X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=screenseqscommand.cpp;h=7ac910d4a74b9fc1bffeacb32f5893941f3eb60f;hb=a6cf29fa4dac0909c7582cb1094151d34093ee76;hp=7a6ea3a5f5cc8f0906c8e49c39d05d1d689f7e51;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp index 7a6ea3a..7ac910d 100644 --- a/screenseqscommand.cpp +++ b/screenseqscommand.cpp @@ -8,7 +8,7 @@ */ #include "screenseqscommand.h" -#include "sequence.hpp" + //********************************************************************************************************************** vector ScreenSeqsCommand::setParameters(){ @@ -16,7 +16,9 @@ vector ScreenSeqsCommand::setParameters(){ 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); @@ -43,8 +45,9 @@ 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, optimize, criteria and processors.\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 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 maxambig parameter allows you to set the maximum number of ambigious bases allowed. The default is -1.\n"; @@ -59,7 +62,7 @@ string ScreenSeqsCommand::getHelpString(){ 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\n"; + helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n"; return helpString; } catch(exception& e) { @@ -78,6 +81,8 @@ ScreenSeqsCommand::ScreenSeqsCommand(){ outputTypes["group"] = tempOutNames; outputTypes["alignreport"] = tempOutNames; outputTypes["accnos"] = tempOutNames; + outputTypes["qfile"] = tempOutNames; + outputTypes["taxonomy"] = tempOutNames; } catch(exception& e) { m->errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand"); @@ -92,6 +97,7 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option) { //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(); @@ -114,6 +120,8 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option) { outputTypes["group"] = tempOutNames; outputTypes["alignreport"] = tempOutNames; outputTypes["accnos"] = tempOutNames; + outputTypes["qfile"] = tempOutNames; + outputTypes["taxonomy"] = 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); @@ -151,6 +159,22 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option) { //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("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; } + } } //check for required parameters @@ -160,19 +184,31 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option) { 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 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); } + alignreport = validParameter.validFile(parameters, "alignreport", true); if (alignreport == "not open") { abort = true; } - else if (alignreport == "not found") { alignreport = ""; } + 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"){ @@ -184,26 +220,26 @@ 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"; } @@ -223,7 +259,12 @@ 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 (namefile == "") { + vector files; files.push_back(fastafile); + parser.getNameFile(files); + } } } @@ -240,35 +281,50 @@ int ScreenSeqsCommand::execute(){ if (abort == true) { if (calledHelp) { return 0; } return 2; } //if the user want to optimize we need to know the 90% mark - vector positions; + 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); } getSummary(positions); } else { - 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 + 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"; int numFastaSeqs = 0; set badSeqNames; int start = time(NULL); - + #ifdef USE_MPI int pid, numSeqsPerProcessor; int tag = 2001; - vector MPIPos; + 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; @@ -305,29 +361,16 @@ 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); @@ -338,27 +381,15 @@ 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 @@ -368,53 +399,10 @@ 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) { remove(goodSeqFile.c_str()); 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); - remove((goodSeqFile + toString(processIDS[i]) + ".temp").c_str()); - - m->appendFiles((badAccnosFile + toString(processIDS[i]) + ".temp"), badAccnosFile); - remove((badAccnosFile + toString(processIDS[i]) + ".temp").c_str()); - } - - if (m->control_pressed) { remove(goodSeqFile.c_str()); 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) { remove(goodSeqFile.c_str()); 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 @@ -452,17 +440,19 @@ int ScreenSeqsCommand::execute(){ if(namefile != "" && groupfile != "") { screenNameGroupFile(badSeqNames); - if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; } + if (m->control_pressed) { m->mothurRemove(goodSeqFile); return 0; } }else if(namefile != "") { screenNameGroupFile(badSeqNames); - if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; } + if (m->control_pressed) { m->mothurRemove(goodSeqFile); return 0; } }else if(groupfile != "") { screenGroupFile(badSeqNames); } // this screens just the group - if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; } + if (m->control_pressed) { m->mothurRemove(goodSeqFile); return 0; } if(alignreport != "") { screenAlignReport(badSeqNames); } + if(qualfile != "") { screenQual(badSeqNames); } + if(taxonomy != "") { screenTaxonomy(badSeqNames); } - if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; } + if (m->control_pressed) { m->mothurRemove(goodSeqFile); return 0; } #ifdef USE_MPI } @@ -492,6 +482,16 @@ int ScreenSeqsCommand::execute(){ 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); } + } m->mothurOut("It took " + toString(time(NULL) - start) + " secs to screen " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); @@ -520,7 +520,7 @@ int ScreenSeqsCommand::screenNameGroupFile(set badSeqNames){ ofstream goodNameOut; m->openOutputFile(goodNameFile, goodNameOut); while(!inputNames.eof()){ - if (m->control_pressed) { goodNameOut.close(); inputNames.close(); remove(goodNameFile.c_str()); return 0; } + if (m->control_pressed) { goodNameOut.close(); inputNames.close(); m->mothurRemove(goodNameFile); return 0; } inputNames >> seqName >> seqList; it = badSeqNames.find(seqName); @@ -566,7 +566,7 @@ int ScreenSeqsCommand::screenNameGroupFile(set badSeqNames){ ofstream goodGroupOut; m->openOutputFile(goodGroupFile, goodGroupOut); while(!inputGroups.eof()){ - if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); remove(goodNameFile.c_str()); remove(goodGroupFile.c_str()); return 0; } + if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); m->mothurRemove(goodNameFile); m->mothurRemove(goodGroupFile); return 0; } inputGroups >> seqName >> group; @@ -602,7 +602,7 @@ int ScreenSeqsCommand::screenNameGroupFile(set badSeqNames){ } } //*************************************************************************************************************** -int ScreenSeqsCommand::getSummary(vector& positions){ +int ScreenSeqsCommand::getSummary(vector& positions){ try { vector startPosition; @@ -611,14 +611,36 @@ int ScreenSeqsCommand::getSummary(vector& positions){ vector ambigBases; vector longHomoPolymer; - 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 + 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, 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{ @@ -626,11 +648,11 @@ 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()); sort(seqLength.begin(), seqLength.end()); @@ -649,6 +671,33 @@ int ScreenSeqsCommand::getSummary(vector& positions){ 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) { @@ -657,13 +706,13 @@ 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; @@ -695,10 +744,10 @@ int ScreenSeqsCommand::driverCreateSummary(vector& startPosition, vector= filePos->end)) { break; } + //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 @@ -717,11 +766,13 @@ 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(); @@ -779,11 +830,53 @@ int ScreenSeqsCommand::createProcessesCreateSummary(vector& startPosition, for (int k = 0; k < tempNum; k++) { in >> temp; longHomoPolymer.push_back(temp); } m->gobble(in); in.close(); - remove(tempFilename.c_str()); + 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"); @@ -805,7 +898,7 @@ int ScreenSeqsCommand::screenGroupFile(set badSeqNames){ ofstream goodGroupOut; m->openOutputFile(goodGroupFile, goodGroupOut); while(!inputGroups.eof()){ - if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); remove(goodGroupFile.c_str()); return 0; } + if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); m->mothurRemove(goodGroupFile); return 0; } inputGroups >> seqName >> group; it = badSeqNames.find(seqName); @@ -819,7 +912,7 @@ int ScreenSeqsCommand::screenGroupFile(set badSeqNames){ m->gobble(inputGroups); } - if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); remove(goodGroupFile.c_str()); return 0; } + 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) { @@ -832,7 +925,7 @@ int ScreenSeqsCommand::screenGroupFile(set badSeqNames){ inputGroups.close(); goodGroupOut.close(); - if (m->control_pressed) { remove(goodGroupFile.c_str()); } + if (m->control_pressed) { m->mothurRemove(goodGroupFile); } return 0; @@ -863,7 +956,7 @@ int ScreenSeqsCommand::screenAlignReport(set badSeqNames){ } while(!inputAlignReport.eof()){ - if (m->control_pressed) { goodAlignReportOut.close(); inputAlignReport.close(); remove(goodAlignReportFile.c_str()); return 0; } + if (m->control_pressed) { goodAlignReportOut.close(); inputAlignReport.close(); m->mothurRemove(goodAlignReportFile); return 0; } inputAlignReport >> seqName; it = badSeqNames.find(seqName); @@ -883,7 +976,7 @@ int ScreenSeqsCommand::screenAlignReport(set badSeqNames){ m->gobble(inputAlignReport); } - if (m->control_pressed) { goodAlignReportOut.close(); inputAlignReport.close(); remove(goodAlignReportFile.c_str()); return 0; } + if (m->control_pressed) { goodAlignReportOut.close(); inputAlignReport.close(); m->mothurRemove(goodAlignReportFile); return 0; } //we were unable to remove some of the bad sequences if (badSeqNames.size() != 0) { @@ -896,7 +989,7 @@ int ScreenSeqsCommand::screenAlignReport(set badSeqNames){ inputAlignReport.close(); goodAlignReportOut.close(); - if (m->control_pressed) { remove(goodAlignReportFile.c_str()); return 0; } + if (m->control_pressed) { m->mothurRemove(goodAlignReportFile); return 0; } return 0; @@ -906,10 +999,133 @@ int ScreenSeqsCommand::screenAlignReport(set badSeqNames){ exit(1); } +} +//*************************************************************************************************************** + +int ScreenSeqsCommand::screenTaxonomy(set badSeqNames){ + try { + ifstream input; + m->openInputFile(taxonomy, input); + string seqName, tax; + set::iterator it; + + string goodTaxFile = outputDir + m->getRootName(m->getSimpleName(taxonomy)) + "good" + m->getExtension(taxonomy); + 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 >> 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 + " 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); + } + +} +//*************************************************************************************************************** + +int ScreenSeqsCommand::screenQual(set badSeqNames){ + try { + ifstream in; + m->openInputFile(qualfile, in); + set::iterator it; + + 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); + + 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){ 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); + } + + 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 + " please correct."); + m->mothurOutEndLine(); + } + } + + if (m->control_pressed) { m->mothurRemove(goodQualFile); return 0; } + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "ScreenSeqsCommand", "screenQual"); + exit(1); + } + } //********************************************************************************************************************** -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); @@ -920,7 +1136,7 @@ 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; @@ -949,9 +1165,9 @@ int ScreenSeqsCommand::driver(linePair* filePos, string goodFName, string badAcc count++; } - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - unsigned long int pos = inFASTA.tellg(); - if ((pos == -1) || (pos >= filePos->end)) { break; } + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + unsigned long long pos = inFASTA.tellg(); + if ((pos == -1) || (pos >= filePos.end)) { break; } #else if (inFASTA.eof()) { break; } #endif @@ -976,7 +1192,7 @@ int ScreenSeqsCommand::driver(linePair* filePos, string goodFName, string badAcc } //********************************************************************************************************************** #ifdef USE_MPI -int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& goodFile, MPI_File& badAccnosFile, vector& MPIPos, set& badSeqNames){ +int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& goodFile, MPI_File& badAccnosFile, vector& MPIPos, set& badSeqNames){ try { string outputString = ""; MPI_Status statusGood; @@ -1056,10 +1272,13 @@ 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(); @@ -1085,8 +1304,10 @@ 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(); remove(tempFile.c_str()); + 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");