_str()); - rename((badAccnosFile + toString(processIDS[0]) + ".temp").c_str(), badAccnosFile.c_str()); - - //append alignment and report files - for(int i=1;iappendFiles((goodSeqFile + toString(processIDS[i]) + ".temp"), goodSeqFile); - m->mothurRemove((goodSeqFile + toString(processIDS[i]) + ".temp")); - - m->appendFiles((badAccnosFile + toString(processIDS[i]) + ".temp"), badAccnosFile); - m->mothurRemove((badAccnosFile + toString(processIDS[i]) + ".temp")); - } - - if (m->control_pressed) { m->mothurRemove(goodSeqFile); return 0; } - - //read badSeqs in because root process doesnt know what other "bad" seqs the children found - ifstream inBad; - int ableToOpen = m->openInputFile(badAccnosFile, inBad, "no error"); - - if (ableToOpen == 0) { - badSeqNames.clear(); - string tempName; - while (!inBad.eof()) { - inBad >> tempName; m->gobble(inBad); - badSeqNames.insert(tempName); - } - inBad.close(); - } - } - #else - numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames); - - if (m->control_pressed) { m->mothurRemove(goodSeqFile); return 0; } - - #endif - + 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 0; } #endif #ifdef USE_MPI @@ -498,7 +502,9 @@ int ScreenSeqsCommand::execute(){ screenNameGroupFile(badSeqNames); if (m->control_pressed) { m->mothurRemove(goodSeqFile); return 0; } }else if(groupfile != "") { screenGroupFile(badSeqNames); } // this screens just the group - + else if (countfile != "") { screenCountFile(badSeqNames); } + + if (m->control_pressed) { m->mothurRemove(goodSeqFile); return 0; } if(alignreport != "") { screenAlignReport(badSeqNames); } @@ -545,6 +551,11 @@ int ScreenSeqsCommand::execute(){ 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(); @@ -566,8 +577,10 @@ int ScreenSeqsCommand::screenNameGroupFile(set badSeqNames){ set badSeqGroups; string seqName, seqList, group; set::iterator it; - - string goodNameFile = outputDir + m->getRootName(m->getSimpleName(namefile)) + "good" + m->getExtension(namefile); + 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); @@ -612,8 +625,10 @@ int ScreenSeqsCommand::screenNameGroupFile(set badSeqNames){ ifstream inputGroups; m->openInputFile(groupfile, inputGroups); - - string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile); + 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); @@ -664,14 +679,25 @@ int ScreenSeqsCommand::getSummary(vector& positions){ vector ambigBases; vector longHomoPolymer; -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - vector positions = m->divideFile(fastafile, processors); - - for (int i = 0; i < (positions.size()-1); i++) { - lines.push_back(new linePair(positions[i], positions[(i+1)])); - } + 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 - lines.push_back(new linePair(0, 1000)); + 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 @@ -682,7 +708,7 @@ int ScreenSeqsCommand::getSummary(vector& positions){ driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]); #else int numSeqs = 0; - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + //#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) if(processors == 1){ numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]); }else{ @@ -690,10 +716,10 @@ int ScreenSeqsCommand::getSummary(vector& positions){ } if (m->control_pressed) { return 0; } - #else - numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]); - if (m->control_pressed) { return 0; } - #endif + //#else + // numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]); + // if (m->control_pressed) { return 0; } + //#endif #endif sort(startPosition.begin(), startPosition.end()); sort(endPosition.begin(), endPosition.end()); @@ -748,13 +774,13 @@ int ScreenSeqsCommand::getSummary(vector& positions){ } } /**************************************************************************************/ -int ScreenSeqsCommand::driverCreateSummary(vector& startPosition, vector& endPosition, vector& seqLength, vector& ambigBases, vector& longHomoPolymer, string filename, linePair* filePos) { +int ScreenSeqsCommand::driverCreateSummary(vector& startPosition, vector& endPosition, vector& seqLength, vector& ambigBases, vector& longHomoPolymer, string filename, linePair filePos) { try { ifstream in; m->openInputFile(filename, in); - in.seekg(filePos->start); + in.seekg(filePos.start); bool done = false; int count = 0; @@ -787,9 +813,9 @@ int ScreenSeqsCommand::driverCreateSummary(vector& startPosition, vectormothurOut("Optimizing sequence: " + toString(count)); m->mothurOutEndLine(); } - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) unsigned long long pos = in.tellg(); - if ((pos == -1) || (pos >= filePos->end)) { break; } + if ((pos == -1) || (pos >= filePos.end)) { break; } #else if (in.eof()) { break; } #endif @@ -808,11 +834,13 @@ int ScreenSeqsCommand::driverCreateSummary(vector& startPosition, vector& startPosition, vector& endPosition, vector& seqLength, vector& ambigBases, vector& longHomoPolymer, string filename) { try { -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - int process = 1; + + int process = 1; int num = 0; - processIDS.clear(); - + 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(); @@ -873,8 +901,50 @@ int ScreenSeqsCommand::createProcessesCreateSummary(vector& startPosition, m->mothurRemove(tempFilename); } - return num; + +#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; + 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]); } + CloseHandle(hThreadArray[i]); + delete pDataArray[i]; + } + #endif + return num; } catch(exception& e) { m->errorOut(e, "ScreenSeqsCommand", "createProcessesCreateSummary"); @@ -890,9 +960,11 @@ int ScreenSeqsCommand::screenGroupFile(set badSeqNames){ m->openInputFile(groupfile, inputGroups); string seqName, group; set::iterator it; - - string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile); - outputNames.push_back(goodGroupFile); outputTypes["group"].push_back(goodGroupFile); + 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()){ @@ -933,7 +1005,72 @@ int ScreenSeqsCommand::screenGroupFile(set badSeqNames){ exit(1); } } +//*************************************************************************************************************** +int ScreenSeqsCommand::screenCountFile(set badSeqNames){ + try { + ifstream in; + m->openInputFile(countfile, in); + set::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 + " 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); + } +} //*************************************************************************************************************** int ScreenSeqsCommand::screenAlignReport(set badSeqNames){ @@ -943,7 +1080,10 @@ int ScreenSeqsCommand::screenAlignReport(set badSeqNames){ string seqName, group; set::iterator it; - string goodAlignReportFile = outputDir + m->getRootName(m->getSimpleName(alignreport)) + "good" + m->getExtension(alignreport); + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(alignreport)); + string goodAlignReportFile = getOutputFileName("alignreport", variables); + outputNames.push_back(goodAlignReportFile); outputTypes["alignreport"].push_back(goodAlignReportFile); ofstream goodAlignReportOut; m->openOutputFile(goodAlignReportFile, goodAlignReportOut); @@ -1006,8 +1146,11 @@ int ScreenSeqsCommand::screenTaxonomy(set badSeqNames){ m->openInputFile(taxonomy, input); string seqName, tax; set::iterator it; - - string goodTaxFile = outputDir + m->getRootName(m->getSimpleName(taxonomy)) + "good" + m->getExtension(taxonomy); + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(taxonomy)); + variables["[extension]"] = m->getExtension(taxonomy); + string goodTaxFile = getOutputFileName("taxonomy", variables); + outputNames.push_back(goodTaxFile); outputTypes["taxonomy"].push_back(goodTaxFile); ofstream goodTaxOut; m->openOutputFile(goodTaxFile, goodTaxOut); @@ -1055,8 +1198,11 @@ int ScreenSeqsCommand::screenQual(set badSeqNames){ ifstream in; m->openInputFile(qualfile, in); set::iterator it; + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(qualfile)); + variables["[extension]"] = m->getExtension(qualfile); + string goodQualFile = getOutputFileName("qfile", variables); - string goodQualFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + "good" + m->getExtension(qualfile); outputNames.push_back(goodQualFile); outputTypes["qfile"].push_back(goodQualFile); ofstream goodQual; m->openOutputFile(goodQualFile, goodQual); @@ -1123,7 +1269,7 @@ int ScreenSeqsCommand::screenQual(set badSeqNames){ } //********************************************************************************************************************** -int ScreenSeqsCommand::driver(linePair* filePos, string goodFName, string badAccnosFName, string filename, set& badSeqNames){ +int ScreenSeqsCommand::driver(linePair filePos, string goodFName, string badAccnosFName, string filename, set& badSeqNames){ try { ofstream goodFile; m->openOutputFile(goodFName, goodFile); @@ -1134,7 +1280,7 @@ int ScreenSeqsCommand::driver(linePair* filePos, string goodFName, string badAcc ifstream inFASTA; m->openInputFile(filename, inFASTA); - inFASTA.seekg(filePos->start); + inFASTA.seekg(filePos.start); bool done = false; int count = 0; @@ -1163,9 +1309,9 @@ int ScreenSeqsCommand::driver(linePair* filePos, string goodFName, string badAcc count++; } - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) unsigned long long pos = inFASTA.tellg(); - if ((pos == -1) || (pos >= filePos->end)) { break; } + if ((pos == -1) || (pos >= filePos.end)) { break; } #else if (inFASTA.eof()) { break; } #endif @@ -1207,7 +1353,6 @@ int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& int length = MPIPos[start+i+1] - MPIPos[start+i]; char* buf4 = new char[length]; - memcpy(buf4, outputString.c_str(), length); MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status); @@ -1270,10 +1415,13 @@ int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, string filename, set& badSeqNames) { try { -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - int process = 0; + + 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(); @@ -1299,8 +1447,10 @@ int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, st } } + 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")); } - return num; -#endif + //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; + while (!inBad.eof()) { + inBad >> tempName; m->gobble(inBad); + badSeqNames.insert(tempName); + } + 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; + for (set::iterator it = pDataArray[i]->badSeqNames.begin(); it != pDataArray[i]->badSeqNames.end(); it++) { badSeqNames.insert(*it); } + 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");