*/
#include "filterseqscommand.h"
+#include "sequence.hpp"
/**************************************************************************************/
-FilterSeqsCommand::FilterSeqsCommand(){
- globaldata = GlobalData::getInstance();
-
- if(globaldata->getFastaFile() != "") { readSeqs = new ReadFasta(globaldata->inputFileName); }
- else if(globaldata->getNexusFile() != "") { readSeqs = new ReadNexus(globaldata->inputFileName); }
- else if(globaldata->getClustalFile() != "") { readSeqs = new ReadClustal(globaldata->inputFileName); }
- else if(globaldata->getPhylipFile() != "") { readSeqs = new ReadPhylip(globaldata->inputFileName); }
-
- readSeqs->read();
- db = readSeqs->getDB();
- numSeqs = db->size();
-
- alignmentLength = db->get(0).getLength();
-
- filter = string(alignmentLength, '1');
-}
-
-/**************************************************************************************/
-
-void FilterSeqsCommand::doHard() {
-
- string hardName = globaldata->getHard();
- string hardFilter = "";
+FilterSeqsCommand::FilterSeqsCommand(string option) {
+ try {
+ abort = false;
+ filterFileName = "";
- ifstream fileHandle;
- openInputFile(hardName, fileHandle);
-
- fileHandle >> hardFilter;
-
- if(hardFilter.length() != filter.length()){
- cout << "The hard filter is not the same length as the alignment: Hard filter will not be applied." << endl;
- }
- else{
- filter = hardFilter;
- }
-
-}
-
-/**************************************************************************************/
-
-void FilterSeqsCommand::doTrump() {
-
- char trump = globaldata->getTrump()[0];
-
- for(int i = 0; i < numSeqs; i++) {
- string curAligned = db->get(i).getAligned();;
-
- for(int j = 0; j < alignmentLength; j++) {
- if(curAligned[j] == trump){
- filter[j] = '0';
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"fasta", "trump", "soft", "hard", "vertical", "outputdir","inputdir", "processors"};
+ 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 (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
- }
- }
-
-}
-
-/**************************************************************************************/
-
-void FilterSeqsCommand::doVertical() {
+
+ //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("hard");
+ //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["hard"] = inputDir + it->second; }
+ }
+ }
+
+ //check for required parameters
+ fasta = validParameter.validFile(parameters, "fasta", false);
+ if (fasta == "not found") { m->mothurOut("fasta is a required parameter for the filter.seqs command."); m->mothurOutEndLine(); abort = true; }
+ else {
+ splitAtDash(fasta, 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]; }
+ }
- vector<int> counts(alignmentLength, 0);
-
- for(int i = 0; i < numSeqs; i++) {
- string curAligned = db->get(i).getAligned();;
-
- for(int j = 0; j < alignmentLength; j++) {
- if(curAligned[j] == '-' || curAligned[j] == '.'){
- counts[j]++;
+ int ableToOpen;
+ ifstream in;
+ ableToOpen = openInputFile(fastafileNames[i], in);
+ if (ableToOpen == 1) {
+ m->mothurOut(fastafileNames[i] + " will be disregarded."); m->mothurOutEndLine();
+ //erase from file list
+ fastafileNames.erase(fastafileNames.begin()+i);
+ i--;
+ }else{
+ string simpleName = getSimpleName(fastafileNames[i]);
+ filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
+ }
+ in.close();
+ }
+
+ //make sure there is at least one valid file left
+ if (fastafileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
}
+
+ if (!abort) {
+ //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(fastafileNames[0]); //if user entered a file with a path then preserve it
+ }
+ }
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+
+ string temp;
+ temp = validParameter.validFile(parameters, "trump", false); if (temp == "not found") { temp = "*"; }
+ trump = temp[0];
+
+ temp = validParameter.validFile(parameters, "soft", false); if (temp == "not found") { soft = 0; }
+ else { soft = (float)atoi(temp.c_str()) / 100.0; }
+
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; }
+ convert(temp, processors);
+
+ hard = validParameter.validFile(parameters, "hard", true); if (hard == "not found") { hard = ""; }
+ else if (hard == "not open") { abort = true; }
+
+ vertical = validParameter.validFile(parameters, "vertical", false); if (vertical == "not found") { vertical = "T"; }
+
+ numSeqs = 0;
+
}
+
}
- for(int i=0;i<alignmentLength;i++){
- if(counts[i] == numSeqs) { filter[i] = '0'; }
+ catch(exception& e) {
+ m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
+ exit(1);
}
}
-/**************************************************************************************/
-
-void FilterSeqsCommand::doSoft() {
+//**********************************************************************************************************************
- int softThreshold = numSeqs * (float)atoi(globaldata->getSoft().c_str()) / 100.0;
-
- vector<int> a(alignmentLength, 0);
- vector<int> t(alignmentLength, 0);
- vector<int> g(alignmentLength, 0);
- vector<int> c(alignmentLength, 0);
- vector<int> x(alignmentLength, 0);
-
- for(int i=0;i<numSeqs;i++){
- string curAligned = db->get(i).getAligned();;
-
- for(int j=0;j<alignmentLength;j++){
- if(toupper(curAligned[j]) == 'A') { a[j]++; }
- else if(toupper(curAligned[j]) == 'T' || toupper(curAligned[i]) == 'U') { t[j]++; }
- else if(toupper(curAligned[j]) == 'G') { g[j]++; }
- else if(toupper(curAligned[j]) == 'C') { c[j]++; }
- }
+void FilterSeqsCommand::help(){
+ try {
+ m->mothurOut("The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file.\n");
+ m->mothurOut("The filter.seqs command parameters are fasta, trump, soft, hard and vertical. \n");
+ m->mothurOut("The fasta parameter is required. You may enter several fasta files to build the filter from and filter, by separating their names with -'s.\n");
+ m->mothurOut("For example: fasta=abrecovery.fasta-amazon.fasta \n");
+ m->mothurOut("The trump parameter .... The default is ...\n");
+ m->mothurOut("The soft parameter .... The default is ....\n");
+ m->mothurOut("The hard parameter .... The default is ....\n");
+ m->mothurOut("The vertical parameter .... The default is T.\n");
+ m->mothurOut("The filter.seqs command should be in the following format: \n");
+ m->mothurOut("filter.seqs(fasta=yourFastaFile, trump=yourTrump, soft=yourSoft, hard=yourHard, vertical=yourVertical) \n");
+ m->mothurOut("Example filter.seqs(fasta=abrecovery.fasta, trump=..., soft=..., hard=..., vertical=T).\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
+
}
-
- for(int i=0;i<alignmentLength;i++){
- if(a[i] < softThreshold && t[i] < softThreshold && g[i] < softThreshold && c[i] < softThreshold){
- filter[i] = '0';
- }
+ catch(exception& e) {
+ m->errorOut(e, "FilterSeqsCommand", "help");
+ exit(1);
}
}
int FilterSeqsCommand::execute() {
try {
-
- if(globaldata->getHard().compare("") != 0) { doHard(); } // has to be applied first!
- if(globaldata->getTrump().compare("") != 0) { doTrump(); }
- if(globaldata->getVertical() == "T") { doVertical(); }
- if(globaldata->getSoft().compare("") != 0) { doSoft(); }
-
- ofstream outfile;
- string filterFile = getRootName(globaldata->inputFileName) + "filter";
- openOutputFile(filterFile, outfile);
-
- outfile << filter << endl;
- outfile.close();
+
+ if (abort == true) { return 0; }
+ vector<string> outputNames;
- string filteredFasta = getRootName(globaldata->inputFileName) + "filter.fasta";
- openOutputFile(filteredFasta, outfile);
-
- for(int i=0;i<numSeqs;i++){
- string curAligned = db->get(i).getAligned();
- outfile << '>' << db->get(i).getName() << endl;
- for(int j=0;j<alignmentLength;j++){
- if(filter[j] == '1'){
- outfile << curAligned[j];
+ ifstream inFASTA;
+ openInputFile(fastafileNames[0], inFASTA);
+
+ Sequence testSeq(inFASTA);
+ alignmentLength = testSeq.getAlignLength();
+ inFASTA.close();
+
+ ////////////create filter/////////////////
+
+ filter = createFilter();
+
+ ofstream outFilter;
+
+ string filterFile = outputDir + filterFileName + ".filter";
+ openOutputFile(filterFile, outFilter);
+ outFilter << filter << endl;
+ outFilter.close();
+ outputNames.push_back(filterFile);
+
+
+ ////////////run filter/////////////////
+
+ numSeqs = 0;
+ for (int i = 0; i < fastafileNames.size(); i++) {
+ ifstream in;
+ openInputFile(fastafileNames[i], in);
+ string filteredFasta = outputDir + getRootName(getSimpleName(fastafileNames[i])) + "filter.fasta";
+ ofstream outFASTA;
+ openOutputFile(filteredFasta, outFASTA);
+ outputNames.push_back(filteredFasta);
+
+
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); outFASTA.close(); for(int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ Sequence seq(in);
+ if (seq.getName() != "") {
+ string align = seq.getAligned();
+ string filterSeq = "";
+
+ for(int j=0;j<alignmentLength;j++){
+ if(filter[j] == '1'){
+ filterSeq += align[j];
+ }
+ }
+
+ outFASTA << '>' << seq.getName() << endl << filterSeq << endl;
+ numSeqs++;
}
+ gobble(in);
}
- outfile << endl;
+ outFASTA.close();
+ in.close();
}
- outfile.close();
int filteredLength = 0;
for(int i=0;i<alignmentLength;i++){
if(filter[i] == '1'){ filteredLength++; }
}
- cout << endl;
- cout << "Length of filtered alignment: " << filteredLength << endl;
- cout << "Number of columns removed: " << alignmentLength-filteredLength << endl;
- cout << "Length of the original alignment: " << alignmentLength << endl;
- cout << "Number of sequences used to construct filter: " << numSeqs << endl;
+ if (m->control_pressed) { for(int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+
+ m->mothurOutEndLine();
+ m->mothurOut("Length of filtered alignment: " + toString(filteredLength)); m->mothurOutEndLine();
+ m->mothurOut("Number of columns removed: " + toString((alignmentLength-filteredLength))); m->mothurOutEndLine();
+ m->mothurOut("Length of the original alignment: " + toString(alignmentLength)); m->mothurOutEndLine();
+ m->mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); m->mothurOutEndLine();
- globaldata->clear();
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for(int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "FilterSeqsCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the FilterSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+/**************************************************************************************/
+string FilterSeqsCommand::createFilter() {
+ try {
+ string filterString = "";
+
+ Filters F;
+
+ if (soft != 0) { F.setSoft(soft); }
+ if (trump != '*') { F.setTrump(trump); }
+
+ F.setLength(alignmentLength);
+
+ if(soft != 0 || isTrue(vertical)){
+ F.initialize();
+ }
+
+ if(hard.compare("") != 0) { F.doHard(hard); }
+ else { F.setFilter(string(alignmentLength, '1')); }
+
+ numSeqs = 0;
+
+ if(trump != '*' || isTrue(vertical) || soft != 0){
+ for (int s = 0; s < fastafileNames.size(); s++) {
+
+ for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ if(processors == 1){
+ ifstream inFASTA;
+ openInputFile(fastafileNames[s], inFASTA);
+ int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+ inFASTA.close();
+
+ numSeqs += numFastaSeqs;
+
+ lines.push_back(new linePair(0, numFastaSeqs));
+
+ driverCreateFilter(F, fastafileNames[s], lines[0]);
+ }else{
+ vector<int> positions;
+
+ ifstream inFASTA;
+ openInputFile(fastafileNames[s], 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();
+
+ int numFastaSeqs = positions.size();
+
+ numSeqs += numFastaSeqs;
+
+ int numSeqsPerProcessor = numFastaSeqs / processors;
+
+ for (int i = 0; i < processors; i++) {
+ long int startPos = positions[ i * numSeqsPerProcessor ];
+ if(i == processors - 1){
+ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
+ }
+ lines.push_back(new linePair(startPos, numSeqsPerProcessor));
+ }
+
+ createProcessesCreateFilter(F, fastafileNames[s]);
+ }
+ #else
+ ifstream inFASTA;
+ openInputFile(fastafileNames[s], inFASTA);
+ int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+ inFASTA.close();
+
+ numSeqs += numFastaSeqs;
+
+ lines.push_back(new linePair(0, numFastaSeqs));
+
+ driverCreateFilter(F, lines[0], fastafileNames[s]);
+ #endif
+
+
+ }
+ }
+
+ F.setNumSeqs(numSeqs);
+
+ if(isTrue(vertical) == 1) { F.doVertical(); }
+ if(soft != 0) { F.doSoft(); }
+
+ filterString = F.getFilter();
+
+ return filterString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "FilterSeqsCommand", "createFilter");
+ exit(1);
+ }
+}
+/**************************************************************************************/
+int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* line) {
+ try {
+
+ ifstream in;
+ openInputFile(filename, in);
+
+ in.seekg(line->start);
+
+ for(int i=0;i<line->numSeqs;i++){
+
+ if (m->control_pressed) { in.close(); return 1; }
+
+ Sequence seq(in);
+ if (seq.getName() != "") {
+ if(trump != '*'){ F.doTrump(seq); }
+ if(isTrue(vertical) || soft != 0){ F.getFreqs(seq); }
+ cout.flush();
+ }
+ }
+
+ in.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "FilterSeqsCommand", "driverCreateFilter");
exit(1);
}
}
+/**************************************************************************************************/
+int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
+ try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ int process = 0;
+ int exitCommand = 1;
+ vector<int> processIDS;
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = vfork();
+
+ 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){
+ driverCreateFilter(F, filename, lines[process]);
+ exit(0);
+ }else { m->mothurOut("unable to spawn the necessary processes."); m->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);
+ }
+
+ return exitCommand;
+#endif
+ }
+ catch(exception& e) {
+ m->errorOut(e, "FilterSeqsCommand", "createProcessesCreateFilter");
+ exit(1);
+ }
+}
/**************************************************************************************/
projects / mothur.git / blobdiff