*/
#include "seqsummarycommand.h"
+#include "sequence.hpp"
//***************************************************************************************************************
-SeqSummaryCommand::SeqSummaryCommand(){
+SeqSummaryCommand::SeqSummaryCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
- if(globaldata->getFastaFile() == "") { cout << "you need to at least enter a fasta file name" << endl; }
+ abort = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"fasta","outputdir","inputdir"};
+ 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; }
+ }
+
+ //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; }
+ }
+ }
+
+ //check for required parameters
+ fastafile = validParameter.validFile(parameters, "fasta", true);
+ if (fastafile == "not open") { abort = true; }
+ else if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the summary.seqs command."); m->mothurOutEndLine(); abort = true; }
+
+ //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(fastafile); //if user entered a file with a path then preserve it
+ }
+
+ }
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SeqCoordCommand class Function SeqCoordCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SeqSummaryCommand", "SeqSummaryCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the SeqCoordCommand class function SeqCoordCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+
+void SeqSummaryCommand::help(){
+ try {
+ m->mothurOut("The summary.seqs command reads a fastafile and ....\n");
+ m->mothurOut("The summary.seqs command parameter is fasta and it is required.\n");
+ m->mothurOut("The summary.seqs command should be in the following format: \n");
+ m->mothurOut("summary.seqs(fasta=yourFastaFile) \n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SeqSummaryCommand", "help");
exit(1);
- }
+ }
}
//***************************************************************************************************************
int SeqSummaryCommand::execute(){
try{
-
+
+ if (abort == true) { return 0; }
+
ifstream inFASTA;
- openInputFile(globaldata->getFastaFile(), inFASTA);
+ openInputFile(fastafile, inFASTA);
int numSeqs = 0;
ofstream outSummary;
- string summaryFile = globaldata->getFastaFile() + ".summary";
+ string summaryFile = outputDir + getSimpleName(fastafile) + ".summary";
openOutputFile(summaryFile, outSummary);
vector<int> startPosition;
outSummary << "seqname\tstart\tend\tnbases\tambigs\tpolymer" << endl;
while(!inFASTA.eof()){
- Sequence current(inFASTA);
- startPosition.push_back(current.getStartPos());
- endPosition.push_back(current.getEndPos());
- seqLength.push_back(current.getNumBases());
- ambigBases.push_back(current.getAmbigBases());
- longHomoPolymer.push_back(current.getLongHomoPolymer());
-
- outSummary << current.getName() << '\t';
- outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
- outSummary << current.getNumBases() << '\t' << current.getAmbigBases() << '\t';
- outSummary << current.getLongHomoPolymer() << endl;
+ if (m->control_pressed) { inFASTA.close(); outSummary.close(); remove(summaryFile.c_str()); return 0; }
- numSeqs++;
+ Sequence current(inFASTA);
+ if (current.getName() != "") {
+ startPosition.push_back(current.getStartPos());
+ endPosition.push_back(current.getEndPos());
+ seqLength.push_back(current.getNumBases());
+ ambigBases.push_back(current.getAmbigBases());
+ longHomoPolymer.push_back(current.getLongHomoPolymer());
+
+ outSummary << current.getName() << '\t';
+ outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
+ outSummary << current.getNumBases() << '\t' << current.getAmbigBases() << '\t';
+ outSummary << current.getLongHomoPolymer() << endl;
+
+ numSeqs++;
+ }
gobble(inFASTA);
}
inFASTA.close();
int ptile97_5 = int(numSeqs * 0.975);
int ptile100 = numSeqs - 1;
- cout << endl;
- cout << "\t\tStart\tEnd\tNBases\tAmbigs\tPolymer" << endl;
- cout << "Minimum:\t" << startPosition[0] << '\t' << endPosition[0] << '\t' << seqLength[0] << '\t' << ambigBases[0] << '\t' << longHomoPolymer[0] << endl;
- cout << "2.5%-tile:\t" << startPosition[ptile0_25] << '\t' << endPosition[ptile0_25] << '\t' << seqLength[ptile0_25] << '\t' << ambigBases[ptile0_25] << '\t' << longHomoPolymer[ptile0_25] << endl;
- cout << "25%-tile:\t" << startPosition[ptile25] << '\t' << endPosition[ptile25] << '\t' << seqLength[ptile25] << '\t' << ambigBases[ptile25] << '\t' << longHomoPolymer[ptile25] << endl;
- cout << "Median: \t" << startPosition[ptile50] << '\t' << endPosition[ptile50] << '\t' << seqLength[ptile50] << '\t' << ambigBases[ptile50] << '\t' << longHomoPolymer[ptile50] << endl;
- cout << "75%-tile:\t" << startPosition[ptile75] << '\t' << endPosition[ptile75] << '\t' << seqLength[ptile75] << '\t' << ambigBases[ptile75] << '\t' << longHomoPolymer[ptile75] << endl;
- cout << "97.5%-tile:\t" << startPosition[ptile97_5] << '\t' << endPosition[ptile97_5] << '\t' << seqLength[ptile97_5] << '\t' << ambigBases[ptile97_5] << '\t' << longHomoPolymer[ptile97_5] << endl;
- cout << "Maximum:\t" << startPosition[ptile100] << '\t' << endPosition[ptile100] << '\t' << seqLength[ptile100] << '\t' << ambigBases[ptile100] << '\t' << longHomoPolymer[ptile100] << endl;
- cout << "# of Seqs:\t" << numSeqs << endl;
+ //to compensate for blank sequences that would result in startPosition and endPostion equalling -1
+ if (startPosition[0] == -1) { startPosition[0] = 0; }
+ if (endPosition[0] == -1) { endPosition[0] = 0; }
+ if (m->control_pressed) { outSummary.close(); remove(summaryFile.c_str()); return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("\t\tStart\tEnd\tNBases\tAmbigs\tPolymer"); m->mothurOutEndLine();
+ m->mothurOut("Minimum:\t" + toString(startPosition[0]) + "\t" + toString(endPosition[0]) + "\t" + toString(seqLength[0]) + "\t" + toString(ambigBases[0]) + "\t" + toString(longHomoPolymer[0])); m->mothurOutEndLine();
+ m->mothurOut("2.5%-tile:\t" + toString(startPosition[ptile0_25]) + "\t" + toString(endPosition[ptile0_25]) + "\t" + toString(seqLength[ptile0_25]) + "\t" + toString(ambigBases[ptile0_25]) + "\t"+ toString(longHomoPolymer[ptile0_25])); m->mothurOutEndLine();
+ m->mothurOut("25%-tile:\t" + toString(startPosition[ptile25]) + "\t" + toString(endPosition[ptile25]) + "\t" + toString(seqLength[ptile25]) + "\t" + toString(ambigBases[ptile25]) + "\t" + toString(longHomoPolymer[ptile25])); m->mothurOutEndLine();
+ m->mothurOut("Median: \t" + toString(startPosition[ptile50]) + "\t" + toString(endPosition[ptile50]) + "\t" + toString(seqLength[ptile50]) + "\t" + toString(ambigBases[ptile50]) + "\t" + toString(longHomoPolymer[ptile50])); m->mothurOutEndLine();
+ m->mothurOut("75%-tile:\t" + toString(startPosition[ptile75]) + "\t" + toString(endPosition[ptile75]) + "\t" + toString(seqLength[ptile75]) + "\t" + toString(ambigBases[ptile75]) + "\t" + toString(longHomoPolymer[ptile75])); m->mothurOutEndLine();
+ m->mothurOut("97.5%-tile:\t" + toString(startPosition[ptile97_5]) + "\t" + toString(endPosition[ptile97_5]) + "\t" + toString(seqLength[ptile97_5]) + "\t" + toString(ambigBases[ptile97_5]) + "\t" + toString(longHomoPolymer[ptile97_5])); m->mothurOutEndLine();
+ m->mothurOut("Maximum:\t" + toString(startPosition[ptile100]) + "\t" + toString(endPosition[ptile100]) + "\t" + toString(seqLength[ptile100]) + "\t" + toString(ambigBases[ptile100]) + "\t" + toString(longHomoPolymer[ptile100])); m->mothurOutEndLine();
+ m->mothurOut("# of Seqs:\t" + toString(numSeqs)); m->mothurOutEndLine();
+
+ outSummary.close();
+
+ if (m->control_pressed) { remove(summaryFile.c_str()); return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut(summaryFile); 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";
- 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";
+ m->errorOut(e, "SeqSummaryCommand", "execute");
exit(1);
}
-
}
//***************************************************************************************************************
projects / mothur.git / blobdiff