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("template");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ string path = hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["template"] = 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; }
- }
}
-
//check for required parameters
- fastafile = validParameter.validFile(parameters, "fasta", true);
- if (fastafile == "not open") { abort = true; }
- else if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.check command."); m->mothurOutEndLine(); abort = true; }
+ fastafile = validParameter.validFile(parameters, "fasta", false);
+ if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.check command."); m->mothurOutEndLine(); abort = true; }
+ else {
+ splitAtDash(fastafile, fastaFileNames);
+
+ //go through files and make sure they are good, if not, then disregard them
+ for (int i = 0; i < fastaFileNames.size(); i++) {
+ if (inputDir != "") {
+ string path = hasPath(fastaFileNames[i]);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
+ }
+
+ int ableToOpen;
+ ifstream in;
+
+ #ifdef USE_MPI
+ int pid;
+ MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+
+ if (pid == 0) {
+ #endif
+
+ ableToOpen = openInputFile(fastaFileNames[i], in);
+ in.close();
+
+ #ifdef USE_MPI
+ for (int j = 1; j < processors; j++) {
+ MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD);
+ }
+ }else{
+ MPI_Status status;
+ MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+ }
+
+ #endif
+
+ if (ableToOpen == 1) {
+ m->mothurOut(fastaFileNames[i] + " will be disregarded."); m->mothurOutEndLine();
+ //erase from file list
+ fastaFileNames.erase(fastaFileNames.begin()+i);
+ i--;
+ }
+ }
+
+ //make sure there is at least one valid file left
+ if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
+ }
//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 = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
templatefile = validParameter.validFile(parameters, "template", true);
if (templatefile == "not open") { abort = true; }
else if (templatefile == "not found") { templatefile = ""; m->mothurOut("template is a required parameter for the chimera.check command."); m->mothurOutEndLine(); abort = true; }
- namefile = validParameter.validFile(parameters, "name", true);
- if (namefile == "not open") { abort = true; }
- else if (namefile == "not found") { namefile = ""; }
+ namefile = validParameter.validFile(parameters, "name", false);
+ if (namefile == "not found") { namefile = ""; }
+ else {
+ splitAtDash(namefile, nameFileNames);
+
+ //go through files and make sure they are good, if not, then disregard them
+ for (int i = 0; i < nameFileNames.size(); i++) {
+ if (inputDir != "") {
+ string path = hasPath(nameFileNames[i]);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { nameFileNames[i] = inputDir + nameFileNames[i]; }
+ }
+
+ int ableToOpen;
+ ifstream in;
+
+ #ifdef USE_MPI
+ int pid;
+ MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+
+ if (pid == 0) {
+ #endif
+
+ ableToOpen = openInputFile(nameFileNames[i], in);
+ in.close();
+
+ #ifdef USE_MPI
+ for (int j = 1; j < processors; j++) {
+ MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD);
+ }
+ }else{
+ MPI_Status status;
+ MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+ }
+
+ #endif
+
+ if (ableToOpen == 1) {
+ m->mothurOut(nameFileNames[i] + " will be disregarded."); m->mothurOutEndLine();
+ //erase from file list
+ nameFileNames.erase(nameFileNames.begin()+i);
+ i--;
+ }
+
+ }
+
+ //make sure there is at least one valid file left
+ if (nameFileNames.size() != 0) {
+ if (nameFileNames.size() != fastaFileNames.size()) {
+ m->mothurOut("Different number of valid name files and fasta files, aborting command."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }
+ }
string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; }
convert(temp, processors);
temp = validParameter.validFile(parameters, "svg", false); if (temp == "not found") { temp = "F"; }
svg = isTrue(temp);
+ if (nameFileNames.size() != 0) { svg = true; }
temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "10"; }
convert(temp, increment);
m->mothurOut("This command was created using the algorythms described in CHIMERA_CHECK version 2.7 written by Niels Larsen. \n");
m->mothurOut("The chimera.check command parameters are fasta, template, processors, ksize, increment, svg and name.\n");
m->mothurOut("The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required. \n");
+ m->mothurOut("You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
m->mothurOut("The template parameter allows you to enter a template file containing known non-chimeric sequences, and is required. \n");
m->mothurOut("The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n");
#ifdef USE_MPI
m->mothurOut("The ksize parameter allows you to input kmersize, default is 7. \n");
m->mothurOut("The svg parameter allows you to specify whether or not you would like a svg file outputted for each query sequence, default is False.\n");
m->mothurOut("The name parameter allows you to enter a file containing names of sequences you would like .svg files for.\n");
+ m->mothurOut("You may enter multiple name files by separating their names with dashes. ie. fasta=abrecovery.svg.names-amzon.svg.names \n");
m->mothurOut("The chimera.check command should be in the following format: \n");
m->mothurOut("chimera.check(fasta=yourFastaFile, template=yourTemplateFile, processors=yourProcessors, ksize=yourKmerSize) \n");
m->mothurOut("Example: chimera.check(fasta=AD.fasta, template=core_set_aligned,imputed.fasta, processors=4, ksize=8) \n");
if (abort == true) { return 0; }
- int start = time(NULL);
-
- chimera = new ChimeraCheckRDP(fastafile, templatefile, namefile, svg, increment, ksize, outputDir);
-
- if (m->control_pressed) { delete chimera; return 0; }
-
- string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "chimeracheck.chimeras";
-
- #ifdef USE_MPI
-
- int pid, end, numSeqsPerProcessor;
- int tag = 2001;
- vector<long> MPIPos;
+ for (int i = 0; i < fastaFileNames.size(); i++) {
+
+ m->mothurOut("Checking sequences from " + fastaFileNames[i] + " ..." ); m->mothurOutEndLine();
- 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 outMPI;
-
- int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
- int inMode=MPI_MODE_RDONLY;
+ int start = time(NULL);
- //char* outFilename = new char[outputFileName.length()];
- //memcpy(outFilename, outputFileName.c_str(), outputFileName.length());
+ string thisNameFile = "";
+ if (nameFileNames.size() != 0) { thisNameFile = nameFileNames[i]; }
- char outFilename[1024];
- strcpy(outFilename, outputFileName.c_str());
+ chimera = new ChimeraCheckRDP(fastaFileNames[i], templatefile, thisNameFile, svg, increment, ksize, outputDir);
- //char* inFileName = new char[fastafile.length()];
- //memcpy(inFileName, fastafile.c_str(), fastafile.length());
+ if (m->control_pressed) { delete chimera; return 0; }
- 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, outFilename, outMode, MPI_INFO_NULL, &outMPI);
+ string outputFileName = outputDir + getRootName(getSimpleName(fastaFileNames[i])) + "chimeracheck.chimeras";
+ outputNames.push_back(outputFileName);
- //delete outFilename;
- //delete inFileName;
+ #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);
- if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); delete chimera; return 0; }
+ MPI_File inMPI;
+ MPI_File outMPI;
+
+ int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
+ int inMode=MPI_MODE_RDONLY;
+
+ char outFilename[1024];
+ strcpy(outFilename, outputFileName.c_str());
- if (pid == 0) { //you are the root process
- MPIPos = setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs
-
- //send file positions to all processes
- for(int i = 1; i < processors; i++) {
- MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
- MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
- }
-
- //figure out how many sequences you have to align
- numSeqsPerProcessor = numSeqs / processors;
- int startIndex = pid * numSeqsPerProcessor;
- if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
+ char inFileName[1024];
+ strcpy(inFileName, fastaFileNames[i].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, outFilename, outMode, MPI_INFO_NULL, &outMPI);
-
- //align your part
- driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; }
- if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); remove(outputFileName.c_str()); delete chimera; return 0; }
+ if (pid == 0) { //you are the root process
+ MPIPos = setFilePosFasta(fastaFileNames[i], numSeqs); //fills MPIPos, returns numSeqs
+
+ //send file positions to all processes
+ for(int j = 1; j < processors; j++) {
+ MPI_Send(&numSeqs, 1, MPI_INT, j, tag, MPI_COMM_WORLD);
+ MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, j, tag, MPI_COMM_WORLD);
+ }
+
+ //figure out how many sequences you have to align
+ numSeqsPerProcessor = numSeqs / processors;
+ int startIndex = pid * numSeqsPerProcessor;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
+
- //wait on chidren
- for(int i = 1; i < processors; i++) {
+ //align your part
+ driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; }
+
+ //wait on chidren
+ for(int j = 1; j < processors; j++) {
+ char buf[4];
+ MPI_Recv(buf, 4, MPI_CHAR, j, tag, MPI_COMM_WORLD, &status);
+ }
+ }else{ //you are a child process
+ MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
+ MPIPos.resize(numSeqs+1);
+ MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
+
+ //figure out how many sequences you have to align
+ numSeqsPerProcessor = numSeqs / processors;
+ int startIndex = pid * numSeqsPerProcessor;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
+
+ //align your part
+ driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; }
+
+ //tell parent you are done.
char buf[4];
- MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
+ strcpy(buf, "done");
+ MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
}
- }else{ //you are a child process
- MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
- MPIPos.resize(numSeqs+1);
- MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
-
- //figure out how many sequences you have to align
- numSeqsPerProcessor = numSeqs / processors;
- int startIndex = pid * numSeqsPerProcessor;
- if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
-
-
- //align your part
- driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
- if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); delete chimera; return 0; }
-
- //tell parent you are done.
- char buf[4];
- strcpy(buf, "done");
- MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
- }
+ //close files
+ MPI_File_close(&inMPI);
+ MPI_File_close(&outMPI);
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+ #else
- //close files
- MPI_File_close(&inMPI);
- MPI_File_close(&outMPI);
- MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
- #else
-
- //break up file
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- if(processors == 1){
+ //break up file
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ if(processors == 1){
+ ifstream inFASTA;
+ openInputFile(fastaFileNames[i], inFASTA);
+ getNumSeqs(inFASTA, numSeqs);
+ inFASTA.close();
+
+ lines.push_back(new linePair(0, numSeqs));
+
+ driver(lines[0], outputFileName, fastaFileNames[i]);
+
+ if (m->control_pressed) {
+ for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); }
+ for (int j = 0; j < lines.size(); j++) { delete lines[j]; } lines.clear();
+ delete chimera;
+ return 0;
+ }
+
+ }else{
+ vector<int> positions;
+ processIDS.resize(0);
+
+ ifstream inFASTA;
+ openInputFile(fastaFileNames[i], 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();
+
+ numSeqs = positions.size();
+
+ int numSeqsPerProcessor = numSeqs / processors;
+
+ for (int j = 0; j < processors; j++) {
+ long int startPos = positions[ j * numSeqsPerProcessor ];
+ if(j == processors - 1){
+ numSeqsPerProcessor = numSeqs - j * numSeqsPerProcessor;
+ }
+ lines.push_back(new linePair(startPos, numSeqsPerProcessor));
+ }
+
+
+ createProcesses(outputFileName, fastaFileNames[i]);
+
+ rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
+
+ //append output files
+ for(int j=1;j<processors;j++){
+ appendFiles((outputFileName + toString(processIDS[j]) + ".temp"), outputFileName);
+ remove((outputFileName + toString(processIDS[j]) + ".temp").c_str());
+ }
+
+ if (m->control_pressed) {
+ for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); }
+ for (int j = 0; j < lines.size(); j++) { delete lines[j]; } lines.clear();
+ delete chimera;
+ return 0;
+ }
+ }
+
+ #else
ifstream inFASTA;
- openInputFile(fastafile, inFASTA);
+ openInputFile(fastaFileNames[i], inFASTA);
getNumSeqs(inFASTA, numSeqs);
inFASTA.close();
-
lines.push_back(new linePair(0, numSeqs));
- driver(lines[0], outputFileName, fastafile);
+ driver(lines[0], outputFileName, fastaFileNames[i]);
if (m->control_pressed) {
- remove(outputFileName.c_str());
- for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
- delete chimera;
- 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); }
- }
+ for (int j = 0; j < lines.size(); j++) { delete lines[j]; } lines.clear();
+ for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); }
+ delete chimera;
+ return 0;
}
- inFASTA.close();
-
- numSeqs = positions.size();
-
- int numSeqsPerProcessor = numSeqs / processors;
-
- for (int i = 0; i < processors; i++) {
- long int startPos = positions[ i * numSeqsPerProcessor ];
- if(i == processors - 1){
- numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor;
- }
- lines.push_back(new linePair(startPos, numSeqsPerProcessor));
- }
-
-
- createProcesses(outputFileName, fastafile);
+ #endif
+ #endif
+ delete chimera;
+ for (int j = 0; j < lines.size(); j++) { delete lines[j]; } lines.clear();
- rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
-
- //append output files
- for(int i=1;i<processors;i++){
- appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
- remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
- }
-
- if (m->control_pressed) {
- remove(outputFileName.c_str());
- for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
- delete chimera;
- return 0;
- }
- }
+ m->mothurOutEndLine(); m->mothurOut("This method does not determine if a sequence is chimeric, but allows you to make that determination based on the IS values."); m->mothurOutEndLine();
+ m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
- #else
- ifstream inFASTA;
- openInputFile(fastafile, inFASTA);
- getNumSeqs(inFASTA, numSeqs);
- inFASTA.close();
- lines.push_back(new linePair(0, numSeqs));
-
- driver(lines[0], outputFileName, fastafile);
-
- if (m->control_pressed) {
- remove(outputFileName.c_str());
- for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
- delete chimera;
- return 0;
- }
- #endif
- #endif
- delete chimera;
- for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
-
- m->mothurOutEndLine(); m->mothurOut("This method does not determine if a sequence is chimeric, but allows you to make that determination based on the IS values."); m->mothurOutEndLine();
+ }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
- m->mothurOut(outputFileName); 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 check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
-
+
return 0;
}
projects / mothur.git / blobdiff