//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; }
+
+ fastafile = validParameter.validFile(parameters, "fasta", false);
+ if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.bellerophon 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; }
}
-
-
- //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.bellerophon command."); 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"){
try {
m->mothurOut("The chimera.bellerophon command reads a fastafile and creates list of potentially chimeric sequences.\n");
m->mothurOut("The chimera.bellerophon command parameters are fasta, filter, correction, processors, window, increment. The fasta parameter is required.\n");
+ m->mothurOut("The fasta parameter is required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
m->mothurOut("The filter parameter allows you to specify if you would like to apply a vertical and 50% soft filter, default=false. \n");
m->mothurOut("The correction parameter allows you to put more emphasis on the distance between highly similar sequences and less emphasis on the differences between remote homologs, default=true.\n");
m->mothurOut("The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n");
m->mothurOut("The window parameter allows you to specify the window size for searching for chimeras, default is 1/4 sequence length. \n");
m->mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default is 25.\n");
m->mothurOut("chimera.bellerophon(fasta=yourFastaFile, filter=yourFilter, correction=yourCorrection, processors=yourProcessors) \n");
- m->mothurOut("Example: chimera.seqs(fasta=AD.align, filter=True, correction=true, window=200) \n");
+ m->mothurOut("Example: chimera.bellerophon(fasta=AD.align, filter=True, correction=true, window=200) \n");
m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
}
catch(exception& e) {
if (abort == true) { return 0; }
- int start = time(NULL);
-
- chimera = new Bellerophon(fastafile, filter, correction, window, increment, processors, outputDir);
-
- string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "bellerophon.chimeras";
- string accnosFileName = outputDir + getRootName(getSimpleName(fastafile)) + "bellerophon.accnos";
- bool hasAccnos = true;
-
- chimera->getChimeras();
-
- if (m->control_pressed) { delete chimera; return 0; }
-
- #ifdef USE_MPI
- MPI_File outMPI;
- MPI_File outMPIAccnos;
-
- int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
-
- //char* outFilename = new char[accnosFileName.length()];
- //memcpy(outFilename, accnosFileName.c_str(), accnosFileName.length());
-
- char outFilename[1024];
- strcpy(outFilename, accnosFileName.c_str());
-
- //char* FileName = new char[outputFileName.length()];
- //memcpy(FileName, outputFileName.c_str(), outputFileName.length());
-
- char FileName[1024];
- strcpy(FileName, outputFileName.c_str());
-
- MPI_File_open(MPI_COMM_WORLD, FileName, outMode, MPI_INFO_NULL, &outMPI); //comm, filename, mode, info, filepointer
- MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
-
- //delete FileName;
- //delete outFilename;
+ for (int i = 0; i < fastaFileNames.size(); i++) {
+
+ m->mothurOut("Checking sequences from " + fastaFileNames[i] + " ..." ); m->mothurOutEndLine();
+
+ int start = time(NULL);
+
+ chimera = new Bellerophon(fastaFileNames[i], filter, correction, window, increment, processors, outputDir);
+
+ string outputFileName = outputDir + getRootName(getSimpleName(fastaFileNames[i])) + "bellerophon.chimeras";
+ string accnosFileName = outputDir + getRootName(getSimpleName(fastaFileNames[i])) + "bellerophon.accnos";
+ bool hasAccnos = true;
+
+ chimera->getChimeras();
+
+ if (m->control_pressed) { delete chimera; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ #ifdef USE_MPI
+ MPI_File outMPI;
+ MPI_File outMPIAccnos;
+
+ int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
+
+ char outFilename[1024];
+ strcpy(outFilename, accnosFileName.c_str());
- numSeqs = chimera->print(outMPI, outMPIAccnos);
-
- MPI_File_close(&outMPI);
- MPI_File_close(&outMPIAccnos);
+ char FileName[1024];
+ strcpy(FileName, outputFileName.c_str());
- #else
+ MPI_File_open(MPI_COMM_WORLD, FileName, outMode, MPI_INFO_NULL, &outMPI); //comm, filename, mode, info, filepointer
+ MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
- ofstream out;
- openOutputFile(outputFileName, out);
-
- ofstream out2;
- openOutputFile(accnosFileName, out2);
-
- numSeqs = chimera->print(out, out2);
- out.close();
- out2.close();
-
- #endif
-
- if (m->control_pressed) { remove(accnosFileName.c_str()); remove(outputFileName.c_str()); delete chimera; return 0; }
+ numSeqs = chimera->print(outMPI, outMPIAccnos);
+
+ MPI_File_close(&outMPI);
+ MPI_File_close(&outMPIAccnos);
+
+ #else
- //delete accnos file if its blank
- if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; }
+ ofstream out;
+ openOutputFile(outputFileName, out);
+
+ ofstream out2;
+ openOutputFile(accnosFileName, out2);
+
+ numSeqs = chimera->print(out, out2);
+ out.close();
+ out2.close();
+
+ #endif
+
+ if (m->control_pressed) { remove(accnosFileName.c_str()); remove(outputFileName.c_str()); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete chimera; return 0; }
+
+ //delete accnos file if its blank
+ if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; }
+
+ m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
+
+ outputNames.push_back(outputFileName);
+ if (hasAccnos) { outputNames.push_back(accnosFileName); }
+
+ delete chimera;
+ }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
- m->mothurOut(outputFileName); m->mothurOutEndLine();
- if (hasAccnos) { m->mothurOut(accnosFileName); 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();
-
- delete chimera;
return 0;
projects / mothur.git / blobdiff