/**************************************************************************************/
-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();
+FilterSeqsCommand::FilterSeqsCommand(string option){
+ try {
+ globaldata = GlobalData::getInstance();
+ abort = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"fasta", "trump", "soft", "hard", "vertical"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ parser = new OptionParser();
+ parser->parse(option, parameters); delete parser;
+
+ ValidParameters* validParameter = new ValidParameters();
+
+ //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; }
+ }
+
+ //check for required parameters
+ fastafile = validParameter->validFile(parameters, "fasta", true);
+ if (fastafile == "not found") { cout << "fasta is a required parameter for the filter.seqs command." << endl; abort = true; }
+ else if (fastafile == "not open") { abort = true; }
+ else {
+ globaldata->setFastaFile(fastafile);
+ }
+
+ //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; }
+
+ 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 = "F"; }
- alignmentLength = db->get(0).getLength();
+ delete validParameter;
+
+ numSeqs = 0;
+
+ }
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function FilterSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the FilterSeqsCommand class function FilterSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
- filter = string(alignmentLength, '1');
+void FilterSeqsCommand::help(){
+ try {
+ cout << "The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file." << "\n";
+ cout << "The filter.seqs command parameters are fasta, trump, soft, hard and vertical. " << "\n";
+ cout << "The fasta parameter is required." << "\n";
+ cout << "The trump parameter .... The default is '.'" << "\n";
+ cout << "The soft parameter .... The default is ...." << "\n";
+ cout << "The hard parameter .... The default is ...." << "\n";
+ cout << "The vertical parameter .... The default is F." << "\n";
+ cout << "The filter.seqs command should be in the following format: " << "\n";
+ cout << "filter.seqs(fasta=yourFastaFile, trump=yourTrump, soft=yourSoft, hard=yourHard, vertical=yourVertical) " << "\n";
+ cout << "Example filter.seqs(fasta=abrecovery.fasta, trump=..., soft=..., hard=..., vertical=T)." << "\n";
+ cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta)." << "\n" << "\n";
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the FilterSeqsCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
}
/**************************************************************************************/
void FilterSeqsCommand::doHard() {
- string hardName = globaldata->getHard();
- string hardFilter = "";
-
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;
- }
+ openInputFile(hard, fileHandle);
+ fileHandle >> filter;
+
}
/**************************************************************************************/
-void FilterSeqsCommand::doTrump() {
-
- char trump = globaldata->getTrump()[0];
+void FilterSeqsCommand::doTrump(Sequence seq) {
- 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';
- }
+ string curAligned = seq.getAligned();
+
+ for(int j = 0; j < alignmentLength; j++) {
+ if(curAligned[j] == trump){
+ filter[j] = '0';
}
}
void FilterSeqsCommand::doVertical() {
- 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]++;
- }
- }
- }
for(int i=0;i<alignmentLength;i++){
- if(counts[i] == numSeqs) { filter[i] = '0'; }
+ if(gap[i] == numSeqs) { filter[i] = '0'; }
}
+
}
/**************************************************************************************/
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]++; }
- }
+ int threshold = int (soft * numSeqs);
+ bool keep = 0;
+
+ for(int i=0;i<alignmentLength;i++){
+ if(a[i] >= threshold) { keep = 1; }
+ else if(t[i] >= threshold) { keep = 1; }
+ else if(g[i] >= threshold) { keep = 1; }
+ else if(c[i] >= threshold) { keep = 1; }
+
+ if(keep == 0) { filter[i] = 0; }
}
+}
- for(int i=0;i<alignmentLength;i++){
- if(a[i] < softThreshold && t[i] < softThreshold && g[i] < softThreshold && c[i] < softThreshold){
- filter[i] = '0';
- }
+/**************************************************************************************/
+
+void FilterSeqsCommand::getFreqs(Sequence seq) {
+
+ string curAligned = seq.getAligned();;
+
+ for(int j=0;j<alignmentLength;j++){
+ if(toupper(curAligned[j]) == 'A') { a[j]++; }
+ else if(toupper(curAligned[j]) == 'T' || toupper(curAligned[j]) == 'U') { t[j]++; }
+ else if(toupper(curAligned[j]) == 'G') { g[j]++; }
+ else if(toupper(curAligned[j]) == 'C') { c[j]++; }
+ else if(curAligned[j] == '-' || curAligned[j] == '.') { gap[j]++; }
}
+
}
/**************************************************************************************/
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(); }
+
+ if (abort == true) { return 0; }
+
+ ifstream inFASTA;
+ openInputFile(fastafile, inFASTA);
+
+ Sequence testSeq(inFASTA);
+ alignmentLength = testSeq.getAlignLength();
+ inFASTA.seekg(0);
+
+ if(soft != 0 || isTrue(vertical)){
+ a.assign(alignmentLength, 0);
+ t.assign(alignmentLength, 0);
+ g.assign(alignmentLength, 0);
+ c.assign(alignmentLength, 0);
+ gap.assign(alignmentLength, 0);
+ }
+
+ if(hard.compare("") != 0) { doHard(); }
+ else { filter = string(alignmentLength, '1'); }
- ofstream outfile;
- string filterFile = getRootName(globaldata->inputFileName) + "filter";
- openOutputFile(filterFile, outfile);
+ if(isTrue(vertical) || soft != 0){
+
+ while(!inFASTA.eof()){
+ Sequence seq(inFASTA);
+ doTrump(seq);
+ if(isTrue(vertical) || soft != 0){ getFreqs(seq); }
+ numSeqs++;
+ cout.flush();
+ }
+
+ }
+ inFASTA.close();
+
+ if(isTrue(vertical) == 1) { doVertical(); }
+ if(soft != 0) { doSoft(); }
- outfile << filter << endl;
- outfile.close();
+ ofstream outFilter;
+ string filterFile = getRootName(fastafile) + "filter";
+ openOutputFile(filterFile, outFilter);
+ outFilter << filter << endl;
+ outFilter.close();
- 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;
+ openInputFile(fastafile, inFASTA);
+ string filteredFasta = getRootName(fastafile) + "filter.fasta";
+ ofstream outFASTA;
+ openOutputFile(filteredFasta, outFASTA);
+
+ numSeqs = 0;
+ while(!inFASTA.eof()){
+ Sequence seq(inFASTA);
+ string align = seq.getAligned();
+ string filterSeq = "";
+
for(int j=0;j<alignmentLength;j++){
if(filter[j] == '1'){
- outfile << curAligned[j];
+ filterSeq += align[j];
}
}
- outfile << endl;
+
+ outFASTA << '>' << seq.getName() << endl << filterSeq << endl;
+ numSeqs++;
+ gobble(inFASTA);
}
- outfile.close();
+ outFASTA.close();
+ inFASTA.close();
+
int filteredLength = 0;
for(int i=0;i<alignmentLength;i++){
projects / mothur.git / blobdiff