*/
#include "filterseqscommand.h"
+#include "sequence.hpp"
/**************************************************************************************/
-FilterSeqsCommand::FilterSeqsCommand(){
+FilterSeqsCommand::FilterSeqsCommand(string option){
+ try {
+ 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)));
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ for (map<string,string>::iterator 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; }
- globaldata = GlobalData::getInstance();
-
- if(globaldata->getFastaFile() == "") { cout << "You must enter a fasta formatted file" << endl; }
- trump = globaldata->getTrump()[0];
- numSeqs = 0;
+ //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 = "T"; }
+
+ 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 T." << "\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);
+ openInputFile(hard, fileHandle);
fileHandle >> filter;
+
+ fileHandle.close();
}
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::doSoft() {
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; }
+ if(a[i] < threshold && t[i] < threshold && g[i] < threshold && c[i] < threshold){ filter[i] = 0; }
}
-
}
/**************************************************************************************/
int FilterSeqsCommand::execute() {
try {
+
+ if (abort == true) { return 0; }
+
ifstream inFASTA;
- openInputFile(globaldata->getFastaFile(), inFASTA);
+ openInputFile(fastafile, inFASTA);
Sequence testSeq(inFASTA);
alignmentLength = testSeq.getAlignLength();
inFASTA.seekg(0);
- if(globaldata->getSoft() != "" || isTrue(globaldata->getVertical())){
+ 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(globaldata->getSoft() != ""){
- soft = (float)atoi(globaldata->getSoft().c_str()) / 100.0;
- }
- if(globaldata->getHard().compare("") != 0) { doHard(); }
- else { filter = string(alignmentLength, '1'); }
+ if(hard.compare("") != 0) { doHard(); }
+ else { filter = string(alignmentLength, '1'); }
- if(globaldata->getTrump().compare("") != 0 || isTrue(globaldata->getVertical()) || globaldata->getSoft().compare("") != 0){
-
- while(!inFASTA.eof()){
+ if(trump != '*' || isTrue(vertical) || soft != 0){
+ while(!inFASTA.eof()){ //read through and create the filter...
Sequence seq(inFASTA);
- if(globaldata->getTrump().compare("") != 0) { doTrump(seq); }
- if(isTrue(globaldata->getVertical()) || globaldata->getSoft().compare("") != 0){ getFreqs(seq); }
+ if(trump != '*'){ doTrump(seq); }
+ if(isTrue(vertical) || soft != 0){ getFreqs(seq); }
numSeqs++;
cout.flush();
}
}
inFASTA.close();
- if(isTrue(globaldata->getVertical()) == 1) { doVertical(); }
- if(globaldata->getSoft().compare("") != 0) { doSoft(); }
+ if(isTrue(vertical) == 1) { doVertical(); }
+ if(soft != 0) { doSoft(); }
ofstream outFilter;
- string filterFile = getRootName(globaldata->inputFileName) + "filter";
+ string filterFile = getRootName(fastafile) + "filter";
openOutputFile(filterFile, outFilter);
outFilter << filter << endl;
outFilter.close();
- openInputFile(globaldata->getFastaFile(), inFASTA);
- string filteredFasta = getRootName(globaldata->inputFileName) + "filter.fasta";
+ openInputFile(fastafile, inFASTA);
+ string filteredFasta = getRootName(fastafile) + "filter.fasta";
ofstream outFASTA;
openOutputFile(filteredFasta, outFASTA);
cout << "Length of the original alignment: " << alignmentLength << endl;
cout << "Number of sequences used to construct filter: " << numSeqs << endl;
- globaldata->clear();
-
return 0;
}
projects / mothur.git / blobdiff