#include "screenseqscommand.h"
#include "sequence.hpp"
+//**********************************************************************************************************************
+vector<string> 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 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);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ScreenSeqsCommand::getHelpString(){
+ try {
+ 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, optimize, criteria and processors.\n";
+ helpString += "The fasta parameter is required.\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";
+ helpString += "The maxhomop parameter allows you to set a maximum homopolymer length. \n";
+ helpString += "The minlength parameter allows you to set and minimum sequence length. \n";
+ helpString += "The maxlength parameter allows you to set and maximum sequence length. \n";
+ helpString += "The processors parameter allows you to specify the number of processors to use while running the command. The default is 1.\n";
+ helpString += "The optimize and criteria parameters allow you set the start, end, maxabig, maxhomop, minlength and maxlength parameters relative to your set of sequences .\n";
+ helpString += "For example optimize=start-end, criteria=90, would set the start and end values to the position 90% of your sequences started and ended.\n";
+ helpString += "The name parameter allows you to provide a namesfile, and the group parameter allows you to provide a groupfile.\n";
+ helpString += "The screen.seqs command should be in the following format: \n";
+ helpString += "screen.seqs(fasta=yourFastaFile, name=youNameFile, group=yourGroupFIle, start=yourStart, end=yourEnd, maxambig=yourMaxambig, \n";
+ helpString += "maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength) \n";
+ helpString += "Example screen.seqs(fasta=abrecovery.fasta, name=abrecovery.names, group=abrecovery.groups, start=..., end=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ScreenSeqsCommand::ScreenSeqsCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ outputTypes["alignreport"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+ outputTypes["qfile"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand");
+ exit(1);
+ }
+}
//***************************************************************************************************************
ScreenSeqsCommand::ScreenSeqsCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string AlignArray[] = {"fasta", "start", "end", "maxambig", "maxhomop", "minlength", "maxlength",
- "name", "group", "alignreport","outputdir","inputdir"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
- ValidParameters validParameter;
+ ValidParameters validParameter("screen.seqs");
map<string,string>::iterator it;
//check to make sure all parameters are valid for command
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ outputTypes["alignreport"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+ outputTypes["qfile"] = tempOutNames;
+
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
it = parameters.find("fasta");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["fasta"] = inputDir + it->second; }
}
it = parameters.find("group");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["group"] = inputDir + it->second; }
}
it = parameters.find("name");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["name"] = inputDir + it->second; }
}
it = parameters.find("alignreport");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["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; }
+ }
+
}
//check for required parameters
fastafile = validParameter.validFile(parameters, "fasta", 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; }
+ if (fastafile == "not found") {
+ fastafile = m->getFastaFile();
+ if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
+ else if (fastafile == "not open") { abort = true; }
+ else { m->setFastaFile(fastafile); }
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
+ else { m->setGroupFile(groupfile); }
+
+ qualfile = validParameter.validFile(parameters, "qfile", true);
+ if (qualfile == "not open") { abort = true; }
+ else if (qualfile == "not found") { qualfile = ""; }
+ else { m->setQualFile(qualfile); }
namefile = validParameter.validFile(parameters, "name", true);
- if (namefile == "not open") { abort = 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 = ""; }
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
outputDir = "";
- outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it
+ outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
}
//check for optional parameter and set defaults
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 = m->getProcessors(); }
+ m->setProcessors(temp);
+ convert(temp, processors);
+
+ temp = validParameter.validFile(parameters, "optimize", false); //optimizing trumps the optimized values original value
+ if (temp == "not found"){ temp = "none"; }
+ m->splitAtDash(temp, optimize);
+
+ //check for invalid optimize options
+ set<string> validOptimizers;
+ validOptimizers.insert("none"); validOptimizers.insert("start"); validOptimizers.insert("end"); validOptimizers.insert("maxambig"); validOptimizers.insert("maxhomop"); validOptimizers.insert("minlength"); validOptimizers.insert("maxlength");
+ for (int i = 0; i < optimize.size(); i++) {
+ if (validOptimizers.count(optimize[i]) == 0) {
+ m->mothurOut(optimize[i] + " is not a valid optimizer. Valid options are start, end, maxambig, maxhomop, minlength and maxlength."); m->mothurOutEndLine();
+ optimize.erase(optimize.begin()+i);
+ i--;
+ }
+ }
+
+ if (optimize.size() == 1) { if (optimize[0] == "none") { optimize.clear(); } }
+
+ temp = validParameter.validFile(parameters, "criteria", false); if (temp == "not found"){ temp = "90"; }
+ convert(temp, criteria);
}
}
exit(1);
}
}
-//**********************************************************************************************************************
-
-void ScreenSeqsCommand::help(){
- try {
- 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, and group.\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 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) {
- m->errorOut(e, "ScreenSeqsCommand", "help");
- exit(1);
- }
-}
-
-//***************************************************************************************************************
-
-ScreenSeqsCommand::~ScreenSeqsCommand(){ /* do nothing */ }
-
//***************************************************************************************************************
int ScreenSeqsCommand::execute(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ //if the user want to optimize we need to know the 90% mark
+ vector<unsigned long int> 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)]));
+ }
+ }
- ifstream inFASTA;
- openInputFile(fastafile, inFASTA);
+ 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<string> badSeqNames;
+ int start = time(NULL);
- string goodSeqFile = outputDir + getRootName(getSimpleName(fastafile)) + "good" + getExtension(fastafile);
- string badSeqFile = outputDir + getRootName(getSimpleName(fastafile)) + "bad" + getExtension(fastafile);
-
- ofstream goodSeqOut; openOutputFile(goodSeqFile, goodSeqOut);
- ofstream badSeqOut; openOutputFile(badSeqFile, badSeqOut);
-
- while(!inFASTA.eof()){
- 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; }
+#ifdef USE_MPI
+ int pid, numSeqsPerProcessor;
+ int tag = 2001;
+ vector<unsigned long int> MPIPos;
+
+ MPI_Status status;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+ MPI_Comm_size(MPI_COMM_WORLD, &processors);
+
+ MPI_File inMPI;
+ MPI_File outMPIGood;
+ MPI_File outMPIBadAccnos;
+
+ int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
+ int inMode=MPI_MODE_RDONLY;
+
+ char outGoodFilename[1024];
+ strcpy(outGoodFilename, goodSeqFile.c_str());
+
+ char outBadAccnosFilename[1024];
+ strcpy(outBadAccnosFilename, badAccnosFile.c_str());
+
+ char inFileName[1024];
+ strcpy(inFileName, fastafile.c_str());
+
+ MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
+ MPI_File_open(MPI_COMM_WORLD, outGoodFilename, outMode, MPI_INFO_NULL, &outMPIGood);
+ MPI_File_open(MPI_COMM_WORLD, outBadAccnosFilename, outMode, MPI_INFO_NULL, &outMPIBadAccnos);
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBadAccnos); return 0; }
+
+ if (pid == 0) { //you are the root process
- if(goodSeq == 1){
- currSeq.printSequence(goodSeqOut);
+ MPIPos = m->setFilePosFasta(fastafile, numFastaSeqs); //fills MPIPos, returns numSeqs
+
+ //send file positions to all processes
+ for(int i = 1; i < processors; i++) {
+ MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
+ MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
}
- else{
- currSeq.printSequence(badSeqOut);
- badSeqNames.insert(currSeq.getName());
+
+ //figure out how many sequences you have to align
+ 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);
+ 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; }
+ //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<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);
+ }*/
}
- gobble(inFASTA);
- }
- if(namefile != "" && groupfile != "") { screenNameGroupFile(badSeqNames); } // this screens both names and groups
- else if(namefile != "") { screenNameGroupFile(badSeqNames); }
- else if(groupfile != "") { screenGroupFile(badSeqNames); } // this screens just the groups
+
+ //close files
+ MPI_File_close(&inMPI);
+ MPI_File_close(&outMPIGood);
+ MPI_File_close(&outMPIBadAccnos);
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+
+#else
+
+ #if 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;i<processors;i++){
+ m->appendFiles((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
+
+#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; m->gobble(iss);
+ badSeqNames.insert(tempName);
+ }
+ #endif
+
+ if(namefile != "" && groupfile != "") {
+ screenNameGroupFile(badSeqNames);
+ if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
+ }else if(namefile != "") {
+ screenNameGroupFile(badSeqNames);
+ if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
+ }else if(groupfile != "") { screenGroupFile(badSeqNames); } // this screens just the group
+
+ if (m->control_pressed) { remove(goodSeqFile.c_str()); return 0; }
+
if(alignreport != "") { screenAlignReport(badSeqNames); }
+ if(qualfile != "") { screenQual(badSeqNames); }
- goodSeqOut.close();
- badSeqOut.close();
- inFASTA.close();
+ if (m->control_pressed) { remove(goodSeqFile.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(goodSeqFile); m->mothurOutEndLine(); outputTypes["fasta"].push_back(goodSeqFile);
+ m->mothurOut(badAccnosFile); m->mothurOutEndLine(); outputTypes["accnos"].push_back(badAccnosFile);
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
-
+ m->mothurOutEndLine();
+
+ //set fasta file as new current fastafile
+ string current = "";
+ itTypes = outputTypes.find("fasta");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+ }
+
+ itTypes = outputTypes.find("name");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
+ }
+
+ itTypes = outputTypes.find("group");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
+ }
+ itTypes = outputTypes.find("qfile");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
+ }
+
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to screen " + toString(numFastaSeqs) + " sequences.");
+ m->mothurOutEndLine();
+
return 0;
}
catch(exception& e) {
//***************************************************************************************************************
-void ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
+int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
+ try {
+ ifstream inputNames;
+ m->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 + m->getRootName(m->getSimpleName(namefile)) + "good" + m->getExtension(namefile);
+ outputNames.push_back(goodNameFile); outputTypes["name"].push_back(goodNameFile);
+
+ ofstream goodNameOut; m->openOutputFile(goodNameFile, goodNameOut);
+
+ while(!inputNames.eof()){
+ if (m->control_pressed) { goodNameOut.close(); inputNames.close(); remove(goodNameFile.c_str()); return 0; }
- string goodNameFile = outputDir + getRootName(getSimpleName(namefile)) + "good" + getExtension(namefile);
- string badNameFile = outputDir + getRootName(getSimpleName(namefile)) + "bad" + getExtension(namefile);
-
- ofstream goodNameOut; openOutputFile(goodNameFile, goodNameOut);
- ofstream badNameOut; openOutputFile(badNameFile, badNameOut);
+ inputNames >> seqName >> seqList;
+ it = badSeqNames.find(seqName);
+
+ if(it != badSeqNames.end()){
+ badSeqNames.erase(it);
+
+ 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));
+ }
+ }
+ else{
+ goodNameOut << seqName << '\t' << seqList << endl;
+ }
+ m->gobble(inputNames);
+ }
+ inputNames.close();
+ goodNameOut.close();
- 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;
- }
+ //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();
+ }
+ }
+
+ if(groupfile != ""){
+
+ ifstream inputGroups;
+ m->openInputFile(groupfile, inputGroups);
+
+ string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
+ outputNames.push_back(goodGroupFile); outputTypes["group"].push_back(goodGroupFile);
+
+ ofstream goodGroupOut; m->openOutputFile(goodGroupFile, goodGroupOut);
+
+ while(!inputGroups.eof()){
+ if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); remove(goodNameFile.c_str()); remove(goodGroupFile.c_str()); return 0; }
+
+ inputGroups >> seqName >> group;
+
+ it = badSeqGroups.find(seqName);
+
+ if(it != badSeqGroups.end()){
+ badSeqGroups.erase(it);
+ }
+ else{
+ goodGroupOut << seqName << '\t' << group << endl;
+ }
+ m->gobble(inputGroups);
+ }
+ inputGroups.close();
+ goodGroupOut.close();
+
+ //we were unable to remove some of the bad sequences
+ if (badSeqGroups.size() != 0) {
+ for (it = badSeqGroups.begin(); it != badSeqGroups.end(); it++) {
+ m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
+ m->mothurOutEndLine();
}
- badSeqGroups.insert(seqList.substr(start,seqList.length()-start));
}
}
- else{
- goodNameOut << seqName << '\t' << seqList << endl;
+
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "screenNameGroupFile");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+int ScreenSeqsCommand::getSummary(vector<unsigned long int>& positions){
+ try {
+
+ vector<int> startPosition;
+ vector<int> endPosition;
+ vector<int> seqLength;
+ vector<int> ambigBases;
+ vector<int> longHomoPolymer;
+
+ vector<unsigned long int> positions = m->divideFile(fastafile, processors);
+
+ for (int i = 0; i < (positions.size()-1); i++) {
+ lines.push_back(new linePair(positions[i], positions[(i+1)]));
+ }
+
+ int numSeqs = 0;
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ if(processors == 1){
+ numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
+ }else{
+ numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile);
+ }
+
+ if (m->control_pressed) { return 0; }
+ #else
+ numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
+ if (m->control_pressed) { return 0; }
+ #endif
+
+ sort(startPosition.begin(), startPosition.end());
+ sort(endPosition.begin(), endPosition.end());
+ sort(seqLength.begin(), seqLength.end());
+ sort(ambigBases.begin(), ambigBases.end());
+ sort(longHomoPolymer.begin(), longHomoPolymer.end());
+
+ //numSeqs is the number of unique seqs, startPosition.size() is the total number of seqs, we want to optimize using all seqs
+ int criteriaPercentile = int(startPosition.size() * (criteria / (float) 100));
+
+ for (int i = 0; i < optimize.size(); i++) {
+ if (optimize[i] == "start") { startPos = startPosition[criteriaPercentile]; m->mothurOut("Optimizing start to " + toString(startPos) + "."); m->mothurOutEndLine(); }
+ else if (optimize[i] == "end") { int endcriteriaPercentile = int(endPosition.size() * ((100 - criteria) / (float) 100)); endPos = endPosition[endcriteriaPercentile]; m->mothurOut("Optimizing end to " + toString(endPos) + "."); m->mothurOutEndLine();}
+ else if (optimize[i] == "maxambig") { maxAmbig = ambigBases[criteriaPercentile]; m->mothurOut("Optimizing maxambig to " + toString(maxAmbig) + "."); m->mothurOutEndLine(); }
+ else if (optimize[i] == "maxhomop") { maxHomoP = longHomoPolymer[criteriaPercentile]; m->mothurOut("Optimizing maxhomop to " + toString(maxHomoP) + "."); m->mothurOutEndLine(); }
+ else if (optimize[i] == "minlength") { int mincriteriaPercentile = int(seqLength.size() * ((100 - criteria) / (float) 100)); minLength = seqLength[mincriteriaPercentile]; m->mothurOut("Optimizing minlength to " + toString(minLength) + "."); m->mothurOutEndLine(); }
+ else if (optimize[i] == "maxlength") { maxLength = seqLength[criteriaPercentile]; m->mothurOut("Optimizing maxlength to " + toString(maxLength) + "."); m->mothurOutEndLine(); }
}
- gobble(inputNames);
+
+ return 0;
}
- inputNames.close();
- goodNameOut.close();
- badNameOut.close();
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "getSummary");
+ exit(1);
+ }
+}
+/**************************************************************************************/
+int ScreenSeqsCommand::driverCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, linePair* filePos) {
+ try {
+
+ ifstream in;
+ m->openInputFile(filename, in);
+
+ in.seekg(filePos->start);
+
+ bool done = false;
+ int count = 0;
+
+ while (!done) {
+
+ if (m->control_pressed) { in.close(); return 1; }
+
+ Sequence current(in); m->gobble(in);
- //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();
+ if (current.getName() != "") {
+ int num = 1;
+ if (namefile != "") {
+ //make sure this sequence is in the namefile, else error
+ map<string, int>::iterator it = nameMap.find(current.getName());
+
+ if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
+ else { num = it->second; }
+ }
+
+ //for each sequence this sequence represents
+ for (int i = 0; i < num; i++) {
+ startPosition.push_back(current.getStartPos());
+ endPosition.push_back(current.getEndPos());
+ seqLength.push_back(current.getNumBases());
+ ambigBases.push_back(current.getAmbigBases());
+ longHomoPolymer.push_back(current.getLongHomoPolymer());
+ }
+
+ count++;
+ }
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ unsigned long int pos = in.tellg();
+ if ((pos == -1) || (pos >= filePos->end)) { break; }
+ #else
+ if (in.eof()) { break; }
+ #endif
+
}
+
+ in.close();
+
+ return count;
}
-
- if(groupfile != ""){
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "driverCreateSummary");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int ScreenSeqsCommand::createProcessesCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename) {
+ try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ int process = 1;
+ int num = 0;
+ processIDS.clear();
- ifstream inputGroups;
- openInputFile(groupfile, inputGroups);
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
+
+ if (pid > 0) {
+ processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
+ process++;
+ }else if (pid == 0){
+ num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[process]);
+
+ //pass numSeqs to parent
+ ofstream out;
+ string tempFile = fastafile + toString(getpid()) + ".num.temp";
+ m->openOutputFile(tempFile, out);
+
+ out << num << endl;
+ out << startPosition.size() << endl;
+ for (int k = 0; k < startPosition.size(); k++) { out << startPosition[k] << '\t'; } out << endl;
+ for (int k = 0; k < endPosition.size(); k++) { out << endPosition[k] << '\t'; } out << endl;
+ for (int k = 0; k < seqLength.size(); k++) { out << seqLength[k] << '\t'; } out << endl;
+ for (int k = 0; k < ambigBases.size(); k++) { out << ambigBases[k] << '\t'; } out << endl;
+ for (int k = 0; k < longHomoPolymer.size(); k++) { out << longHomoPolymer[k] << '\t'; } out << endl;
+
+ out.close();
+
+ exit(0);
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
+ }
+
+ num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<processIDS.size();i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ //parent reads in and combine Filter info
+ for (int i = 0; i < processIDS.size(); i++) {
+ string tempFilename = fastafile + toString(processIDS[i]) + ".num.temp";
+ ifstream in;
+ m->openInputFile(tempFilename, in);
+
+ int temp, tempNum;
+ in >> tempNum; m->gobble(in); num += tempNum;
+ in >> tempNum; m->gobble(in);
+ for (int k = 0; k < tempNum; k++) { in >> temp; startPosition.push_back(temp); } m->gobble(in);
+ for (int k = 0; k < tempNum; k++) { in >> temp; endPosition.push_back(temp); } m->gobble(in);
+ for (int k = 0; k < tempNum; k++) { in >> temp; seqLength.push_back(temp); } m->gobble(in);
+ for (int k = 0; k < tempNum; k++) { in >> temp; ambigBases.push_back(temp); } m->gobble(in);
+ for (int k = 0; k < tempNum; k++) { in >> temp; longHomoPolymer.push_back(temp); } m->gobble(in);
+
+ in.close();
+ remove(tempFilename.c_str());
+ }
+
+ return num;
+#endif
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "createProcessesCreateSummary");
+ exit(1);
+ }
+}
- string goodGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "good" + getExtension(groupfile);
- string badGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "bad" + getExtension(groupfile);
+//***************************************************************************************************************
+
+int ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
+ try {
+ ifstream inputGroups;
+ m->openInputFile(groupfile, inputGroups);
+ string seqName, group;
+ set<string>::iterator it;
- ofstream goodGroupOut; openOutputFile(goodGroupFile, goodGroupOut);
- ofstream badGroupOut; openOutputFile(badGroupFile, badGroupOut);
+ string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
+ outputNames.push_back(goodGroupFile); outputTypes["group"].push_back(goodGroupFile);
+ ofstream goodGroupOut; m->openOutputFile(goodGroupFile, goodGroupOut);
while(!inputGroups.eof()){
- inputGroups >> seqName >> group;
+ if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); remove(goodGroupFile.c_str()); return 0; }
- it = badSeqGroups.find(seqName);
+ inputGroups >> seqName >> group;
+ it = badSeqNames.find(seqName);
- if(it != badSeqGroups.end()){
- badSeqGroups.erase(it);
- badGroupOut << seqName << '\t' << group << endl;
+ if(it != badSeqNames.end()){
+ badSeqNames.erase(it);
}
else{
goodGroupOut << seqName << '\t' << group << endl;
}
- gobble(inputGroups);
+ m->gobble(inputGroups);
}
- inputGroups.close();
- goodGroupOut.close();
- badGroupOut.close();
+ if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); remove(goodGroupFile.c_str()); return 0; }
+
//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.");
+ 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();
+
+ if (m->control_pressed) { remove(goodGroupFile.c_str()); }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "screenGroupFile");
+ exit(1);
}
}
//***************************************************************************************************************
-void ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
+int ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
+ try {
+ ifstream inputAlignReport;
+ m->openInputFile(alignreport, inputAlignReport);
+ string seqName, group;
+ set<string>::iterator it;
+
+ string goodAlignReportFile = outputDir + m->getRootName(m->getSimpleName(alignreport)) + "good" + m->getExtension(alignreport);
+ outputNames.push_back(goodAlignReportFile); outputTypes["alignreport"].push_back(goodAlignReportFile);
+ ofstream goodAlignReportOut; m->openOutputFile(goodAlignReportFile, goodAlignReportOut);
- ifstream inputGroups;
- openInputFile(groupfile, inputGroups);
- 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);
+ while (!inputAlignReport.eof()) { // need to copy header
+ char c = inputAlignReport.get();
+ goodAlignReportOut << c;
+ if (c == 10 || c == 13){ break; }
+ }
+
+ while(!inputAlignReport.eof()){
+ if (m->control_pressed) { goodAlignReportOut.close(); inputAlignReport.close(); remove(goodAlignReportFile.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);
+ }
+ else{
+ goodAlignReportOut << seqName << '\t' << line;
+ }
+ m->gobble(inputAlignReport);
+ }
+
+ if (m->control_pressed) { goodAlignReportOut.close(); inputAlignReport.close(); remove(goodAlignReportFile.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 alignreport file does not include the sequence " + *it + " please correct.");
+ m->mothurOutEndLine();
+ }
+ }
+
+ inputAlignReport.close();
+ goodAlignReportOut.close();
+
+ if (m->control_pressed) { remove(goodAlignReportFile.c_str()); return 0; }
+
+ return 0;
- ofstream goodGroupOut; openOutputFile(goodGroupFile, goodGroupOut);
- ofstream badGroupOut; openOutputFile(badGroupFile, badGroupOut);
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "screenAlignReport");
+ exit(1);
+ }
- while(!inputGroups.eof()){
- inputGroups >> seqName >> group;
- it = badSeqNames.find(seqName);
+}
+//***************************************************************************************************************
+
+int ScreenSeqsCommand::screenQual(set<string> badSeqNames){
+ try {
+ ifstream in;
+ m->openInputFile(qualfile, in);
+ set<string>::iterator it;
- if(it != badSeqNames.end()){
- badSeqNames.erase(it);
- badGroupOut << seqName << '\t' << group << endl;
+ 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(); remove(goodQualFile.c_str()); 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);
}
- else{
- goodGroupOut << seqName << '\t' << group << endl;
+
+ in.close();
+ goodQual.close();
+
+ //we were unable to remove some of the bad sequences
+ if (badSeqNames.size() != 0) {
+ for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
+ m->mothurOut("Your qual file does not include the sequence " + *it + " please correct.");
+ m->mothurOutEndLine();
+ }
}
- gobble(inputGroups);
+
+ if (m->control_pressed) { remove(goodQualFile.c_str()); return 0; }
+
+ 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();
- }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "screenQual");
+ exit(1);
}
- inputGroups.close();
- goodGroupOut.close();
- badGroupOut.close();
-
}
+//**********************************************************************************************************************
-//***************************************************************************************************************
+int ScreenSeqsCommand::driver(linePair* filePos, string goodFName, string badAccnosFName, string filename, set<string>& badSeqNames){
+ try {
+ ofstream goodFile;
+ m->openOutputFile(goodFName, goodFile);
+
+ ofstream badAccnosFile;
+ m->openOutputFile(badAccnosFName, badAccnosFile);
+
+ ifstream inFASTA;
+ m->openInputFile(filename, inFASTA);
-void ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
-
- 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);
+ inFASTA.seekg(filePos->start);
+
+ bool done = false;
+ int count = 0;
- 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 (!done) {
+
+ if (m->control_pressed) { return 0; }
+
+ Sequence currSeq(inFASTA); m->gobble(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{
+ badAccnosFile << currSeq.getName() << endl;
+ badSeqNames.insert(currSeq.getName());
+ }
+ count++;
+ }
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ unsigned long int pos = inFASTA.tellg();
+ if ((pos == -1) || (pos >= filePos->end)) { break; }
+ #else
+ if (inFASTA.eof()) { break; }
+ #endif
+
+ //report progress
+ if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); }
+ }
+ //report progress
+ if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); }
+
+
+ goodFile.close();
+ inFASTA.close();
+ badAccnosFile.close();
+
+ return count;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "driver");
+ exit(1);
}
+}
+//**********************************************************************************************************************
+#ifdef USE_MPI
+int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& goodFile, MPI_File& badAccnosFile, vector<unsigned long int>& MPIPos, set<string>& badSeqNames){
+ try {
+ string outputString = "";
+ MPI_Status statusGood;
+ MPI_Status statusBadAccnos;
+ MPI_Status status;
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
- 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{
+
+ 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;
+ }
+ }
+
+ //report progress
+ if((i) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(i)); m->mothurOutEndLine(); }
+ }
+
+ return 1;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "driverMPI");
+ exit(1);
+ }
+}
+#endif
+/**************************************************************************************************/
+
+int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, string filename, set<string>& badSeqNames) {
+ try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ int process = 0;
+ int num = 0;
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
+
+ if (pid > 0) {
+ processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
+ process++;
+ }else if (pid == 0){
+ num = driver(lines[process], goodFileName + toString(getpid()) + ".temp", badAccnos + toString(getpid()) + ".temp", filename, badSeqNames);
+
+ //pass numSeqs to parent
+ ofstream out;
+ string tempFile = filename + toString(getpid()) + ".num.temp";
+ m->openOutputFile(tempFile, out);
+ out << num << endl;
+ out.close();
+
+ exit(0);
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
}
- if(it != badSeqNames.end()){
- badSeqNames.erase(it);
- badAlignReportOut << 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);
}
- else{
- goodAlignReportOut << seqName << '\t' << line;
+
+ for (int i = 0; i < processIDS.size(); i++) {
+ ifstream in;
+ string tempFile = filename + toString(processIDS[i]) + ".num.temp";
+ m->openInputFile(tempFile, in);
+ if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
+ in.close(); remove(tempFile.c_str());
}
- gobble(inputAlignReport);
+
+ return num;
+#endif
}
-
- //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();
- }
+ catch(exception& e) {
+ m->errorOut(e, "ScreenSeqsCommand", "createProcesses");
+ exit(1);
}
-
- inputAlignReport.close();
- goodAlignReportOut.close();
- badAlignReportOut.close();
-
}
//***************************************************************************************************************
projects / mothur.git / blobdiff