else {
//valid paramters for this command
- string Array[] = {"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantile", "mask", "numwanted", "ksize", "svg", "name", "match","mismatch", "divergence", "minsim", "parents", "iters" };
+ string Array[] = {"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantile", "mask",
+ "numwanted", "ksize", "svg", "name", "match","mismatch", "divergence", "minsim","mincov","minbs", "minsnp","parents", "iters","outputdir","inputdir", "search","realign" };
vector<string> myArray (Array, Array+(sizeof(Array)/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("template");
+ //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["template"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("conservation");
+ //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["conservation"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("quantile");
+ //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["quantile"] = 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 = ""; mothurOut("fasta is a required parameter for the chimera.seqs command."); 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
+ }
+
templatefile = validParameter.validFile(parameters, "template", true);
if (templatefile == "not open") { abort = true; }
else if (templatefile == "not found") { templatefile = ""; }
maskfile = validParameter.validFile(parameters, "mask", false);
if (maskfile == "not found") { maskfile = ""; }
else if (maskfile != "default") {
+ if (inputDir != "") {
+ string path = hasPath(maskfile);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { maskfile = inputDir + maskfile; }
+ }
+
ifstream in;
int ableToOpen = openInputFile(maskfile, in);
if (ableToOpen == 1) { abort = true; }
svg = isTrue(temp);
temp = validParameter.validFile(parameters, "window", false);
- if ((temp == "not found") && (method == "chimeraslayer")) { temp = "100"; }
+ if ((temp == "not found") && (method == "chimeraslayer")) { temp = "50"; }
else if (temp == "not found") { temp = "0"; }
convert(temp, window);
temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found") { temp = "-4"; }
convert(temp, mismatch);
- temp = validParameter.validFile(parameters, "divergence", false); if (temp == "not found") { temp = "1.0"; }
+ temp = validParameter.validFile(parameters, "divergence", false); if (temp == "not found") { temp = "1.007"; }
convert(temp, divR);
temp = validParameter.validFile(parameters, "minsim", false); if (temp == "not found") { temp = "90"; }
convert(temp, minSimilarity);
- temp = validParameter.validFile(parameters, "parents", false); if (temp == "not found") { temp = "5"; }
+ temp = validParameter.validFile(parameters, "mincov", false); if (temp == "not found") { temp = "70"; }
+ convert(temp, minCoverage);
+
+ temp = validParameter.validFile(parameters, "minbs", false); if (temp == "not found") { temp = "90"; }
+ convert(temp, minBS);
+
+ temp = validParameter.validFile(parameters, "minsnp", false); if (temp == "not found") { temp = "10"; }
+ convert(temp, minSNP);
+
+ temp = validParameter.validFile(parameters, "parents", false); if (temp == "not found") { temp = "3"; }
convert(temp, parents);
- temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
+ temp = validParameter.validFile(parameters, "realign", false); if (temp == "not found") { temp = "f"; }
+ realign = isTrue(temp);
+
+ search = validParameter.validFile(parameters, "search", false); if (search == "not found") { search = "distance"; }
+
+ temp = validParameter.validFile(parameters, "iters", false);
+ if ((temp == "not found") && (method == "chimeraslayer")) { temp = "100"; }
+ else if (temp == "not found") { temp = "1000"; }
convert(temp, iters);
temp = validParameter.validFile(parameters, "increment", false);
- if ((temp == "not found") && ((method == "chimeracheck") || (method == "chimeraslayer"))) { temp = "10"; }
+ if ((temp == "not found") && (method == "chimeracheck")) { temp = "10"; }
+ else if ((temp == "not found") && (method == "chimeraslayer")) { temp = "5"; }
else if (temp == "not found") { temp = "25"; }
convert(temp, increment);
temp = validParameter.validFile(parameters, "numwanted", false);
- if ((temp == "not found") && (method == "chimeraslayer")) { temp = "10"; }
+ if ((temp == "not found") && (method == "chimeraslayer")) { temp = "15"; }
else if (temp == "not found") { temp = "20"; }
convert(temp, numwanted);
+ if ((search != "distance") && (search != "blast") && (search != "kmer")) { mothurOut(search + " is not a valid search."); mothurOutEndLine(); abort = true; }
-
- if (((method != "bellerophon")) && (templatefile == "")) { mothurOut("You must provide a template file with the pintail, ccode or chimeracheck methods."); mothurOutEndLine(); abort = true; }
+ if (((method != "bellerophon")) && (templatefile == "")) { mothurOut("You must provide a template file with the pintail, ccode, chimeraslayer or chimeracheck methods."); mothurOutEndLine(); abort = true; }
}
//"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantile", "mask", "numwanted", "ksize", "svg", "name"
//mothurOut("chimera.seqs ASSUMES that your sequences are ALIGNED and if using a template that the template file sequences are the same length as the fasta file sequences.\n\n");
mothurOut("The chimera.seqs command reads a fastafile and creates list of potentially chimeric sequences.\n");
- mothurOut("The chimera.seqs command parameters are fasta, filter, correction, processors, mask, method, window, increment, template, conservation, quantile, numwanted, ksize, svg, name, iters.\n");
+ mothurOut("The chimera.seqs command parameters are fasta, filter, correction, processors, mask, method, window, increment, template, conservation, quantile, numwanted, ksize, svg, name, iters, search, realign.\n");
mothurOut("The fasta parameter is always required and template is required if using pintail, ccode or chimeracheck.\n");
mothurOut("The filter parameter allows you to specify if you would like to apply a vertical and 50% soft filter. \n");
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.\n");
mothurOut("The svg parameter allows you to specify whether or not you would like a svg file outputted for each query sequence.\n");
mothurOut("The name parameter allows you to enter a file containing names of sequences you would like .svg files for.\n");
mothurOut("The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method.\n");
+ mothurOut("The minsim parameter allows you .... \n");
+ mothurOut("The mincov parameter allows you to specify minimum coverage by closest matches found in template. Default is 70, meaning 70%. \n");
+ mothurOut("The minbs parameter allows you to specify minimum bootstrap support for calling a sequence chimeric. Default is 90, meaning 90%. \n");
+ mothurOut("The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 10) \n");
+ mothurOut("The search parameter allows you to specify search method for finding the closest parent. Choices are distance, blast, and kmer, default distance. -used only by chimeraslayer. \n");
+ mothurOut("The realign parameter allows you to realign the query to the potential paretns. Choices are true or false, default false. -used only by chimeraslayer. \n");
mothurOut("NOT ALL PARAMETERS ARE USED BY ALL METHODS. Please look below for method specifics.\n\n");
mothurOut("Details for each method: \n");
mothurOut("\tpintail: \n");
mothurOut("\t\tparameters: fasta=required, template=required, filter=F, mask=no mask, processors=1, window=10% of length, numwanted=20\n");
mothurOut("\tchimeracheck: \n");
mothurOut("\t\tparameters: fasta=required, template=required, processors=1, increment=10, ksize=7, svg=F, name=none\n\n");
+ mothurOut("\tchimeraslayer: \n");
+ mothurOut("\t\tparameters: fasta=required, template=required, processors=1, increment=10, mask=no mask, numwanted=10, match=5, mismatch=-4, divergence=1.0, minsim=90, parents=5, iters=1000, window=100. \n\n");
mothurOut("The chimera.seqs command should be in the following format: \n");
mothurOut("chimera.seqs(fasta=yourFastaFile, filter=yourFilter, correction=yourCorrection, processors=yourProcessors, method=bellerophon) \n");
mothurOut("Example: chimera.seqs(fasta=AD.align, filter=True, correction=true, method=bellerophon, window=200) \n");
if (abort == true) { return 0; }
- if (method == "bellerophon") { chimera = new Bellerophon(fastafile); }
- else if (method == "pintail") { chimera = new Pintail(fastafile, templatefile); }
- else if (method == "ccode") { chimera = new Ccode(fastafile, templatefile); }
- else if (method == "chimeracheck") { chimera = new ChimeraCheckRDP(fastafile, templatefile); }
- else if (method == "chimeraslayer") { chimera = new ChimeraSlayer(fastafile, templatefile); }
+ int start = time(NULL);
+
+ if (method == "bellerophon") { chimera = new Bellerophon(fastafile, outputDir); }
+ else if (method == "pintail") { chimera = new Pintail(fastafile, outputDir); }
+ else if (method == "ccode") { chimera = new Ccode(fastafile, outputDir); }
+ else if (method == "chimeracheck") { chimera = new ChimeraCheckRDP(fastafile, outputDir); }
+ else if (method == "chimeraslayer") { chimera = new ChimeraSlayer(search, realign, fastafile); }
else { mothurOut("Not a valid method."); mothurOutEndLine(); return 0; }
//set user options
if (maskfile == "default") { mothurOut("I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013."); mothurOutEndLine(); }
- //saves time to avoid generating it
chimera->setCons(consfile);
-
- //saves time to avoid generating it
chimera->setQuantiles(quanfile);
-
chimera->setMask(maskfile);
chimera->setFilter(filter);
chimera->setCorrection(correction);
chimera->setDivR(divR);
chimera->setParents(parents);
chimera->setMinSim(minSimilarity);
+ chimera->setMinCoverage(minCoverage);
+ chimera->setMinBS(minBS);
+ chimera->setMinSNP(minSNP);
chimera->setIters(iters);
+ chimera->setTemplateFile(templatefile);
+
+ string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + method + maskfile + ".chimeras";
+ string accnosFileName = outputDir + getRootName(getSimpleName(fastafile)) + method + maskfile + ".accnos";
+
-
- //find chimeras
- chimera->getChimeras();
+ if ((method != "bellerophon") && (method != "chimeracheck")) {
+ if (chimera->getUnaligned()) {
+ mothurOut("Your template sequences are different lengths, please correct."); mothurOutEndLine();
+ delete chimera;
+ return 0;
+ }
+ }else if (method == "bellerophon") {//run bellerophon separately since you need to read entire fastafile to run it
+ chimera->getChimeras();
+
+ ofstream out;
+ openOutputFile(outputFileName, out);
+
+ ofstream out2;
+ openOutputFile(accnosFileName, out2);
+
+ chimera->print(out, out2);
+ out.close();
+ out2.close();
+
+ return 0;
+ }
- string outputFileName = getRootName(fastafile) + method + maskfile + ".chimeras";
- ofstream out;
- openOutputFile(outputFileName, out);
+ //some methods need to do prep work before processing the chimeras
+ chimera->doPrep();
- //print results
- chimera->print(out);
+ templateSeqsLength = chimera->getLength();
- out.close();
+ ofstream outHeader;
+ string tempHeader = outputDir + getRootName(getSimpleName(fastafile)) + method + maskfile + ".chimeras.tempHeader";
+ openOutputFile(tempHeader, outHeader);
+
+ chimera->printHeader(outHeader);
+ outHeader.close();
+
+
+ //break up file
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ if(processors == 1){
+ ifstream inFASTA;
+ openInputFile(fastafile, inFASTA);
+ numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+ inFASTA.close();
+
+ lines.push_back(new linePair(0, numSeqs));
+
+ driver(lines[0], outputFileName, fastafile, accnosFileName);
+
+ }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();
+
+ 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, accnosFileName);
+
+ rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
+ rename((accnosFileName + toString(processIDS[0]) + ".temp").c_str(), accnosFileName.c_str());
+
+ //append alignment and report files
+ for(int i=1;i<processors;i++){
+ appendOutputFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
+ remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
+
+ appendOutputFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName);
+ remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());
+
+ }
+ }
+
+ #else
+ ifstream inFASTA;
+ openInputFile(candidateFileNames[s], inFASTA);
+ numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+ inFASTA.close();
+ lines.push_back(new linePair(0, numSeqs));
+
+ driver(lines[0], outputFileName, fastafile, accnosFileName);
+ #endif
+ //mothurOut("Output File Names: ");
+ //if ((filter) && (method == "bellerophon")) { mothurOut(
+ //if (outputDir == "") { fastafile = getRootName(fastafile) + "filter.fasta"; }
+ // else { fastafile = outputDir + getRootName(getSimpleName(fastafile)) + "filter.fasta"; }
+
+ appendOutputFiles(tempHeader, outputFileName);
+
+ remove(outputFileName.c_str());
+ rename(tempHeader.c_str(), outputFileName.c_str());
+
delete chimera;
+ if (method == "chimeracheck") { remove(accnosFileName.c_str()); mothurOutEndLine(); mothurOut("This method does not determine if a sequence is chimeric, but allows you to make that determination based on the IS values."); mothurOutEndLine(); }
+
+ mothurOutEndLine(); mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); mothurOutEndLine();
+
return 0;
}
errorOut(e, "ChimeraSeqsCommand", "execute");
exit(1);
}
+}//**********************************************************************************************************************
+
+int ChimeraSeqsCommand::driver(linePair* line, string outputFName, string filename, string accnos){
+ try {
+ ofstream out;
+ openOutputFile(outputFName, out);
+
+ ofstream out2;
+ openOutputFile(accnos, out2);
+
+ ifstream inFASTA;
+ openInputFile(filename, inFASTA);
+
+ inFASTA.seekg(line->start);
+
+ for(int i=0;i<line->numSeqs;i++){
+
+ Sequence* candidateSeq = new Sequence(inFASTA); gobble(inFASTA);
+
+ if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
+
+ if ((candidateSeq->getAligned().length() != templateSeqsLength) && (method != "chimeracheck")) { //chimeracheck does not require seqs to be aligned
+ mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); mothurOutEndLine();
+ }else{
+ //find chimeras
+ chimera->getChimeras(candidateSeq);
+
+ //print results
+ chimera->print(out, out2);
+ }
+ }
+ delete candidateSeq;
+
+ //report progress
+ if((i+1) % 100 == 0){ mothurOut("Processing sequence: " + toString(i+1)); mothurOutEndLine(); }
+ }
+ //report progress
+ if((line->numSeqs) % 100 != 0){ mothurOut("Processing sequence: " + toString(line->numSeqs)); mothurOutEndLine(); }
+
+ out.close();
+ out2.close();
+ inFASTA.close();
+
+ return 1;
+ }
+ catch(exception& e) {
+ errorOut(e, "ChimeraSeqsCommand", "driver");
+ exit(1);
+ }
}
+
/**************************************************************************************************/
+void ChimeraSeqsCommand::createProcesses(string outputFileName, string filename, string accnos) {
+ try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ int process = 0;
+ // processIDS.resize(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){
+ driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp");
+ exit(0);
+ }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
+ }
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<processors;i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+#endif
+ }
+ catch(exception& e) {
+ errorOut(e, "ChimeraSeqsCommand", "createProcesses");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+void ChimeraSeqsCommand::appendOutputFiles(string temp, string filename) {
+ try{
+
+ ofstream output;
+ ifstream input;
+
+ openOutputFileAppend(temp, output);
+ openInputFile(filename, input, "noerror");
+
+ while(char c = input.get()){
+ if(input.eof()) { break; }
+ else { output << c; }
+ }
+
+ input.close();
+ output.close();
+ }
+ catch(exception& e) {
+ errorOut(e, "ChimeraSeqsCommand", "appendOuputFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+
projects / mothur.git / blobdiff