//***************************************************************************************************************
-ScreenSeqsCommand::ScreenSeqsCommand(string option){
+ScreenSeqsCommand::ScreenSeqsCommand(string option) {
try {
abort = false;
else {
//valid paramters for this command
string AlignArray[] = {"fasta", "start", "end", "maxambig", "maxhomop", "minlength", "maxlength",
- "name", "group", "alignreport"};
+ "name", "group", "alignreport","processors","outputdir","inputdir"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
+ map<string,string>::iterator it;
//check to make sure all parameters are valid for command
- for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //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 = 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 = 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 = 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 = 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; }
+ }
+ }
+
//check for required parameters
fastafile = validParameter.validFile(parameters, "fasta", true);
- if (fastafile == "not found") { cout << "fasta is a required parameter for the screen.seqs command." << endl; abort = true; }
+ if (fastafile == "not found") { m->mothurOut("fasta is a required parameter for the screen.seqs command."); m->mothurOutEndLine(); abort = true; }
else if (fastafile == "not open") { abort = true; }
groupfile = validParameter.validFile(parameters, "group", true);
if (alignreport == "not open") { abort = true; }
else if (alignreport == "not found") { alignreport = ""; }
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
+ outputDir = "";
+ outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it
+ }
+
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
string temp;
temp = validParameter.validFile(parameters, "maxlength", false); if (temp == "not found") { temp = "-1"; }
convert(temp, maxLength);
+
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; }
+ convert(temp, processors);
+
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ScreenSeqsCommand class Function ScreenSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the ScreenSeqsCommand class function ScreenSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
void ScreenSeqsCommand::help(){
try {
- cout << "The screen.seqs command reads a fastafile and creates ....." << "\n";
- cout << "The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, and group." << "\n";
- cout << "The fasta parameter is required." << "\n";
- cout << "The start parameter .... The default is -1." << "\n";
- cout << "The end parameter .... The default is -1." << "\n";
- cout << "The maxambig parameter .... The default is -1." << "\n";
- cout << "The maxhomop parameter .... The default is -1." << "\n";
- cout << "The minlength parameter .... The default is -1." << "\n";
- cout << "The maxlength parameter .... The default is -1." << "\n";
- cout << "The name parameter allows you to provide a namesfile, and the group parameter allows you to provide a groupfile." << "\n";
- cout << "The screen.seqs command should be in the following format: " << "\n";
- cout << "screen.seqs(fasta=yourFastaFile, name=youNameFile, group=yourGroupFIle, start=yourStart, end=yourEnd, maxambig=yourMaxambig, " << "\n";
- cout << "maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength) " << "\n";
- cout << "Example screen.seqs(fasta=abrecovery.fasta, name=abrecovery.names, group=abrecovery.groups, start=..., end=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...)." << "\n";
- cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta)." << "\n" << "\n";
+ m->mothurOut("The screen.seqs command reads a fastafile and creates .....\n");
+ m->mothurOut("The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, group and processors.\n");
+ m->mothurOut("The fasta parameter is required.\n");
+ m->mothurOut("The start parameter .... The default is -1.\n");
+ m->mothurOut("The end parameter .... The default is -1.\n");
+ m->mothurOut("The maxambig parameter .... The default is -1.\n");
+ m->mothurOut("The maxhomop parameter .... The default is -1.\n");
+ m->mothurOut("The minlength parameter .... The default is -1.\n");
+ m->mothurOut("The maxlength parameter .... The default is -1.\n");
+ m->mothurOut("The processors parameter allows you to specify the number of processors to use while running the command. The default is 1.\n");
+ m->mothurOut("The name parameter allows you to provide a namesfile, and the group parameter allows you to provide a groupfile.\n");
+ m->mothurOut("The screen.seqs command should be in the following format: \n");
+ m->mothurOut("screen.seqs(fasta=yourFastaFile, name=youNameFile, group=yourGroupFIle, start=yourStart, end=yourEnd, maxambig=yourMaxambig, \n");
+ m->mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength) \n");
+ m->mothurOut("Example screen.seqs(fasta=abrecovery.fasta, name=abrecovery.names, group=abrecovery.groups, start=..., end=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ScreenSeqsCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ScreenSeqsCommand", "help");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the ScreenSeqsCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//***************************************************************************************************************
if (abort == true) { return 0; }
- ifstream inFASTA;
- openInputFile(fastafile, inFASTA);
+ string goodSeqFile = outputDir + getRootName(getSimpleName(fastafile)) + "good" + getExtension(fastafile);
+ string badSeqFile = outputDir + getRootName(getSimpleName(fastafile)) + "bad" + getExtension(fastafile);
+ string badAccnosFile = outputDir + getRootName(getSimpleName(fastafile)) + "bad.accnos";
+ int numFastaSeqs = 0;
set<string> badSeqNames;
+ int start = time(NULL);
- string goodSeqFile = getRootName(fastafile) + "good" + getExtension(fastafile);
- string badSeqFile = getRootName(fastafile) + "bad" + getExtension(fastafile);
-
- ofstream goodSeqOut; openOutputFile(goodSeqFile, goodSeqOut);
- ofstream badSeqOut; openOutputFile(badSeqFile, badSeqOut);
-
- 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);
+#ifdef USE_MPI
+ int pid, end, numSeqsPerProcessor;
+ int tag = 2001;
+ vector<long> 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 outMPIBad;
+ 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 outBadFilename[1024];
+ strcpy(outBadFilename, badSeqFile.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, outBadFilename, outMode, MPI_INFO_NULL, &outMPIBad);
+ 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(&outMPIBad); MPI_File_close(&outMPIBadAccnos); return 0; }
+
+ if (pid == 0) { //you are the root process
+
+ MPIPos = 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, outMPIBad, outMPIBadAccnos, MPIPos, badSeqNames);
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBadAccnos); MPI_File_close(&outMPIBad); 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);
+ 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, outMPIBad, outMPIBadAccnos, MPIPos, badSeqNames);
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBad); 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<string>::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);
+ }*/
}
- else{
- currSeq.printSequence(badSeqOut);
- badSeqNames.insert(currSeq.getName());
+
+ //close files
+ MPI_File_close(&inMPI);
+ MPI_File_close(&outMPIGood);
+ MPI_File_close(&outMPIBad);
+ MPI_File_close(&outMPIBadAccnos);
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+
+#else
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ if(processors == 1){
+ ifstream inFASTA;
+ openInputFile(fastafile, inFASTA);
+ getNumSeqs(inFASTA, numFastaSeqs);
+ inFASTA.close();
+
+ lines.push_back(new linePair(0, numFastaSeqs));
+
+ driver(lines[0], goodSeqFile, badSeqFile, badAccnosFile, fastafile, badSeqNames);
+
+ if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
+
+ }else{
+ vector<int> positions;
+ processIDS.resize(0);
+
+ ifstream inFASTA;
+ openInputFile(fastafile, inFASTA);
+
+ string input;
+ while(!inFASTA.eof()){
+ input = getline(inFASTA);
+ if (input.length() != 0) {
+ if(input[0] == '>'){ long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
+ }
+ }
+ inFASTA.close();
+
+ numFastaSeqs = positions.size();
+
+ int numSeqsPerProcessor = numFastaSeqs / processors;
+
+ for (int i = 0; i < processors; i++) {
+ long int startPos = positions[ i * numSeqsPerProcessor ];
+ if(i == processors - 1){
+ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
+ }
+ lines.push_back(new linePair(startPos, numSeqsPerProcessor));
+ }
+
+ createProcesses(goodSeqFile, badSeqFile, badAccnosFile, fastafile, badSeqNames);
+
+ rename((goodSeqFile + toString(processIDS[0]) + ".temp").c_str(), goodSeqFile.c_str());
+ rename((badSeqFile + toString(processIDS[0]) + ".temp").c_str(), badSeqFile.c_str());
+ rename((badAccnosFile + toString(processIDS[0]) + ".temp").c_str(), badAccnosFile.c_str());
+
+ //append alignment and report files
+ for(int i=1;i<processors;i++){
+ appendFiles((goodSeqFile + toString(processIDS[i]) + ".temp"), goodSeqFile);
+ remove((goodSeqFile + toString(processIDS[i]) + ".temp").c_str());
+
+ appendFiles((badSeqFile + toString(processIDS[i]) + ".temp"), badSeqFile);
+ remove((badSeqFile + toString(processIDS[i]) + ".temp").c_str());
+
+ appendFiles((badAccnosFile + toString(processIDS[i]) + ".temp"), badAccnosFile);
+ remove((badAccnosFile + toString(processIDS[i]) + ".temp").c_str());
+ }
+
+ if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
+
+ //read badSeqs in because root process doesnt know what other "bad" seqs the children found
+ ifstream inBad;
+ int ableToOpen = openInputFile(badAccnosFile, inBad, "no error");
+
+ if (ableToOpen == 0) {
+ badSeqNames.clear();
+ string tempName;
+ while (!inBad.eof()) {
+ inBad >> tempName; gobble(inBad);
+ badSeqNames.insert(tempName);
+ }
+ inBad.close();
+ }
}
- gobble(inFASTA);
- }
- if(namefile != "") { screenNameGroupFile(badSeqNames); }
- if(groupfile != "") { screenGroupFile(badSeqNames); }
- if(alignreport != "") { screenAlignReport(badSeqNames); }
+ #else
+ ifstream inFASTA;
+ openInputFile(fastafile, inFASTA);
+ getNumSeqs(inFASTA, numFastaSeqs);
+ inFASTA.close();
+
+ lines.push_back(new linePair(0, numFastaSeqs));
+
+ driver(lines[0], goodSeqFile, badSeqFile, badAccnosFile, fastafile, badSeqNames);
+
+ if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
+
+ #endif
+
+#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;
+ while (!iss.eof()) {
+ iss >> tempName; gobble(iss);
+ badSeqNames.insert(tempName);
+ }
+ #endif
+
+ if(namefile != "" && groupfile != "") {
+ screenNameGroupFile(badSeqNames);
+ if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
+ }else if(namefile != "") {
+ screenNameGroupFile(badSeqNames);
+ if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
+ }else if(groupfile != "") { screenGroupFile(badSeqNames); } // this screens just the group
- goodSeqOut.close();
- badSeqOut.close();
- inFASTA.close();
+ if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
+
+ if(alignreport != "") { screenAlignReport(badSeqNames); }
+
+ if (m->control_pressed) { remove(goodSeqFile.c_str()); remove(badSeqFile.c_str()); return 0; }
+
+ #ifdef USE_MPI
+ }
+ #endif
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ m->mothurOut(goodSeqFile); m->mothurOutEndLine();
+ m->mothurOut(badSeqFile); m->mothurOutEndLine();
+ m->mothurOut(badAccnosFile); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+ m->mothurOutEndLine();
+
+ 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 ScreenSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ScreenSeqsCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the ScreenSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
}
//***************************************************************************************************************
-void ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
+int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
+ try {
+ ifstream inputNames;
+ openInputFile(namefile, inputNames);
+ set<string> badSeqGroups;
+ string seqName, seqList, group;
+ set<string>::iterator it;
- ifstream inputNames;
- openInputFile(namefile, inputNames);
- set<string> badSeqGroups;
- string seqName, seqList, group;
- set<string>::iterator it;
+ string goodNameFile = outputDir + getRootName(getSimpleName(namefile)) + "good" + getExtension(namefile);
+ string badNameFile = outputDir + getRootName(getSimpleName(namefile)) + "bad" + getExtension(namefile);
+
+ outputNames.push_back(goodNameFile); outputNames.push_back(badNameFile);
+
+ ofstream goodNameOut; openOutputFile(goodNameFile, goodNameOut);
+ ofstream badNameOut; openOutputFile(badNameFile, badNameOut);
+
+ while(!inputNames.eof()){
+ if (m->control_pressed) { goodNameOut.close(); badNameOut.close(); inputNames.close(); remove(goodNameFile.c_str()); remove(badNameFile.c_str()); return 0; }
- string goodNameFile = getRootName(namefile) + "good" + getExtension(namefile);
- string badNameFile = getRootName(namefile) + "bad" + getExtension(namefile);
-
- ofstream goodNameOut; openOutputFile(goodNameFile, goodNameOut);
- ofstream badNameOut; openOutputFile(badNameFile, badNameOut);
-
- while(!inputNames.eof()){
- inputNames >> seqName >> seqList;
- it = badSeqNames.find(seqName);
-
- if(it != badSeqNames.end()){
- badSeqNames.erase(it);
- badNameOut << seqName << '\t' << seqList << endl;
- if(namefile != ""){
- int start = 0;
- for(int i=0;i<seqList.length();i++){
- if(seqList[i] == ','){
- badSeqGroups.insert(seqList.substr(start,i-start));
- start = i+1;
- }
+ inputNames >> seqName >> seqList;
+ it = badSeqNames.find(seqName);
+
+ if(it != badSeqNames.end()){
+ badSeqNames.erase(it);
+ badNameOut << seqName << '\t' << seqList << endl;
+ if(namefile != ""){
+ int start = 0;
+ for(int i=0;i<seqList.length();i++){
+ if(seqList[i] == ','){
+ badSeqGroups.insert(seqList.substr(start,i-start));
+ start = i+1;
+ }
+ }
+ badSeqGroups.insert(seqList.substr(start,seqList.length()-start));
}
- badSeqGroups.insert(seqList.substr(start,seqList.length()-start));
}
+ else{
+ goodNameOut << seqName << '\t' << seqList << endl;
+ }
+ gobble(inputNames);
}
- else{
- goodNameOut << seqName << '\t' << seqList << endl;
+ inputNames.close();
+ goodNameOut.close();
+ badNameOut.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 namefile does not include the sequence " + *it + " please correct.");
+ m->mothurOutEndLine();
+ }
}
- gobble(inputNames);
- }
- inputNames.close();
- goodNameOut.close();
- badNameOut.close();
+
+ if(groupfile != ""){
+
+ ifstream inputGroups;
+ openInputFile(groupfile, inputGroups);
+
+ string goodGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "good" + getExtension(groupfile);
+ string badGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "bad" + getExtension(groupfile);
+
+ outputNames.push_back(goodGroupFile); outputNames.push_back(badGroupFile);
+
+ ofstream goodGroupOut; openOutputFile(goodGroupFile, goodGroupOut);
+ ofstream badGroupOut; openOutputFile(badGroupFile, badGroupOut);
+
+ while(!inputGroups.eof()){
+ if (m->control_pressed) { goodGroupOut.close(); badGroupOut.close(); inputGroups.close(); remove(goodNameFile.c_str()); remove(badNameFile.c_str()); remove(goodGroupFile.c_str()); remove(badGroupFile.c_str()); return 0; }
+
+ inputGroups >> seqName >> group;
+
+ it = badSeqGroups.find(seqName);
+
+ if(it != badSeqGroups.end()){
+ badSeqGroups.erase(it);
+ badGroupOut << seqName << '\t' << group << endl;
+ }
+ else{
+ goodGroupOut << seqName << '\t' << group << endl;
+ }
+ gobble(inputGroups);
+ }
+ inputGroups.close();
+ goodGroupOut.close();
+ badGroupOut.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 namefile does not include the sequence " + *it + " please correct.");
+ m->mothurOutEndLine();
+ }
+ }
+ }
+
+ return 0;
- if(groupfile != ""){
-
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "screenNameGroupFile");
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+
+int ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
+ try {
ifstream inputGroups;
openInputFile(groupfile, inputGroups);
-
- string goodGroupFile = getRootName(groupfile) + "good" + getExtension(groupfile);
- string badGroupFile = getRootName(groupfile) + "bad" + getExtension(groupfile);
+ string seqName, group;
+ set<string>::iterator it;
+
+ string goodGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "good" + getExtension(groupfile);
+ string badGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "bad" + getExtension(groupfile);
+
+ outputNames.push_back(goodGroupFile); outputNames.push_back(badGroupFile);
ofstream goodGroupOut; openOutputFile(goodGroupFile, goodGroupOut);
ofstream badGroupOut; openOutputFile(badGroupFile, badGroupOut);
while(!inputGroups.eof()){
- inputGroups >> seqName >> group;
+ if (m->control_pressed) { goodGroupOut.close(); badGroupOut.close(); inputGroups.close(); remove(goodGroupFile.c_str()); remove(badGroupFile.c_str()); return 0; }
- it = badSeqGroups.find(seqName);
+ inputGroups >> seqName >> group;
+ it = badSeqNames.find(seqName);
- if(it != badSeqGroups.end()){
- badSeqGroups.erase(it);
+ if(it != badSeqNames.end()){
+ badSeqNames.erase(it);
badGroupOut << seqName << '\t' << group << endl;
}
else{
}
gobble(inputGroups);
}
+
+ if (m->control_pressed) { goodGroupOut.close(); badGroupOut.close(); inputGroups.close(); remove(goodGroupFile.c_str()); remove(badGroupFile.c_str()); 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 + " please correct.");
+ m->mothurOutEndLine();
+ }
+ }
+
inputGroups.close();
goodGroupOut.close();
badGroupOut.close();
+
+ if (m->control_pressed) { remove(goodGroupFile.c_str()); remove(badGroupFile.c_str()); }
+
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "screenGroupFile");
+ exit(1);
}
}
//***************************************************************************************************************
-void ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
-
- ifstream inputGroups;
- openInputFile(groupfile, inputGroups);
- string seqName, group;
- set<string>::iterator it;
-
- string goodGroupFile = getRootName(groupfile) + "good" + getExtension(groupfile);
- string badGroupFile = getRootName(groupfile) + "bad" + getExtension(groupfile);
-
- ofstream goodGroupOut; openOutputFile(goodGroupFile, goodGroupOut);
- ofstream badGroupOut; openOutputFile(badGroupFile, badGroupOut);
-
- while(!inputGroups.eof()){
- inputGroups >> seqName >> group;
- it = badSeqNames.find(seqName);
+int ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
+ try {
+ ifstream inputAlignReport;
+ openInputFile(alignreport, inputAlignReport);
+ string seqName, group;
+ set<string>::iterator it;
+
+ string goodAlignReportFile = outputDir + getRootName(getSimpleName(alignreport)) + "good" + getExtension(alignreport);
+ string badAlignReportFile = outputDir + getRootName(getSimpleName(alignreport)) + "bad" + getExtension(alignreport);
- if(it != badSeqNames.end()){
- badSeqNames.erase(it);
- badGroupOut << seqName << '\t' << group << endl;
+ outputNames.push_back(goodAlignReportFile); outputNames.push_back(badAlignReportFile);
+
+ ofstream goodAlignReportOut; openOutputFile(goodAlignReportFile, goodAlignReportOut);
+ ofstream badAlignReportOut; openOutputFile(badAlignReportFile, badAlignReportOut);
+
+ while (!inputAlignReport.eof()) { // need to copy header
+ char c = inputAlignReport.get();
+ goodAlignReportOut << c;
+ badAlignReportOut << c;
+ if (c == 10 || c == 13){ break; }
+ }
+
+ while(!inputAlignReport.eof()){
+ if (m->control_pressed) { goodAlignReportOut.close(); badAlignReportOut.close(); inputAlignReport.close(); remove(goodAlignReportFile.c_str()); remove(badAlignReportFile.c_str()); return 0; }
+
+ inputAlignReport >> seqName;
+ it = badSeqNames.find(seqName);
+ string line;
+ while (!inputAlignReport.eof()) { // need to copy header
+ char c = inputAlignReport.get();
+ line += c;
+ if (c == 10 || c == 13){ break; }
+ }
+
+ if(it != badSeqNames.end()){
+ badSeqNames.erase(it);
+ badAlignReportOut << seqName << '\t' << line;
+ }
+ else{
+ goodAlignReportOut << seqName << '\t' << line;
+ }
+ gobble(inputAlignReport);
}
- else{
- goodGroupOut << seqName << '\t' << group << endl;
+
+ if (m->control_pressed) { goodAlignReportOut.close(); badAlignReportOut.close(); inputAlignReport.close(); remove(goodAlignReportFile.c_str()); remove(badAlignReportFile.c_str()); 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 file does not include the sequence " + *it + " please correct.");
+ m->mothurOutEndLine();
+ }
}
- gobble(inputGroups);
+
+ inputAlignReport.close();
+ goodAlignReportOut.close();
+ badAlignReportOut.close();
+
+ if (m->control_pressed) { remove(goodAlignReportFile.c_str()); remove(badAlignReportFile.c_str()); return 0; }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "screenAlignReport");
+ exit(1);
}
- inputGroups.close();
- goodGroupOut.close();
- badGroupOut.close();
}
+//**********************************************************************************************************************
-//***************************************************************************************************************
+int ScreenSeqsCommand::driver(linePair* line, string goodFName, string badFName, string badAccnosFName, string filename, set<string>& badSeqNames){
+ try {
+ ofstream goodFile;
+ openOutputFile(goodFName, goodFile);
+
+ ofstream badFile;
+ openOutputFile(badFName, badFile);
+
+ ofstream badAccnosFile;
+ openOutputFile(badAccnosFName, badAccnosFile);
+
+ ifstream inFASTA;
+ openInputFile(filename, inFASTA);
-void ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
-
- ifstream inputAlignReport;
- openInputFile(alignreport, inputAlignReport);
- string seqName, group;
- set<string>::iterator it;
+ inFASTA.seekg(line->start);
- string goodAlignReportFile = getRootName(alignreport) + "good" + getExtension(alignreport);
- string badAlignReportFile = getRootName(alignreport) + "bad" + getExtension(alignreport);
-
- ofstream goodAlignReportOut; openOutputFile(goodAlignReportFile, goodAlignReportOut);
- ofstream badAlignReportOut; openOutputFile(badAlignReportFile, badAlignReportOut);
-
- while (!inputAlignReport.eof()) { // need to copy header
- char c = inputAlignReport.get();
- goodAlignReportOut << c;
- badAlignReportOut << c;
- if (c == 10 || c == 13){ break; }
+ for(int i=0;i<line->numSeqs;i++){
+
+ if (m->control_pressed) { return 0; }
+
+ Sequence currSeq(inFASTA);
+ if (currSeq.getName() != "") {
+ 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(goodFile);
+ }
+ else{
+ currSeq.printSequence(badFile);
+ badAccnosFile << currSeq.getName() << endl;
+ badSeqNames.insert(currSeq.getName());
+ }
+ }
+ gobble(inFASTA);
+ }
+
+
+ goodFile.close();
+ inFASTA.close();
+ badFile.close();
+ badAccnosFile.close();
+
+ return 1;
+ }
+ 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& badFile, MPI_File& badAccnosFile, vector<long>& MPIPos, set<string>& badSeqNames){
+ try {
+ string outputString = "";
+ MPI_Status statusGood;
+ MPI_Status statusBad;
+ MPI_Status statusBadAccnos;
+ MPI_Status status;
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
- while(!inputAlignReport.eof()){
- inputAlignReport >> seqName;
- it = badSeqNames.find(seqName);
- string line;
- while (!inputAlignReport.eof()) { // need to copy header
- char c = inputAlignReport.get();
- line += c;
- if (c == 10 || c == 13){ break; }
+ for(int i=0;i<num;i++){
+
+ if (m->control_pressed) { return 0; }
+
+ //read next sequence
+ 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);
+
+ 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
+ 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){
+ outputString = ">" + currSeq.getName() + "\n" + currSeq.getAligned() + "\n";
+
+ //print good seq
+ length = outputString.length();
+ char* buf2 = new char[length];
+ memcpy(buf2, outputString.c_str(), length);
+
+ MPI_File_write_shared(goodFile, buf2, length, MPI_CHAR, &statusGood);
+ delete buf2;
+ }
+ else{
+ outputString = ">" + currSeq.getName() + "\n" + currSeq.getAligned() + "\n";
+
+ //print bad seq to fasta
+ length = outputString.length();
+ char* buf2 = new char[length];
+ memcpy(buf2, outputString.c_str(), length);
+
+ MPI_File_write_shared(badFile, buf2, length, MPI_CHAR, &statusBad);
+ delete buf2;
+
+ badSeqNames.insert(currSeq.getName());
+
+ //write to bad accnos file
+ outputString = currSeq.getName() + "\n";
+
+ length = outputString.length();
+ char* buf3 = new char[length];
+ memcpy(buf3, outputString.c_str(), length);
+
+ MPI_File_write_shared(badAccnosFile, buf3, length, MPI_CHAR, &statusBadAccnos);
+ delete buf3;
+ }
+ }
}
+
+ return 1;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "driverMPI");
+ exit(1);
+ }
+}
+#endif
+/**************************************************************************************************/
+
+int ScreenSeqsCommand::createProcesses(string goodFileName, string badFileName, string badAccnos, string filename, set<string>& badSeqNames) {
+ try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ int process = 0;
+ int exitCommand = 1;
- if(it != badSeqNames.end()){
- badSeqNames.erase(it);
- badAlignReportOut << seqName << '\t' << line;;
+ //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){
+ exitCommand = driver(lines[process], goodFileName + toString(getpid()) + ".temp", badFileName + toString(getpid()) + ".temp", badAccnos + toString(getpid()) + ".temp", filename, badSeqNames);
+ exit(0);
+ }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
}
- else{
- goodAlignReportOut << seqName << '\t' << line;
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<processors;i++) {
+ int temp = processIDS[i];
+ wait(&temp);
}
- gobble(inputAlignReport);
+
+ return exitCommand;
+#endif
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "createProcesses");
+ exit(1);
}
- inputAlignReport.close();
- goodAlignReportOut.close();
- badAlignReportOut.close();
-
}
//***************************************************************************************************************
projects / mothur.git / blobdiff