* Mothur
*
* Created by Thomas Ryabin on 5/4/09.
- * Copyright 2009 __MyCompanyName__. All rights reserved.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "filterseqscommand.h"
-#include <iostream>
-#include <fstream>
/**************************************************************************************/
-void FilterSeqsCommand::doTrump() {
- //trump = globaldata->getTrump();
-//
-// for(int i = 0; i < db->size(); i++) {
-// Sequence cur = db->get(i);
-// string curAligned = cur.getAligned();
-//
-// for(int j = 0; j < curAligned.length-1; j++) {
-// string curChar = curAligned.substr(j, j+1);
-//
-// if(curChar.compare(trump) == 0)
-// columnsToRemove[j] = true;
-// }
-// }
+
+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"; }
+
+ 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);
+ }
+}
+
+//**********************************************************************************************************************
+
+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() {
+
+ ifstream fileHandle;
+ openInputFile(hard, fileHandle);
+
+ fileHandle >> filter;
+
+}
+
+/**************************************************************************************/
+
+void FilterSeqsCommand::doTrump(Sequence seq) {
+
+ string curAligned = seq.getAligned();
+
+ for(int j = 0; j < alignmentLength; j++) {
+ if(curAligned[j] == trump){
+ filter[j] = '0';
+ }
+ }
+
+}
+
+/**************************************************************************************/
+
+void FilterSeqsCommand::doVertical() {
+
+ for(int i=0;i<alignmentLength;i++){
+ if(gap[i] == numSeqs) { filter[i] = '0'; }
+ }
+
}
/**************************************************************************************/
+
void FilterSeqsCommand::doSoft() {
- //soft = atoi(globaldata->getSoft().c_str());
-// vector<vector<int> > columnSymbolSums;
-// vector<vector<string> > columnSymbols;
-// for(int i = 0; i < db->get(0).getLength(); i++) {
-// vector<string> symbols;
-// vector<int> sums;
-// columnSymbols[i] = symbols;
-// columnSymbolSums[i] = sums;
-// }
-//
-// for(int i = 0; i < db->size(); i++) {
-// Sequence cur = db->get(i);
-// string curAligned = cur.getAligned();
-//
-// for(int j = 0; j < curAligned.length-1; j++) {
-// string curChar = curAligned.substr(j, j+1);
-// vector<string> curColumnSymbols = columnSymbols[j];
-//
-// bool newSymbol = true;
-//
-// for(int k = 0; j < curColumnSymbols.size(); j++)
-// if(curChar.compare(curColumnSymbols[k]) == 0) {
-// newSymbol = false;
-// columnSymbolSums[j][k]++;
-// }
-//
-// if(newSymbol) {
-// columnSymbols.push_back(curChar);
-// columnSymbolSums[j].push_back(1);
-// }
-// }
-// }
-//
-// for(int i = 0; i < columnSymbolSums.size(); i++) {
-// int totalSum = 0;
-// int max = 0;
-// vector<int> curColumn = columnSymbolSums[i];
-//
-// for(int j = 0; j < curColumn.size(); j++) {
-// int curSum = curColumn[j];
-// if(curSum > max)
-// max = curSum;
-// totalSum += curSum;
-// }
-//
-// if((double)max/(double)totalSum * 100 < soft)
-// columnsToRemove[i] = true;
-// }
+
+ 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; }
+ }
+}
+
+/**************************************************************************************/
+
+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]++; }
+ }
+
}
-void FilterSeqsCommand::doFilter() {}
+
/**************************************************************************************/
+
int FilterSeqsCommand::execute() {
try {
- globaldata = GlobalData::getInstance();
- filename = globaldata->inputFileName;
+
+ if (abort == true) { return 0; }
- if(globaldata->getFastaFile().compare("") != 0) {
- readFasta = new ReadFasta(filename);
- readFasta->read();
- db = readFasta->getDB();
- }
+ ifstream inFASTA;
+ openInputFile(fastafile, inFASTA);
- else if(globaldata->getNexusFile().compare("") != 0) {
- readNexus = new ReadNexus(filename);
- readNexus->read();
- db = readNexus->getDB();
- }
+ Sequence testSeq(inFASTA);
+ alignmentLength = testSeq.getAlignLength();
+ inFASTA.seekg(0);
- else if(globaldata->getClustalFile().compare("") != 0) {
- readClustal = new ReadClustal(filename);
- readClustal->read();
- db = readClustal->getDB();
+ 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'); }
- else if(globaldata->getPhylipFile().compare("") != 0) {
- readPhylip = new ReadPhylip(filename);
- readPhylip->read();
- db = readPhylip->getDB();
- }
-
- for(int i = 0; i < db->get(0).getLength(); i++)
- columnsToRemove[i] = false;
-
- // Trump
- if(globaldata->getTrump().compare("") != 0) {
+ 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();
- // Soft
- if(globaldata->getSoft().compare("") != 0) {}
+ if(isTrue(vertical) == 1) { doVertical(); }
+ if(soft != 0) { doSoft(); }
+ ofstream outFilter;
+ string filterFile = getRootName(fastafile) + "filter";
+ openOutputFile(filterFile, outFilter);
+ outFilter << filter << endl;
+ outFilter.close();
-
+
+ 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'){
+ filterSeq += align[j];
+ }
+ }
+
+ outFASTA << '>' << seq.getName() << endl << filterSeq << endl;
+ numSeqs++;
+ gobble(inFASTA);
+ }
+ outFASTA.close();
+ inFASTA.close();
- // Filter
- //if(globaldata->getFilter().compare("") != 0) {
-//
-// filter = globaldata->getFilter();
-// ifstream filehandle;
-// openInputFile(filter, filehandle);
-//
-// char c;
-// int count = 0;
-// while(!filehandle.eof()) {
-// c = filehandle.get();
-// if(c == '0')
-// columnsToRemove[count] = true;
-// count++;
-// }
-// }
+ 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;
+
+ globaldata->clear();
-
-
return 0;
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the DeconvoluteCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
catch(...) {
- cout << "An unknown error has occurred in the DeconvoluteCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "An unknown error has occurred in the FilterSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
}
+
/**************************************************************************************/
projects / mothur.git / blobdiff