/**************************************************************************************/
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();
+ if(globaldata->getFastaFile() == "") { cout << "You must enter a fasta formatted file" << endl; }
+ trump = globaldata->getTrump()[0];
+ numSeqs = 0;
- filter = string(alignmentLength, '1');
}
/**************************************************************************************/
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;
- }
-
+ 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(); }
+ ifstream inFASTA;
+ openInputFile(globaldata->getFastaFile(), inFASTA);
+
+ Sequence testSeq(inFASTA);
+ alignmentLength = testSeq.getAlignLength();
+ inFASTA.seekg(0);
+
+ if(globaldata->getSoft() != "" || isTrue(globaldata->getVertical())){
+ a.assign(alignmentLength, 0);
+ t.assign(alignmentLength, 0);
+ g.assign(alignmentLength, 0);
+ c.assign(alignmentLength, 0);
+ gap.assign(alignmentLength, 0);
+ }
+ if(globaldata->getSoft() != ""){
+ soft = (float)atoi(globaldata->getSoft().c_str()) / 100.0;
+ }
+
+ if(globaldata->getHard().compare("") != 0) { doHard(); }
+ else { filter = string(alignmentLength, '1'); }
- ofstream outfile;
- string filterFile = getRootName(globaldata->inputFileName) + "filter";
- openOutputFile(filterFile, outfile);
+ if(globaldata->getTrump().compare("") != 0 || isTrue(globaldata->getVertical()) || globaldata->getSoft().compare("") != 0){
+
+ while(!inFASTA.eof()){
+ Sequence seq(inFASTA);
+ if(globaldata->getTrump().compare("") != 0) { doTrump(seq); }
+ if(isTrue(globaldata->getVertical()) || globaldata->getSoft().compare("") != 0){ getFreqs(seq); }
+ numSeqs++;
+ cout.flush();
+ }
+
+ }
+ inFASTA.close();
+
+ if(isTrue(globaldata->getVertical()) == 1) { doVertical(); }
+ if(globaldata->getSoft().compare("") != 0) { doSoft(); }
- outfile << filter << endl;
- outfile.close();
+ ofstream outFilter;
+ string filterFile = getRootName(globaldata->inputFileName) + "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(globaldata->getFastaFile(), inFASTA);
+ string filteredFasta = getRootName(globaldata->inputFileName) + "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