X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqsummarycommand.cpp;h=a2500949a9c207a5975b5734050533c1d1ea317f;hb=9b53f130ac9af5e95444ce2e817fce25ed19ff03;hp=c328a041267d01e21ed2e99780f18de486571685;hpb=f687723a8357916e86a05116978e6869b039ce36;p=mothur.git diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp index c328a04..a250094 100644 --- a/seqsummarycommand.cpp +++ b/seqsummarycommand.cpp @@ -8,13 +8,14 @@ */ #include "seqsummarycommand.h" - +#include "counttable.h" //********************************************************************************************************************** vector SeqSummaryCommand::setParameters(){ try { CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta); - CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname); + CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pname); + CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pcount); CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors); CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); @@ -33,8 +34,9 @@ string SeqSummaryCommand::getHelpString(){ try { string helpString = ""; helpString += "The summary.seqs command reads a fastafile and summarizes the sequences.\n"; - helpString += "The summary.seqs command parameters are fasta, name and processors, fasta is required, unless you have a valid current fasta file.\n"; + helpString += "The summary.seqs command parameters are fasta, name, count and processors, fasta is required, unless you have a valid current fasta file.\n"; helpString += "The name parameter allows you to enter a name file associated with your fasta file. \n"; + helpString += "The count parameter allows you to enter a count file associated with your fasta file. \n"; helpString += "The summary.seqs command should be in the following format: \n"; helpString += "summary.seqs(fasta=yourFastaFile, processors=2) \n"; helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n"; @@ -123,6 +125,14 @@ SeqSummaryCommand::SeqSummaryCommand(string option) { //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["name"] = inputDir + it->second; } } + + it = parameters.find("count"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["count"] = inputDir + it->second; } + } } //initialize outputTypes @@ -142,6 +152,13 @@ SeqSummaryCommand::SeqSummaryCommand(string option) { if (namefile == "not open") { namefile = ""; abort = true; } else if (namefile == "not found") { namefile = ""; } else { m->setNameFile(namefile); } + + countfile = validParameter.validFile(parameters, "count", true); + if (countfile == "not open") { abort = true; countfile = ""; } + else if (countfile == "not found") { countfile = ""; } + else { m->setCountTableFile(countfile); } + + if ((countfile != "") && (namefile != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name."); 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"){ @@ -153,11 +170,12 @@ SeqSummaryCommand::SeqSummaryCommand(string option) { m->setProcessors(temp); m->mothurConvert(temp, processors); - if (namefile == "") { - vector files; files.push_back(fastafile); - parser.getNameFile(files); - } - + if (countfile == "") { + if (namefile == "") { + vector files; files.push_back(fastafile); + parser.getNameFile(files); + } + } } } catch(exception& e) { @@ -186,6 +204,11 @@ int SeqSummaryCommand::execute(){ vector longHomoPolymer; if (namefile != "") { nameMap = m->readNames(namefile); } + else if (countfile != "") { + CountTable ct; + ct.readTable(countfile); + nameMap = ct.getNameMap(); + } if (m->control_pressed) { return 0; } @@ -344,7 +367,7 @@ int SeqSummaryCommand::execute(){ int size = startPosition.size(); //find means - float meanStartPosition, meanEndPosition, meanSeqLength, meanAmbigBases, meanLongHomoPolymer; + double meanStartPosition, meanEndPosition, meanSeqLength, meanAmbigBases, meanLongHomoPolymer; meanStartPosition = 0; meanEndPosition = 0; meanSeqLength = 0; meanAmbigBases = 0; meanLongHomoPolymer = 0; for (int i = 0; i < size; i++) { meanStartPosition += startPosition[i]; @@ -353,6 +376,7 @@ int SeqSummaryCommand::execute(){ meanAmbigBases += ambigBases[i]; meanLongHomoPolymer += longHomoPolymer[i]; } + //this is an int divide so the remainder is lost meanStartPosition /= (float) size; meanEndPosition /= (float) size; meanLongHomoPolymer /= (float) size; meanSeqLength /= (float) size; meanAmbigBases /= (float) size; @@ -380,7 +404,7 @@ int SeqSummaryCommand::execute(){ m->mothurOut("Maximum:\t" + toString(startPosition[ptile100]) + "\t" + toString(endPosition[ptile100]) + "\t" + toString(seqLength[ptile100]) + "\t" + toString(ambigBases[ptile100]) + "\t" + toString(longHomoPolymer[ptile100]) + "\t" + toString(ptile100+1)); m->mothurOutEndLine(); m->mothurOut("Mean:\t" + toString(meanStartPosition) + "\t" + toString(meanEndPosition) + "\t" + toString(meanSeqLength) + "\t" + toString(meanAmbigBases) + "\t" + toString(meanLongHomoPolymer)); m->mothurOutEndLine(); - if (namefile == "") { m->mothurOut("# of Seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); } + if ((namefile == "") && (countfile == "")) { m->mothurOut("# of Seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); } else { m->mothurOut("# of unique seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); m->mothurOut("total # of seqs:\t" + toString(startPosition.size())); m->mothurOutEndLine(); } if (m->control_pressed) { m->mothurRemove(summaryFile); return 0; } @@ -420,21 +444,21 @@ int SeqSummaryCommand::driverCreateSummary(vector& startPosition, vectorcontrol_pressed) { in.close(); outSummary.close(); return 1; } Sequence current(in); m->gobble(in); - + if (current.getName() != "") { int num = 1; - if (namefile != "") { + if ((namefile != "") || (countfile != "")) { //make sure this sequence is in the namefile, else error map::iterator it = nameMap.find(current.getName()); - if (it == nameMap.end()) { m->mothurOut("[ERROR]: '" + current.getName() + "' is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; } + if (it == nameMap.end()) { m->mothurOut("[ERROR]: '" + current.getName() + "' is not in your name or count file, please correct."); m->mothurOutEndLine(); m->control_pressed = true; } else { num = it->second; } } @@ -505,11 +529,11 @@ int SeqSummaryCommand::MPICreateSummary(int start, int num, vector& startPo if (current.getName() != "") { int num = 1; - if (namefile != "") { + if ((namefile != "") || (countfile != "")) { //make sure this sequence is in the namefile, else error map::iterator it = nameMap.find(current.getName()); - if (it == nameMap.end()) { cout << "[ERROR]: " << current.getName() << " is not in your namefile, please correct." << endl; m->control_pressed = true; } + if (it == nameMap.end()) { cout << "[ERROR]: " << current.getName() << " is not in your name or count file, please correct." << endl; m->control_pressed = true; } else { num = it->second; } } @@ -626,14 +650,17 @@ int SeqSummaryCommand::createProcessesCreateSummary(vector& startPosition, vector pDataArray; DWORD dwThreadIdArray[processors-1]; HANDLE hThreadArray[processors-1]; - + + bool hasNameMap = false; + if ((namefile !="") || (countfile != "")) { hasNameMap = true; } + //Create processor worker threads. for( int i=0; istart, lines[i]->end, namefile, nameMap); + seqSumData* tempSum = new seqSumData(filename, (sumFile+extension), m, lines[i]->start, lines[i]->end, hasNameMap, nameMap); pDataArray.push_back(tempSum); //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.